title: Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex

city: Vienna

first: Jakob

last: Schnabl

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

summary: Nuclear Argonaute proteins, guided by their bound small RNAs to nascent target transcripts, mediate cotranscriptional silencing of transposons and repetitive genomic loci through heterochromatin formation. The molecular mechanisms involved in this process are incompletely understood. Here, we show that the SFiNX complex, a silencing mediator downstream from nuclear Piwi-piRNA complexes in Drosophila, facilitates cotranscriptional silencing as a homodimer. The dynein light chain protein Cut up/LC8 mediates SFiNX dimerization, and its function can be bypassed by a heterologous dimerization domain, arguing for a constitutive SFiNX dimer. Dimeric, but not monomeric SFiNX, is capable of forming molecular condensates in a nucleic acid-stimulated manner. Mutations that prevent SFiNX dimerization result in loss of condensate formation in vitro and the inability of Piwi to initiate heterochromatin formation and silence transposons in vivo. We propose that multivalent SFiNX-nucleic acid interactions are critical for heterochromatin establishment at piRNA target loci in a cotranscriptional manner.

overall_design: Cut and Run H3K9me3 profiling of OSCs with panx knockdown and transfection of Panx[wildtype] plasmid or Panx[dLC8-mut] plasmid

first: Juncheng

first: Ulrich

last: Hohmann

first: Maja

last: Gehre

first: Julia

last: Batki

first: Veselin

middle: I

last: Andreev

first: Kim

last: Purkhauser

first: Nina

last: Fasching

first: Peter

last: Duchek

first: Maria

last: Novatchkova

first: Karl

last: Mechtler

first: Clemens

last: Plaschka

first: Dinshaw

last: Patel

first: Julius

last: Brennecke


title: Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions

status: Public on Dec 31 2020

city: Raleigh

first: Lisa

last: Van den Broeck

state: NORTH CAROLINA

address: 112 Derieux Place

department: Plant and Microbial Biology

country: USA

institute: North Carolina State University

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome wide differential gene expression analysis after DDX21 knockdown in MYCN-amplified human neuroblastoma BE(2)-C cells

status: Public on Jan 01 2021

city: Kensington

first: Pei

last: Liu

address: C25 Lowy Cancer Research Centre

country: Australia

institute: CCIA

summary:
Genome wide differential gene expression analysis after DDX21 knockdown by treatment with DOX in MYCN-amplified human neuroblastoma BE(2)-C cells stably transfected with DOX-indicible control shRNA, DDX21 shRNA-1 or DDX21 shRNA-2
DDX21 increases neuroblastoma cell proliferation by activating CEP55 gene transcription and increases its expression.
We identified that knocking N-Myc increases DDX21 gene expression, therefore, we performed affymetrix micoarray studies to investigate what are the downstream target genes of DDX21.

overall_design: We performed Affymetrix gene_array in DOX-inducible control, DDX21 shRNA-1 or DDX21 shRNA-2 BE(2)-C cells after treatment with control or DOX for 32 hours.

middle: Y

first: Tao

first: Nicholas

last: Ho


title: Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions [an3]

summary: We performed a transcriptome analysis on the meristematic root tissue from the loss-of-function line an3 and WT plants.

overall_design: Three biological replicates of an3 and WT seeds were plated. After 5 days of growth, ∼5 mm of an3 and WT root tips were collected. RNA was extracted using the Qiagen RNeasy Micro kit and libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced on an Illumina HiSeq 2500 with 100 bp single-end reads. Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al, 2019). Specifically, TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al., 2015) for genome alignment, and Cufflinks (Trapnell et al., 2012) for differential expression analysis.

first: L

first: A

middle: P

last: Fisher

first: R

last: Sozzani


title: E-cadherin marks the early commitment of murine hematopoietic progenitors to the basophil and mast cell fate

city: Boston

first: Anaïs

last: Wanet

state: MA

address: 3 Blackfan circle

department: Hematology Oncology

institute: BIDMC

summary: E-cadherin is a calcium-dependent cell-cell adhesion molecule extensively studied for its involvement in tissue formation, epithelial cell behavior and suppression of cancer; however its expression in the hematopoietic system hasn't received much attention. Combining single-cell RNA sequencing analyses and immunophenotyping, we revealed expression of E-cadherin in the basophil and mast cell lineages. No defect in basophil and mast cell differentiation was observed in mice lacking E-cadherin in the hematopoietic system, supporting that E-cadherin is not required per se for basophil and mast cell differentiation. Yet, we evidenced that granulocyte-monocyte progenitors expressing high levels of E-cadherin have an enriched capacity to differentiate into basophils and mast cells. Importantly, E-cadherin expression is observed on committed progenitors prior to the expression of  other reported markers of these lineages. We named those progenitors pro-BMPs (pro- basophil and mast cells progenitors). Using RNA-sequencing, we demonstrated the transcriptional priming of pro-BMPs to the basophil and mast cell lineages.

overall_design: 4 hematopoietic populations (DN-GMPs, Pro-BMPs, Pre-BMPs, Basophils) were isolated from the bone marrow of 3 C57Bl/6J mice (independent triplicates) and RNAseq was performed.

first: Anais

first: Mahmoud

last: Bassal

first: Daniel

middle: G

last: Tenen


title: Epigenomic profiles of African American Transthyretin Val122Ile carriers reveals putatively dysregulated amyloid mechanisms

city: New Haven

first: Gita

middle: A

last: Pathak

state: CT

address: 333 cedar St

institute: Yale University

type: Methylation profiling by genome tiling array

summary: The Val122Ile mutation in Transthyretin (TTR) gene causes a rare, difficult to diagnose hereditary form of cardiac amyloidosis. This mutation is most common in the United States and mainly present in people of African descent. The carriers have an increased risk of congestive heart failure, peripheral edema, and several other non-cardiac phenotypes such as carpal tunnel syndrome, and arthroplasty which are top reasons for ambulatory/outpatient surgeries in the country.  We conducted first-ever epigenome-wide association study in Val122Ile carriers of African descent for heart disease (HD) and multiple outpatient surgeries (OS) - an early disease indicator. DNA was extracted from whole blood of Yale-Penn participants using the EZ-96 DNA methylation kit (Zymo Research, CA, USA). DNA methylation was assayed using the Illumina Infinium MethylationEPIC chip quantifying >850,000 CpG sites and imaged on the Illumina iScan system at YCGA. The methylation intensity data (*.idat files) was exported for analysis using the manufacturer's recommended protocol using the GenomeStudio methylation module.

overall_design: Epigenomic differences were tested with respect to the history of heart disease (N=90 controls; 6 cases; Males-47%) and 10 or more outpatient surgeries (N=94 controls, 2 cases; Males-46%) in 96 individuals who were carriers of Val122Ile mutation.

first: Renato

last: Polimanti


title: Intracerebral Hemorrhage Induces MicroRNA and Target Genes within Six Hours: An Integrated Analysis of miRNA-seq and mRNA-seq in Swine ICH

city: Cincinnati

first: Xiang

last: Zhang

state: OH

address: 160 Panzeca Way, Kettering Room 336

department: Environmental and Public Health Sciences

institute: University of Cincinnati

type: Non-coding RNA profiling by high throughput sequencing

summary:
Introduction:  Intracerebral hemorrhage (ICH) is a severe neurological disorder with no proven treatment. microRNA  (miRNA) are short, noncoding nucleic acids that are critical regulators gene expression and promising novel therapeutic targets. Our prior research of mRNA-seq in swine demonstrated that ICH increased inflammatory gene expression within six hours of onset. We now present findings from an integrated analysis of miRNA-seq and mRNA-seq in peripheral blood mononuclear cells (PBMCs) from swine ICH. We tested the hypothesis that ICH would induce miRNA within six hours  and that differentially expressed (DE) inflammatory genes would be targets of the DE miRNA.
Methods: In 10 pigs, one PBMC sample was collected immediately prior to ICH induction and a second six hours later; miRNA-seq and mRNA-seq were performed. To determine the miRNA that primarily regulated the DE mRNA, an aggregate score was calculated for each miRNA of interest that incorporated the combined summary statistics of its DE target mRNA. Networks of molecular interactions were generated for the target mRNA and the combined miRNA/target mRNA.
Results:  A total of 227 miRNA were identified with alignment to the Sus scrofa (swine) genome, and 46 were DE (FDR <0.05). When analyzed with the aggregate scoring calculation, the miRNA that were most essential for regulating the DE mRNA included the following, all of which were downregulated post-ICH: miR-29a, miR-29b, miR-31, miR-34c, miR-125a, miR-132, miR-142, miR-150, miR-151a, miR-181a, and miR-186. A highly connected network  of interactions was generated from these miRNA and their target mRNA.
Conclusion:  ICH strongly induced numerous miRNA/mRNA targets  in swine PBMCs within six hours of onset. To our knowledge, this is the first integrated analysis of miRNA-seq and mRNA-seq in any study of ICH and the first report of miRNA in swine ICH. Further research is needed to determine whether these miRNA are potential therapeutic targets, including analyzing interventions such as miRNA overexpression or inhibition

overall_design: PBMC sample was collected immediately prior to ICH induction and a second six hours later; miRNA-seq were performed to identify differentially expressed miRNA. Combined with our prior RNA-seq data, a highly connected network  of interactions was generated from these miRNA and their target mRNA.

first: Kyle

middle: B

last: Walsh

first: Kip

last: Zimmerman

first: Carl

last: Langefeld

last: Woo

first: Opeolu

last: Adeoye


title: Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions [w5C6]

first: Lisa

summary: We performed a transcriptome analysis on FACS-sorted GFP positive cells from pCYCD6;1-GFP, wox5xpCYCD6;1-GFP, and pWOX5-GFP, and the GFP negative cells from pWOX5-GFP to obtain CEI specific transcriptional profiles in a WT and in a wox5 mutant background.

overall_design: Four biological replicates of pWOX5:erGFP, pCYCD6:GUS-GFP, and wox5 x pCYCD6:GUS-GFP seeds were plated. After 5 days of growth, approximately 1mm of the root tip was collected and protoplasted as described (Birnbaum et al., 2005). GFP positive and negative cells were collected using a MoFlo cell sorter into a vial containing a solution of beta-mercaptoethanol and RLT buffer. RNA was extracted using the Qiagen RNeasy Micro kit. Libraries were prepared using the SMART-Seq v3 Ultra Low RNA Input Kit for Sequencing and the Low Library Prep Kit v1 from Clontech. Libraries were sequenced on an Illumina HiSeq 2500 with 100 bp single-end reads. Gene expression analysis of raw RNA-seq data was performed using the TuxNet interface (Spurney et al., 2019). Specifically, TuxNet uses ea-utils fastq-mcf (Aronesty, 2011, Aronesty, 2013) for preprocessing, hisat2 (Kim et al., 2015) for genome alignment, and Cufflinks (Trapnell et al., 2012) for differential expression analysis.


title: Combined Inhibition of Gaq and MEK Enhances Therapeutic Efficacy in Uveal Melanoma

city: New York

first: Tyler

last: Hitchman

state: NY

address: 417 E 68th Street

department: HOPP

institute: MSKCC

summary: We developed an isogenic melanocytic cellular system and systematically examined the hotspot mutations in GNAQ (e.g., G48V, R183Q, Q209L) and CYSLTR2 (e.g. L129Q) in human uveal melanoma. Biochemical and cell viability assays validated YM-254890 as a potent inhibitor of cell signaling and growth. Human uveal melanoma cells and mouse models recapitulated this finding, indicating that YM is also effective in vivo. Combination of YM and MEK inhibition leads to further decreases in MAPK pathway gene expression and cell viability. Furthermore, our cellular and mouse models show that combination leads to long term signaling inhibition and significant decreases in tumor burden.

overall_design: Transcriptome analysis of melan-a cells (mouse) and two variant lines all in duplicate. Parental melan-a cells were compared to melan-a cells  overexpressing GNAQ Q209L or KRAS G12V.

middle: D

first: Yu

last: Chen


title: A Molecular Signature associated with prolonged survival in Glioblastoma patients treated with Regorafenib [miRNA-seq]

city: Verona

first: Marzia

last: Rossato

address: Strada Le Grazie 15

department: Biotechnology

country: Italy

institute: University of Verona

summary: Background: Patients with glioblastoma (GBM) have a dramatically poor prognosis. The recent REGOMA trial suggested an overall survival benefit of regorafenib in recurrent GBM patients. Considering the extreme genetic heterogeneity of GBMs, we aimed to identify molecular biomarkers predictive of differential response to the drug. The study provides evidence that a signature based on the expression of five biomarkers could help identifying a subgroup of GBM patients exhibiting a striking survival advantage when treated with regorafenib. Despite the presented results must be confirmed in larger replication cohorts, the study highlights potential biomarker options to help guiding the clinical decision among regorafenib and other treatments in patients with relapsing GBM.    Methods.Total RNA was extracted from tumor samples of patients enrolled in the REGOMA trial. Genome-wide transcriptome and miRNA profiles were associated with patients' Overall Survival (OS) and Progression Free Survival (PFS). Results. At first step, a set of 11 gene transcripts (HIF1A, CTSK, SLC2A1, KLHL12, CDKN1A, CA12, WDR1, CD53, CBR4, NIFK-AS1, RAB30-DT) and 10 miRNAs (miR-93-5p, miR-203a-3p, miR-17-5p, let-7c-3p, miR-101-3p, miR-3607-3p, miR-6516-3p, miR-301a-3p, miR-23b-3p, miR-222-3p) was filtered by comparing survival between regorafenib and lomustine arms. As second step, a minisignature of two gene transcripts (HIF1A, CDKN1A) and three miRNAs (miR-3607-3p, miR-301a-3p, miR-93-5p) identified a subgroup of patients showing prolonged survival after regorafenib administration (median OS range 10.6 - 20.8 months).    Conclusions. The study provides evidence that a signature based on the expression of five biomarkers could help identifying a subgroup of GBM patients exhibiting a striking survival advantage when treated with regorafenib. Despite the presented results must be confirmed in larger replication cohorts, the study highlights potential biomarker options to help guiding the clinical decision among regorafenib and other treatments in patients with relapsing GBM.

overall_design: Among anti-angiogenic drugs for second-line therapy of patients with glioblastoma (GBM), regorafenib has gained interest after the REGOMA clinical trial reported an overall survival advantage of the patients of the regorafenib arm compared to those enrolled in the lomustine arm. Considering the huge molecular variability among GBM tumors, we investigated by genome-wide analyses whether expression levels of transcripts and miRNAs could help identifying patients with specific advantage or disadvantage in the choice of regorafenib as second-line therapy.

first: Alessandra

last: Santangelo

first: Giuseppe

last: Lombardi

first: Vittorina

last: Zagonel

first: Giulio

last: Cabrini


title: miR-497 Reduction and the Increase of its Family Member miR-424 Leads to the Dysregulation of Multiple Inflammation Related Gene in Synovial Fibroblasts with Rheumatoid Arthritis

city: xi'an

first: SI

last: WANG

state: shaanxi

address: no.76 yanta west road

country: China

institute: xi'an jiaotong university

summary:
Objectives: Mounting evidence has demonstrated that microRNAs (miRNAs) participate in rheumatoid arthritis (RA). The role of highly conserved miR-15/107 family in RA was not clarified yet, and hence investigated in this study.
Methods: Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to evaluate the expression of miRNAs and genes. Cell counting kit 8 (CCK-8) and FACS were used to detect proliferation and apoptosis. Protein expression was detected by using Western blotting. mRNA deep sequencing and cytokine antibody array were used to analyze differentially expressed genes, signaling pathways and cytokines.
Results: In RA patients, the expression of miR-15a, miR-103, miR-497 and miR-646 was increased, while miR-424 was decreased. miR-424 and miR-497 were further investigated and the results showed that they could regulate multiple genes in rheumatoid arthritis synovial fibroblast (RASF) and affect signaling pathways. At the protein level, miR-497 mimic has an effect on all the selected inflammation related genes while miR-424 inhibitor only affects part of genes. miR-497 mimic has obvious effects on proliferation and apoptosis of RASF rather than miR-424 inhibitor. DICER1 was found to positively regulate miR-424 and miR-497, while DICER1 was also negatively regulated by miR-424. The increase of miR-424 could reduce miR-497 expression, thus forming a loop, which helps explain the dysregulated miR-424 and miR-497 condition in RA.
Conclusion: Our study clarified the effects of miR-15/107 family members miR-424 and miR-497 on cell proliferation and apoptosis in RA and proposed miR-424-DICER1-miR-497 feedback loop which provided novel ideas and new inspiration for miRNA research and RA therapy.

overall_design: Examine differentially expressed genes after transfection of miRNA mimics in synovial fibroblasts

first: Si

last: Wang

first: Congshan

last: Jiang

first: Shemin

last: Lu


title: Quantification of tRNA-derived fragments in Arabidopsis and rice

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

summary: Here, we adopt a method that combines tRNA-seq and cp-RNA-seq to identify and quantify tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncovers complex tRFs repertoire and the dynamic expressions of tRNA genes in plants.

sample_organism:
Arabidopsis thaliana
Oryza sativa

platform_organism:
Arabidopsis thaliana
Oryza sativa

overall_design: We constructed five Arabidopsis tRNA-seq libraries sampling from various vegetative and reproductive tissues, and seven rice libraries from shoots, roots and panicles. As abiotic stresses potentially induce tRFs levels, the rice seedlings with salt and cold treatments were also subjected to tRNA-seqs. Two biological replicates for each sample were performed.

first: Weijiang

last: Luan


title: Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [ChIP-seq, Cut&Run]

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcription factors regulate gene networks controlling normal hematopoiesis and are frequently deregulated in acute myeloid leukemia (AML). Critical to our understanding of the mechanism of cellular transformation by oncogenic transcription factors is the ability to define their direct gene targets. However, gene network cascades can change within minutes to hours, making it difficult to distinguish direct from secondary or compensatory transcriptional changes by traditional methodologies. Utilizing CRISPR-based genome editing, we inserted a degron tag into the endogenous AML1-ETO locus of Kasumi-1 cells, as well as overexpressed a degradable AML1-ETO protein in CD34+ human cord blood cells. This allowed rapid AML1-ETO protein degradation upon addition of a proteolysis targeting chimera (PROTAC). Furthermore, by combining rapid degradation with nascent transcript analysis (PRO-seq), RNA-seq and Cut&Run, we have defined the core AML1-ETO regulatory network. De-repression of this small set of genes set off a cascade of transcriptional events resulting in myeloid differentiation.

overall_design: Cut&Run was performed to define genome-wide binding of AML1-ETO-FKBP12F36V-2xHA in both Kasumi-1 cells and CD34+ cord blood cultures. Cut&Run using anti-ETO confirmed that the FKBP-2xHA tag had not altered AML1-ETO binding. ChIP-seq for H3K27ac was performed before and after 24 hr dTAG treatment.

first: Kristy

middle: R

last: Stengel

first: Clare

middle: L

last: Spielman

first: Monica

last: Bomber

middle: W


title: Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO


title: FATC domain deletion compromises ATM protein stability, lymphocyte development, and promotes lymphomagenesis

first: Xiaobin

middle: Summer

state: NEW YORK

address: 1130 Siant Nicholas Ave, Room 501

department: Institute for Cancer Genetics

institute: Columbia University Medical Center

summary: ATM kinase is a master regulator of the DNA damage response and loss of ATM leads to primary immunodeficiency and greatly increased risk for lymphoid malignancies. The FATC domain is conserved in Phosphatidylinositol-3-kinase-related protein kinases (PIKKs). Truncation mutation in the FATC domain (R3047X) selectively compromised reactive oxygen species-induced ATM activation in cell-free assays. Here we show that in mouse models, knock-in ATM-R3057X (AtmRX, corresponding to R3047X in human ATM) mutation severely compromises ATM protein stability, and causes T cell development and B cell immunoglobulin class switch recombination defects and infertility resembling ATM-null. The residual ATM R3057X protein retains minimal, yet functional measurable, DNA damage-induced checkpoint activation and significantly delays lymphomagenesis in AtmRX/RX mice compared to Atm-/-. Together, these results support a physiological role of the FATC domain in ATM protein stability and show that minimal ATM activity can prevent growth retardation and delay tumorigenesis without restoring lymphocyte development and fertility.

overall_design: To determine how ATM-RX protein affects the repair phase of CSR, we analyzed thousands of CSR and internal deletion junctions from activated AtmRX/RX, Atm+/+, and Atm-/- control B cells using the high-throughput genome-wide translocation sequencing (HTGTS) technology. Since all our experimental mice carry the preassembled IgH on the 129  background, we replaced the IgH switch region (from JH4 to the last Cα exon, chr12 114, 494, 415–114, 666, 816) of the C57/BL6-based mm9 with the corresponding region in the AJ851868.3 (NCBI gene accession no. AJ851868.3) 129 IgH sequence (1415966–1592715) to generate the mm9sr (switch region replacement) genome.  1. Hu J, et al. (2016) Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 11:853–871. Together, the increased translocation (+ oriented junction), preferential loss of Sμ-Sε junctions, and the increased MH usage in the HTGTS analyses of AtmRX/RX B cells indicate that the R3057X mutation impairs the DNA repair function of ATM during CSR, similar to the loss of ATM.

first: Maja

last: Milanovic

first: Demis

last: Menolfi

first: Shan

last: Zha


title: Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [RNA-seq]

overall_design: RNA-seq was performed using biological replicates. For Kasumi-1 cell samples, parental cells as well as untreated AML1-ETO-FKB12F36V cells served as negative controls. Cells were harvested at 2, 4, 8, and 24 hr post-treatment with dTAG-47 to induce AML1-ETO-FKBP12F36V degradation. For CD34+ human cord blood cultures expressing AML1-ETO-FKBP12F36V, RNA-seq was performed on biological replicates treated with dTAG-47 for 4 hours and compared with DMSO-treated control samples.


title: A Molecular Signature associated with prolonged survival in Glioblastoma patients treated with Regorafenib

first: Marzia

last: Rossato


title: Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [PRO-seq]

overall_design: PRO-seq was performed on biological replicates. Parental Kasumi-1 cells (wild-type AML1-ETO) or untreated Kasumi-1 cells expressing AML1-ETO-FKBP12F36V served as negative controls. Cells were harvested at 30 min, 1 hr, 2 hr, 6 hr and 24 hr post-treatment with 500 nM dTAG-47, as well as at 24 hours following treatment with 100 nM GSK2879552 or 500nM dTAG-47 + 100 nM GSK2879552. Nuclei were isolated from cells for nuclear run-ons.


title: Centromeric R loops contribute to defects in kinetochore assembly and chromosomal instability

city: Syracuse

first: Wenyi

last: Feng

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

summary: We mapped ssDNA formation in WT and hpr1delta cells at permissive (30C) and non-permissive (37C) temperature. We showed that hpr1 cells accumulate ssDNA show elevated levels of ssDNA at centromeric regions. Additionally, we show replication fork-associated ssDNA at origins of replication is more confined to the origins in hpr1 cells than WT cells, suggesting a defect in replication fork progression.

overall_design: We queried the yeast genome for ssDNA production in WT and hpr1delta cells. G1-arrested cells were released into S phase at 30C and 37C and collected at 10, 15, 20, and 25 min. Each S phase sample was paired with a G1 control sample and subject to ssDNA labeling with Cy3 and Cy5, respectively, prior to co-hybridization to the same microarray. The level of ssDNA was quantified as the ratio of Cy3 signals to Cy5 signals for every probe position on the microarray, after normalization.

first: Jie

last: Peng

first: Arijita

last: Chakraborty


title: Combined Inhibition of Gaq and MEK Enhances Therapeutic Efficacy in Uveal Melanoma.

first: Tyler

last: Hitchman

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Transcriptome analysis of three different cell lines (one mouse and two human)  all in duplicate. Melan-a cells were treated with Vehicle, YM-254890, or Trametinib for 4 or 24 hours. OMM1.3 and Mel202 cells were treated with Vehicle, YM-254890, Trametinib, or Combination for 24 hours.

first: Yu

last: Chen


title: An aberrant cytoplasmic intron retention programme is a blueprint for ALS-related RBP mislocalization

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

country: Switzerland

institute: Idiap Research Institute

summary: We recently described aberrant cytoplasmic SFPQ intron-retaining transcripts (IRTs) and concurrent SFPQ protein mislocalization as a new hallmark of amyotrophic lateral sclerosis (ALS). However the generalizability and potential roles of cytoplasmic IRTs in health and disease remain unclear. Here, using time-resolved deep-sequencing of nuclear and cytoplasmic fractions of hiPSCs undergoing motor neurogenesis, we reveal that ALS-causing VCP gene mutations lead to compartment-specific aberrant accumulation of IRTs. Specifically, we identify >100 IRTs with increased cytoplasmic (but not nuclear) abundance in ALS samples. Furthermore, these aberrant cytoplasmic IRTs possess sequence-specific attributes and differential predicted binding affinity to RNA binding proteins (RBPs). Remarkably, TDP-43, SFPQ and FUS - RBPs known for nuclear-to-cytoplasmic mislocalization in ALS - avidly and specifically bind to this aberrant cytoplasmic pool of IRTs, as opposed to any individual IRT. Our data are therefore consistent with a novel role for cytoplasmic IRTs in regulating compartment-specific protein abundance. This study provides new molecular insight into potential pathomechanisms underlying ALS and highlights aberrant cytoplasmic IRTs as potential therapeutic targets.

overall_design: Bulk RNA-seq from fractionated cells at different timepoints throughout a 35-day differentiation protocol that converted iPSC cells to highly enriched motor neurons.

first: Giulia

last: Tyzack

first: Jacob

last: Neeves

first: Pierre

last: Klein

first: Hamish

last: Crerar

first: Doaa

middle: M

last: Taha

first: Oliver

last: Ziff

first: Nicholas

last: Luscombe

first: Rickie

last: Patani


title: Selective mRNA translation governs the tumor-associated macrophage  phenotype

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

summary: Tumor-associated macrophages (TAMs) continuously tune their immune modulatory properties, but how gene expression programs coordinate this is largely unknown. Selective mRNA translation facilitates reshaping of proteomes without changes in abundance of corresponding mRNAs and plays pivotal roles in regulating immune cell plasticity. Using polysome-profiling developed for small samples we show that, during tumor growth, gene expression in TAMs is predominately modulated via mRNA-selective changes in translational efficiencies targeting key cellular functions including cell proliferation and metabolism. These changes in translational efficiencies paralleled accumulation of immunosuppressive macrophages with augmented phosphorylation of eIF4E, a target of the MNK1 and MNK2 kinases, whose altered phosphorylation selectively modulates mRNA translation. Furthermore, suppression of MNK2-signaling reprogrammed immunosuppressive macrophages towards a pro-inflammatory phenotype with the ability to activate CD8+ T cells. Thus, selective changes of mRNA translation depending on MNK2-signaling represents a key node regulating macrophage immunosuppressive functions.

overall_design: Macrophages were sorted from tumors of different sizes and translatomes and transcriptomes were compared using polysome-profiling


title: Lung response to crystalline nanocellulose exposure in rats

city: Morgantown

first: Christina

last: Umbright

state: WV

address: 1095 Willowdale Road

department: HELD

institute: DHHS/PHS/CDC/NIOSH

summary: Crystalline nanocellulose (CNC) is an emerging nanomaterial with multiple commercial and industrial applications. Occupational exposure to CNC during the production and/or use of products containing the nanomaterial potentially resulting in adverse health effects among workers is possible. Therefore, there is an immediate need to determine the toxicity potential of CNC. Rats were exposed to either air or CNC (20 mg/m^3, 6 hours/day, 5 days/week, 14 days) and lung toxicity was determined one day following termination of the exposures. Compared to the control rats, the CNC exposed rats exhibited moderate changes in lung histology. Lactate dehydrogenase activity and the number of phagocytes present in the bronchoalveolar lavage were higher in the CNC exposed rats, compared with the controls. Global gene expression profiling identified 531 genes whose expressions were significantly different (fold change >1.5 and FDR p <0.05) in the lungs of the CNC exposed rats, compared with the controls. In summary, the data demonstrated the induction of pulmonary toxicity and global gene expression changes in the lungs of the rats in response to inhalation exposure to CNC.

overall_design: Rats (n=6) were exposed by whole body inhalation to air or crystalline nanocellulose (20 mg/m3, 6 hours/day for 5 days/week for a total of 14 days of exposure). One day after the final exposure, lung tissue was collected, and Next Generation Sequencing was performed on the lungs of 6 rats per treatment group (air/crystalline nanocellulose).

first: Tina

last: Sager

first: Pius

last: Joseph


title: RNA Seq of Pseudomonas aeruginosa PAO1 exposed to DAS and DAE

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling of control of P. aeruginosa PAO1 (RNA-seq) to transcriptome profiling of DAS-treated and DAE-treated P. aeruginosa PAO1 and to evaluate protocols for optimal high-throughput data analysis.
Results: The transcriptome sequencing data of control, DAS-treated and DAE-treated groups were compared and analyzed in the form of the following: DAE vs DAS, control vs DAS, and control vs DAE. The details of the differentially expressed genes among the three groups showed that the amount of differential expressed genes between DAE-treated group and DAS-treated group was high (total 2195, up-regulated 1608, down-regulated 587). There were many differentially expressed genes in the PAO1 strain after DAS treatment (total 2771, up-regulated 1905, down-regulated 866), while the amount of differentially expressed genes after DAE treatment was relatively small (total 770, up-regulated 349, down-regulated 421).

overall_design: Methods: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 1.0E8 CFU/mL. Diallyl sulfide and diallyl ether were then added at a concentration of either 0 (control) or 0.63 μl/mL, respectively, in triplicate. All nine experiment groups were incubated in a water bath shaker at 37C with a shaking rate of 180 rpm for 5 h. Cells were then sampled and centrifuged from the three control groups and three farnesol treatment groups, respectively. The cell precipitates were separately snap-frozen at -80C.  Total RNA was isolated from cells using Trizol (Life Technologies, USA) according to the manufacturer’s protocol.

first: Wen-Ru

first: Tao-Hua

last: Zeng


title: Expression profiling in OVCAR8 cells following treatment with relaxin-2 (RLN2)

city: Toronto

first: Rob

last: Rottapel

state: ON

address: 101 College Street, Room 12-704

department: Medical Biophysics

country: Canada

institute: University Health Network

summary: The relaxin-RXFP1 signaling loop promotes survival and proliferation in a panel of high-grade serous ovarian (HGSOC) cancer cell lines. Knockdown of either the relaxin receptor-1(RXFP1) or relaxin-2 (RLN2) decreased growth and tumorigenicity and increased apoptosis in dependent HGSOC cell lines. Transcriptome profiling of relaxin-dependent HGSOC cells using RNA-Seq revealed genes with altered expression levels following relaxin treatment. This included components of the Notch signaling pathway (NOTCH1 and NOTCH3), Wnt signaling (DVL1, LRP5, BCL9) and extracellular matrix regulation (VEGF-A, MMP9, MMP23). Collectively, genes and pathways upregulated by relaxin provide insight into the mechanisms by which it sustains proliferation of dependent cells.

overall_design: Whole genome transcriptome analysis in OVCAR8 cells treated with recombinant human relaxin-2 (RLN2). OVCAR8 cells were plated in 6-well format. 24 hours later, cells were starved in RPMI containing 0% FBS for 16 hr. Cells were either untreated or treated with human recombinant RLN2 (50ng/mL, Phoenix Pharmaceuticals 035-62) in triplicate for 8 hours. Cells were harvested and RNA was purified using Trizol extraction.

first: Helen

last: Burston

first: Robert


title: Transcriptome profile of fibroblasts in chronic thromboembolic pulmonary hypertension

city: Vienna

first: Smriti

last: Sharma

address: Spitalgasse 23

department: Internal Medicine II, Cardiology

institute: Medical University of Vienna

summary: The hallmark of chronic thromboembolic pulmonary hypertension (CTEPH) is fibrotic transformation of pulmonary arterial thrombus, leading to mechanical obstruction of pulmonary arteries. We report the transcriptome profile of fibroblasts isolated from pairs of CTEPH thrombus and pulmonary artery adventitia of the same patient. Fibroblasts isolated from CTEPH thrombus demonstrated upregulation of genes associated with the TGF-β pathway indicating that TGF-β upregulation is associated with the intravascular remodeling process.

overall_design: RNA-seq of fibroblasts isolated from pairs of CTEPH thrombus and pulmonary artery adventitia from 4 CTEPH patients.

first: Adelheid

last: Panzenboeck

first: Bernhard

last: Moser

first: Shahrokh

last: Taghavi

first: Walter

last: Klepetko

first: Irene

last: Lang


title: Multifactorial stress combination

city: Memphis

first: Soham

last: Sengupta

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

summary: We report the differences in gene expression when Arabidopsis seedlings are subjected to different stressors, impacting alone or in combinations of 2, 3 or 4 factors at a time

overall_design: 10-day-old Col seedlings growing under different stress treatments as describe below were analyzed for RNAseq in triplicates

first: Sara

last: Zandalinas

first: Felix

last: Fritschi

first: Rajeev

middle: K

last: Azad

first: Ron

last: Mittler


title: miRNA sequencing profile of isolated Kit+ interstital cells of Cajal (ICC) in Leptin mutant mice

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 N Virginia St

department: Physiology & Cell Biology

institute: University of Nevada, Reno

summary: We report the high-throughput miRNA sequencing of isolated colonic and jejunal Kit+ interstitial cells of Cajal (ICC) from Lepob/ob;KitcopGFP mice, which develop type 2 diabetes, and Lepob/+;KitcopGFP mice which are non-diabetic counterparts and control

overall_design: Global transcriptomic profiling of miRNA produced in isolated ICC

first: Chanjae

last: Park


title: miRNA sequencing profile of human plasma samples from healthy, diabetic, and gastroparesis patients

summary: We report the high-throughput miRNA sequencing of plasma isolated from human patients with type 2 diabetes & gastroparesis, idiopathic gastroparesis alone, and healthy control patients.

overall_design: Global transcriptomic profiling of miRNA isolated from human serum

first: Andres

last: Blackmore

first: Se

middle: E

last: Ha


title: A Molecular Signature associated with prolonged survival in Glioblastoma patients treated with Regorafenib [RNA-seq]

first: Marzia

last: Rossato

overall_design: Among anti-angiogenic drugs for second-line therapy of patients with glioblastoma (GBM), regorafenib has gained interest after the REGOMA clinical trial reported an overall survival advantage of the patients of the regorafenib arm compared to those enrolled in the lomustine arm. Considering the huge molecular variability among GBM tumors, we investigated by genome-wide analyses whether expression levels of transcripts and miRNAs could help identifying patients with specific advantage or disadvantage in the choice of regorafenib as second-line therapy.

first: Alessandra

last: Santangelo

first: Giuseppe

last: Lombardi

first: Vittorina

last: Zagonel

first: Giulio

last: Cabrini


title: Expression data from Arabidopsis plants overexpressing CLE2 in roots

city: Tokyo

first: Dichao

last: Ma

address: 1-1-1 Yayoi, Bunkyo-ku

department: Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

summary: Plant hormones and small secretory peptides often function as environmental stress mediators. Some recent reports indicate that small secretory peptides, such as CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE), also function as mediators of environmental stimuli. CLE2 is induced in roots by light depriviation. Plants without functional CLE2 showed a chlorosis phenotype when grown under shade.  Here, we identified specific genes downstream of CLE2 in roots and shoots with transformed Arabidopsis plants.

overall_design: To identify specific genes downstream of CLE2, GeneChip analyses were performed using roots and shoots separately collected from arabidopsis seedlings, roots of which were treated with estrogen or DMSO for 24h.


title: Transcriptome analysis for comparing the overlap mis-regulated genes between impα triple and lhp1-3 mutants.

city: Austin

first: Sibum

last: Sung

state: TX

institute: University of Texas at Austin

summary: We performed transcriptomic analysis to check the overlap mis-regulated genes between impα triple and lhp1 mutants. Overall, 87.64% genes differentially expressed in lhp1-3 are also differentially expressed in impα triple. We also observed that the number of DEGs in impα triple mutants are greater than that in lhp1-3 mutants, which is expected given that IMPα 1, 2 and 3 should also be necessary for other nucleus-localized proteins.

overall_design: Comparision of differently expressed genes in impα triple and lhp1-3 mutants

first: Bordiya

last: Yogendra

first: Zhao

last: Bo


title: The Aging Microenvironment Drives Alveolar Macrophage Changes in Aging

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The DEL-1–β3 integrin axis promotes Runx-1–dependent Foxp3 expression and regulatory T cell responses at mucosal barrier sites

city: Philadelphia

first: George

last: Hajishengallis

state: PA

address: School of Dental Medicine

institute: University of Pennsylvania

summary: Foxp3+CD4+ regulatory T cells (Tregs) are critical for immune homeostasis and respond to local tissue cues, which control their stability and function. We explored here whether DEL-1, which, like Tregs, increases during resolution of inflammation, promotes Treg responses. DEL-1 enhanced Treg numbers and function at barrier sites (oral and lung mucosa). The underlying mechanism was dissected using mice lacking DEL-1 or expressing a point mutant thereof, or mice with CD4-specific deletion of the transcription factor Runx1, identified by RNA-seq analysis of the DEL-1-induced Treg transcriptome. Specifically, through interaction with avβ3-integrin, DEL-1 promoted induction of Runx1-dependent Foxp3 expression and conferred stability of Foxp3 expression upon Treg restimulation in the absence of exogenous TGFβ1. Additionally, DEL-1 increased RUNX1 and FOXP3 expression in human conventional T cells promoting their conversion into induced Tregs with increased TSDR demethylation, increased stability and suppressive activity. We thus uncovered a DEL-1-avβ3-Runx1 axis that promotes Treg responses at barrier sites and offers novel therapeutic options for modulating inflammatory/autoimmune disorders.

overall_design: We examined gene expression by RNA-seq in Tregs treated with DEL-1-Fc or Fc control

first: Xiaofei

last: Li

last: Colamatteo

first: Lydia

last: Kalafati

first: Tetsuhiro

last: Kajikawa

first: Hui

last: Wang

first: Jong-Hyung

last: Lim

first: Khalil

last: Bdeir

first: Xiang

last: Yu

first: Clorinda

last: Fusco

first: Antonio

last: Porcellini

first: Salvatore

last: De Simone

last: Matarese

first: Triantafyllos

last: Chavakis

first: Veronica

last: De Rosa


title: Transcriptome changes during Endothelial to Mesenchymal Transition (EndMT) using a TGF-b2 and IL-1b in vitro model of EndMT in HUVEC and HPAEC

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

summary: Endothelial-to-mesenchymal transition (EndMT) is a dynamic transformation process that has a functional impact upon pathological vascular remodelling. However, the molecular mechanisms that govern EndMT remain largely unknown. We modelled this process in vitro by exposing human primary endothelial cells to a combination of transforming growth factor-β2 (TGF- β2) and interleukin-1β (IL-1β). RNAseq was carried out to analyse the change of gene expression during the transition and define the transcriptional architecture of EndMT.

overall_design: HUVEC (Human umbilical vein endothelial cells) cells were treated with TGF-β2 (10 ng/ml) alone, IL-1β (1ng/ml) alone as well as combined TGF-β2 and IL-1β for 7 consecutive days. HPAEC (Human pulmonary artery endothelial cells) cells were co-treated with TGF-β2 and IL-1β for 7 consecutive days. Control samples correspond to time-matched untreated cells. All treatments were carried out in triplicates and total RNAs were extracted for RNAseq. Ribosomal-depleted stranded libraries were prepared by Beckman Coulter Genomics using the TruSeq Stranded Total RNA kit with Ribo-Zero Gold. Libraries were sequenced with Illumina at an average of 50 million reads per samples (paired end 2 x 125bp).

first: Axelle

last: Caudrillier

first: João

last: Monteiro

first: Lin

last: Deng

first: Andrew

middle: H

last: Baker


title: Janus-faced nature of light in the cold acclimation processes of maize

city: Martonvásár

first: Imre

last: Majláth

state: Fejér

address: Brunszvik u. 2.

department: Plant Physiology

country: Hungary

institute: Centre for Agricultural Research, Hungarian Academy of Sciences

summary: Earlier findings indicated that light plays a critical role in the development of frost tolerance in winter cereals. However, the exact mechanism is still poorly understood. In the present work the effects of light during the cold acclimation period were studied in chilling-sensitive maize plants. The results show that although exposure to relatively high light intensities during cold acclimation at 15 °C causes various stress symptoms, it enhances the effectiveness of acclimation to chilling conditions (5 °C in the light). Interestingly, certain stress responses were light-dependent not only in the leaves, but also in the roots. A microarray study was also conducted to achieve a better understanding of the interaction of low temperature and light intensity during the cold hardening period. Numerous genes significantly differentially expressed were observed in almost all assimilation and metabolic pathways. Acclimation at moderately low temperature and low light intensity reduced the level of soluble sugars, while chilling increased it. Greater accumulation during hardening was detected at relatively high light intensity. It seems that the photoinhibition induced by low temperature is a necessary evil for cold acclimation processes in plants.

overall_design: Control and cold-induced maize plants were sampling at different growth light intensities

first: Gabriella

last: Szalai


title: Long non-coding RNA MIR503HG controls endothelial-to-mesenchymal transition

summary: Endothelial-to-mesenchymal transition (EndMT) is a dynamic transformation process that has a functional impact upon pathological vascular remodelling. The molecular mechanisms that govern EndMT remain largely unknown. By induction of EndMT in human primary endothelial cells (EC), using a combination of transforming growth factor-β2 (TGF-b2) and interleukin-1b (IL-1β), we identified the dramatic loss of the lncRNA MIR503HG, as a common signature across multiple primary EC types. Targeted depletion of MIR503HG spontaneously induced EndMT. Overexpression of MIR503HG repressed EndMT despite TGF-β2 and IL-1β co-stimulation. RNA-seq was carried out to identify the changes in gene expression induced by MIR503HG overexpression. We showed that over 25% of the EndMT-transcriptome signature was inhibited upon MIR503HG overexpression. Crucially, phenotypic changes induced by MIR503HG were independent of the functional regulation of miR-503 and miR-424, both harbored within the MIR503HG locus. Collectively, we identify the lncRNA MIR503HG as an essential regulator of EndMT.

overall_design: To analyse the effect of MIR503HG overexpression during EndMT, we performed RNA-Seq on control and EndMT (TGFβ2 and IL1β) HUVEC cells overexpressing MIR503HG isoform 2 (ENST00000440570.5) using lentiviral transfection. Untransfected cells and cells transfected with an empty vector were used as controls. Each condition was carried out in triplicates.


title: RNA expression of memory NK subsets

city: hong kong

first: wenwei

last: tu

address: L7-55, lab block, 21 sassoon road.

department: Paediatrics & Adolescent Medicine

country: Hong Kong

institute: University of Hong Kong

summary: we compared and reported RNA expression difference in memory and non-memory NK cell subsets

overall_design: RNA transcriptone sequencing on memory and naïve NKp46+NKG2A+ NK cell subsets

first: Wenwei

last: Tu


title: Hippocampus-Cerebellum Axis Specific Transcriptomic Stratification to Discriminate Mild from Moderate TBI

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: The variations of psycho- and physiological deficits caused by TBI correlate with the degree of brain injury. However, the objective stratification of TBI is yet elusive. A modified closed-head injury Marmarou model was used based on the release of a 500 gram steel slug on top of the rat skull from a height of 100 cm or 120 cm to induce differential injury models for mild TBI and moderate TBI, respectively. The skull was covered by a helmet to mimic the warfighter’s condition in theater. The hippocampus was at the focal point of injury, and the cerebellum, was susceptible to diffused shock (secondary injury). The HC-CB axis coordinates visuomotor performance, which is known to be vulnerable to TBI. The rats that received moderate TBI showed deficient visuomotor performance by the Barnes maze test for longer time periods than those inflicted with mild TBI. The time resolved and HC-CB specific transcriptomic analysis focused on genes that enabled discrimination of mild from moderate TBI at 14d post injury which is equivalent to nearly 1.5 years of human lifetime. The functional analysis elucidated an active healing mechanism in the HC exposed to mild TBI. In contrast, moderate TBI caused delayed healing and active cell death in the HC. In conclusion, the graded brain injuries differentially implicated the HC-CB axis, despite the use of a helmet to reduce the impact. Time resolved functional dynamics informed the distinct consequences of mild vs. moderate TBI.

overall_design: A modified closed-head injury Marmarou model was used based on the release of a 500 gram steel slug on top of the rat skull from a height of 100 cm or 120 cm to induce differential injury models for mild TBI and moderate TBI.

first: Nabarun

last: Chakraborty

first: Rasha

last: Hammamieh

first: Stacy-Ann

last: Miller

first: Michelle

last: Condlin

first: Marti

last: Jett

first: Andrei

last: Loban

first: Angus

last: Scrimgeour


title: Expression data from human breast cancer cell MDA-MB-231 stably expressing MYOSIN10 shRNA versus scramble shRNA

city: Changchun

first: Rangjuan

last: Cao

state: jilin

address: 5268 Renmin Street

department: Institute of Genetics and Cytology

institute: Northeeast Normal University

summary:
We used MYOSIN10 shRNA to stably silence the expression of endogenous MYOSIN10 in Breast cancer cell MDA-MB-231. To investigate the inner change of cells with silenced MYOSIN10, we conducted a genome-wide screening for all potential genes affected by MYOSIN10 shRNA using Affymetrix Human Genome U133 plus 2.0 array.
We showed genes affected by MYOSIN10 knockdown in breast cancer cell MDA-MB-231

overall_design: Three group MDA-MB-231 cells stably expressing MYOSIN10 shRNA and scramble shRNA

first: Xiaojuan

last: Zhu


title: Transcripts identified by microarray analysis that were deregulated in E14.5 Tbx18cre/+;Gata2fl/fl (Gata2cKO) ureters

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

summary: Evaluation of the transcriptional changes in E14.5 ureters upon loss of Gata2 in the ureteric mesenchyme.

overall_design: Total RNA from dissected ureters of E14.5 Tbx18cre/+;Gata2fl/fl and control mice was analyzed by microarray analysis.


title: Adapted Y-50049 vs. Wild type Y-12632 in response to furfural-HMF challenge

city: Peoria

first: Z Lewis

last: Liu

address: 1815 N University

institute: USDA-ARS

summary: Transcriptional profiling of adapted tolerant industrial yeast Saccharomyces cerevisiae NRRL Y-50049 compared with its parental wild type NRRL Y-12632 in response to challenge of furfural and HMF each at 20 mM. Y-50049 is able to detoxify toxic furan aldehydes in situ while produce ethanol. Under the same conditions, the wild type Y-12632 was repressed and unable to grow and function.

overall_design: Two-condition experiment, Y-50049 vs Y-12632 cells. Biological replicates: 2. Independently grown and harvested. Sample time-point at 0, 0.2, 0.5, 1, 2, 18, 24, and 28 hours. Triplicated array with 48 replications of reference control genes. Pre-scan mini array applied.

first: Z

first: Menggen

last: Ma


title: The Aging Microenvironment Drives Alveolar Macrophage Changes in Aging  [RNA-Seq]

first: Ziyou

last: Ren

summary: Our study shows that the aging lung microenvironment shapes the transcriptional phenotype of alveolar macrophages during aging.  Except during acute injury when alveolar macrophage differentiation is incomplete, cellular ontogeny makes little difference in determining the transcriptional response of alveolar macrophages.  Studies with parabiosis suggest the age-related changes in the alveolar microenvironment occur independently of circulating factors or cells.  Our findings suggest that changes that target the microenvironment, for example metformin, senolytics or others might indirectly improve macrophage function during aging.

overall_design: RNA sequencing files from 273 samples of 7 different experiments to investigate the ontogeny and aging microenvironment in alveolar macrophage identity

first: Alexandra

last: McQuattie-Pimentel

first: Thomas

last: Stoeger

first: Paul

last: Reyfman

first: Benjamin

last: Singer

first: Alexander

last: Misharin

first: Scott

last: Budinger


title: Gene expression profile of MX-1 breast cancer cell line and chemoresistant sublines of them

status: Public on Dec 30 2020

city: Vilnius

first: Raimonda

last: Kubiliūtė

state: Saulėtekis

address: Sauletekio al., 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Breast cancer is a leading cause of cancer-related deaths among women in the Western world. Anthracyclines, including doxorubicin (DOX), along with taxanes, cyclophosphamide and platinum compounds are the main chemotherapeutic agents applied for breast cancer treatment. However, chemoresistance is the major cause of the disease progression following chemotherapy. Drug resistance can be either inherent or acquired during the treatment, but most possibly the interaction of both mechanisms drives the rapid development of treatment refractory cancer. In the present study, the mechanisms of acquired cellular chemoresistance were studied in breast cancer cell line MX-1 exposed to gradually increasing concentration of the chemotherapeutic compound DOX (MX-1/D). Nongenotoxic phosphorganic compound tetraphenylphosphonium cation (TPP+) – a potent substrate and activator for ABCB1 transporter – was used in the cell line model of intrinsic chemoresistance (MX-1/T). Finally, DOX highly resistant cell subline was derived from ABCB1-activated, TPP+ pretreated cells (MX-1/TD). Chemoresistance in all cell sublines was closely associated with the EMT, and the ABCB1 hyperexpression was a possibly trigger of this process.

overall_design: Gene expression profile was analyzed in the parental MX-1 cells and chemoresistant MX-1/D (cultured with 80 nM of doxorubicin), MX-1/T (cultured with ABCB1 transporter activator TPP+ (128 nM)) and MX-1/TD (MX-1/T cells cultured in media supplemented with up to 1280 nM of doxorubicin for a week). Two biological replicates were performed for the each sample.

last: Kubiliute

first: Sonata

last: Jarmalaite


title: Gene expression profiles of bulk tumor tissues of intrahepatic cholangiocarcinoma

city: Daejeon

first: Su-Hyung

last: Park

address: 291 Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We report the gene expression profiles of bulk tumor tissues of intrahepatic cholangiocarcinoma


title: Single-cell RNA sequence of ovarian tissues at E16.5, postnatal day 0 (PD0) and postnatal day 3 (PD3) with C57/BL6J mouse

city: Qingdao

first: Jun-Jie

last: Wang

state: Shandong

address: Changcheng 700

department: Qingdao Agricultural University

institute: College of Life Sciences

summary: The ovarian tissues at E16.5, postnatal 0 day (PD0 ) and 3 days (PD3) in mice were collected to perform single-cell RNA sequence (scRNA-seq) in this study. The transcriptome landscape of different cell types contributed to discern the intrinsic mechanism of early folliculogenesis, and the developmental stage-specific germline and somatic cells were defined to reveal their genetic programs along with follicle development as well as their regulative molecules and interaction signals. Synthetically, this single cell transcriptomic map of germ cells and granulosa cells would be deemed as a fundamental genetic programs of primordial follicle assembly in mice.

overall_design: Construction of transcriptome landscape of germ cells and granulosa cells from time-series ovaries from germline cyst to primordial follicle in mice

first: Wei

last: Shen


title: Hypoxia and oxygenation induce a metabolic switch between the pentose phosphate pathway and glycolysis in glioma stem-like cells

city: Hamburg

first: Katrin

last: Lamszus

address: Martinistrasse 52

institute: UKE

summary: Oxygen fluctuation during tissue remodeling imposes a major metabolic challenge in human tumors. Stem-like tumor cells in glioblastomas are believed to possess extraordinary metabolic flexibility, enabling them to initiate growth even under non-permissive conditions. To identify adaptive response mechanism, we compared the effects of acute and chronic hypoxia versus oxygenation on stem-like glioblastoma (GS) cells. GS cell lines were established and propagated either under normoxia (21% O2) or hypoxia (1% O2) and subsequently exposed to acute normoxia or hypoxia, respectively. Gene expression profiling revealed that acute hypoxia predominantly induced metabolic pathways and cell cycle arrest, whereas chronic hypoxia activated neurodevelopmental processes. In particular, we found increased expression of glycolytic enzymes, especially of the preparatory phase of glycolysis, under acute hypoxia, whereas pentose phosphate pathway (PPP) enzymes were downregulated. The opposite was found for acute oxygenation of hypoxic GS cells. Findings were confirmed by qPCR and immunoblot analyses. Despite downregulation by hypoxia, expression of PPP enzymes is increased in GBMs compared to normal brain, whereas expression of hypoxia-inducible enzymes of the parallel preparatory phase of glycolysis is decreased. Immunohistochemistry revealed strong staining for PPP enzymes in the bulk of GBM tissue, especially in highly proliferative areas, but not in pseudopalisading (hypoxic) cells. Glycolytic enzymes displayed an inverse pattern. Mass spectrometric analysis using [1,2-13C2]-D-glucose showed reduced glucose flux through the PPP under hypoxia in favor of flux through glycolysis. Acute and chronic hypoxia increased cell migration but reduced proliferation, whereas normoxia had opposite effects. Our findings extend Warburg’s observations by showing that in most tumor cells the PPP, which supplies metabolites for biomass production, is favored over the parallel preparatory phase of glycolysis, but is suppressed under acute severe hypoxia, causing a switch to direct glycolysis to protect against hypoxic stress.

overall_design: Total RNA was extracted from the following samples: 4 glioblastomas, 4 normoxic cell lines and 4 hypoxic cell lines established from the 4 original tumors, 4 normoxic cell lines exposed to hypoxia for 48 hrs, 4 hypoxic cell lines exposed to normoxia for 48 hrs

first: Annegret

last: Kathagen


title: Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia

status: Public on Dec 27 2020

city: Guangzhou

first: Xiuqin

last: Bao

address: No. 1838, Guangzhou avenue north, baiyun district, Guangzhou

institute: Southern Medical University


title: Spatiotemporal female reproductive tract gene expression in Drosophila melanogaster

status: Public on Dec 29 2020

city: Syracuse NY

first: Caitlin

last: McDonough

address: 107 College Place, 114 Life Science Complex

department: Syracuse University Biology Department

institute: Syracuse University

summary: In order to better understand the female reproductive tract (FRT) we conducted a systematic, comprehensive investigation of the FRT in a tssue-specific manner at three time points relative to mating. By characterizing the transcriptional relationships among discrete FRT tissues across time we advance the understanding of the molecular genetics of FRT functions.

overall_design: RNAseq of five FRT tissues (bursa, oviduct, seminal receeptacle, spermatheca, and parovaria) as well as the FRT-associated fat body in unmated females as well as females 6hrs and 24hrs post-mating

last: McDonough-Goldstein


title: Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia [ChIP-seq]

summary: The fetal-to-adult hemoglobin switch is regulated in a developmental stage-specific manner and reactivation of fetal hemoglobin (HbF) has therapeutic potential for β-hemoglobinopathies. Although BCL11A and ZBTB7A interact with their coregulators, reportedly mediating most γ-globin transcriptional silencing in erythroid in trans, and in cis, the molecular mechanism underlying the epigenetic dysregulation of the switch remains largely unclear. Here we showed that epigenetic inactivation of an ETS2 repressor factor (ERF) reactivates γ-globin expression during stress erythropoiesis, and ERF depletion elevates γ-globin in erythroid cells and in erythroid progenies from the edited HSPCs engrafted into immunodeficient mice. ERF represses γ-globin by directly binding to two motifs regulating HBG expression, independently of the major HbF repressors BCL11A and ZBTB7A. We further uncovered that an lncRNA, RP11-196G18.23 mediates ERF promoter hypermethylation resulting in reactivation of g-globin. Herein, the epigenetic alterations were identified as novel modulators ameliorating the severity of b-thalassemia, thus providing novel therapeutic targets for β-hemoglobinopathies.

overall_design: Examination of transcription factor ERF in HUDEP-2 cells. Input DNA served as control.

first: Xinhua

last: Zhang

first: Liren

first: Zhongju

first: Jin

last: Huang

first: Qianqian

first: Yuhua

last: Ye

first: Yongqiong

last: Liu

first: Diyu

last: Chen

first: Yangjin

last: Zuo

first: Qifa

first: Binbin

first: Jianpei

last: Fang

first: Jinquan

last: Lao

first: Xiaoqin

last: Feng

first: Yafeng

last: Li

first: Ryo

last: Kurita

first: Yukio

last: Nakamura

first: Weiwei

last: Yu

first: Cunxiang

last: Ju

first: Narla

last: Mohandas

first: Dali

first: Cunyou

last: Zhao

first: Xiangmin

last: Xu

first: Chunbo


title: Gene expression profiling of NKG2C+ NK cells generated from inflammatory CD34+DNAM-1brCXCR4+  and Lin-CD34- CD16+CD56- blood precursors

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

institute: Ospedale Pediatrico Bambino Gesù

summary:
There is limited knowledge on the origin and development of the ample spectrum of human NK cells, particularly of specialized NK subsets. Here, we characterized the NK cell progeny of CD34+DNAM-1bright CXCR4+ precursors that reside in healthy bone marrow and circulate in the peripheral blood (PB) of patients with chronic infections/inflammation. including HIV, HCV or HCMV reactivation after HSC transplantation. Unlike conventional CD34+ precursors they rapidly differentiated in vitro into cytotoxic, IFNγ-secreting CD94/NKG2C+KIR+CD57+ maturing NK cell progenies with HCMV-inhibiting activity. Progeny characterization led also to identification of an additional new PB Lin-CD56-CD16+ precursor giving rise to the same CD94/NKG2C+KIR+CD57+ maturing NK cell progenies. Microarray analysis of NK cell progenies revealed a signature compatible with maturing adaptive NK cells. In vivo circulation of multiple common lymphocyte precursors with rapid development to NKG2C+ NK cell progeny is steadily occurring and may thus be a crucial resource for the prompt control of HCMV.
We used microarray to compare the transcriptional profiles of human NKG2C+ NK cells derived from i) CD34+DNAM1brightCXCR4+ precursors, ii) Lin-CD34-CD16+CD56- precursors, iii) peripheral blood.

overall_design: 13 samples of NKG2C+ NK cells derived from mature peripheral blood NK cells (n = 3), CD34+DNAM-1brCXCR4+ progenies (n = 2) and  Lin-CD34- CD16+CD56- progenies (n = 8) were analyzed using Clariom D Pico human array (Affymetrix).

first: Federica

last: Bozzano

first: Maria

last: Ascierto

first: Lorenzo

last: Moretta

last: De Maria


title: The Aging Microenvironment Drives Alveolar Macrophage Changes in Aging [Bisulfite-Seq]

first: Ziyou

last: Ren

overall_design: Four bisulfite-Seq (reduced representation) of flow sorting of alveolar macrophages from mice treated with bone marrow chimeras to allow knowing the origin of pulmonary macrophages (TRAMs vs. Mo-AMs)

first: Alexandra

last: McQuattie-Pimentel

first: Benjamin

last: Singer

first: Alexander

last: Misharin

first: Scott

last: Budinger


title: Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia [RNA-seq]

first: Xiuqin

last: Bao

overall_design: Total RNA were extracted from ERF KO (n=3) or wild type (WT, n=2) HUDEP-2 cells and performed by deep sequencing, using Illumina.

first: Xinhua

last: Zhang

first: Liren

last: Wang

first: Zhongju

first: Jin

last: Huang

first: Qianqian

first: Yuhua

last: Ye

first: Yongqiong

last: Liu

first: Diyu

last: Chen

first: Yangjin

last: Zuo

first: Qifa

first: Binbin

first: Jianpei

last: Fang

first: Jinquan

last: Lao

first: Xiaoqin

last: Feng

first: Yafeng

last: Li

first: Ryo

last: Kurita

first: Yukio


title: A comparative analysis of reactive Müller glia gene expression after light damage and microRNA-depleted Müller glia – focus on microRNAs

status: Public on Dec 24 2020

city: New York

first: Stefanie

last: Wohl

state: NY

address: 33w 42nd Street

department: Biological and Vision Sciences

institute: SUNY Optometry

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

overall_design: Refer to individual Series


title: A comparative analysis of reactive Müller glia gene expression after light damage and microRNA-depleted Müller glia – focus on microRNAs [Affymetrix]

summary: In order to identify the mRNAs in adult light damaged Muller glia of the the neural retina, Müller glia from Hes-5 GFP reporter mice that were crossed with Swiss Webster mice were isolated by means of fluorescent activated cell sorting and analyzed their mRNAs using the Mouse Gene 1.0 ST microarray (Affymetrix). Differentially expressed genes were analyzed and compared to the genes found upregulated in the Dicer-cKO mouse (Wohl at el., 2017). miRNA:mRNA target tools were used to find potential miRNA targets of Muller glia miRNAs.

overall_design: MG from 10 light damaged and 12 undamaged retinas were FACS-purified, the RNA extracted and mRNA expression was analysed using the Mouse Gene 1.0 ST microarray (Affymetrix). Fold change of gene expression was plotted from log2 relative expression of light damaged Muller glia minus log2 relative expression from control Muller glia to dinf differetnially expressed genes after light damage.

first: Seoyoung

last: Kang

first: Daniel

last: Larbi

first: Monica

last: Andrade

first: Sara

last: Reardon

first: Thomas

last: Reh


title: Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 3333 Burnet Ave MLC7013

department: Experimental Hematology and Cancer Biology

institute: CINCINNATI CHILDRENS HOSP MED CTR

summary: The mechanistic target of rapamycin (mTOR) is a central regulator of cell growth and an attractive anti-cancer target that integrates diverse signals to control cell proliferation. Previous studies using mTOR inhibitors have shown that mTOR targeting suppresses gene expression and cell proliferation. To date, however, mTOR targeted therapies in cancer have seen very limited efficacy, and one key issue is related to the development of evasive resistance. In this manuscript, through the use of a gene targeting mouse model, we have found that inducible deletion of mTOR in hematopoietic stem cells (HSCs) results in a loss of quiescence and increased proliferation. Adaptive to the mTOR loss, mTOR-/- HSCs increase chromatin accessibility and activate global gene expression, contrary to the effects of short-term inhibition by mTOR inhibitors. Mechanistically, such genomic changes are due to a rewiring and adaptive activation of the ERK/MNK/eIF4E signaling pathway that enhances the protein translation of RNA polymerase II (RNAP II), which in turn leads to increased c-Myc gene expression, allowing the HSCs to thrive despite loss of a functional mTOR pathway. This adaptive mechanism can also be utilized by leukemia cells undergoing long-term mTOR inhibitor treatment to confer resistance to mTOR drug targeting. The resistance can then be counteracted by MNK, CDK9, or c-Myc inhibition. These results provide new insights into the physiological role of mTOR in mammalian stem cell regulation and implicate a novel mechanism of evasive resistance in the context of mTOR targeting.

overall_design: 4 Control, 4 KO mutant

first: Cuiqing

last: Fan


title: IL-31 signaling in pulmonary fibrosis

status: Public on Dec 23 2020

first: Anil

last: Jegga

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Pulmonary fibrosis (PF) is associated with many chronic lung diseases including Systemic sclerosis (SSc), Idiopathic Pulmonary Fibrosis (IPF) and Cystic Fibrosis (CF) which are characterized by the progressive accumulation of mesenchymal cells and formation of scar tissue. Th2 T cell-derived cytokines including IL-4 and IL-13 have been shown to contribute to inflammation and fibrotic remodeling in multiple tissues. Interleukin-31 (IL-31) is a newly identified cytokine that is predominantly produced by CD4 Th2 T cells, but its signaling receptor IL-31RA is primarily expressed by non-hematopoietic cells. However, the potential role of the IL-31-IL31RA axis in pulmonary inflammation and fibrosis has remained largely unknown. To determine the role of IL-31 signaling in pulmonary fibrosis, wildtype, and IL-31RA knockout mice were treated with bleomycin and measured changes in total lung transcripts using RNA-seq. The total lung transcriptome analysis showed a significant reduction in fibrosis-associated gene transcripts including extracellular matrix and epithelial cell-associated gene networks.

overall_design: mRNA profiles of IL-31 RA wild type, knock-out mice treated with bleomycin and measured changes in total lung transcripts.

first: Dan

middle: J

last: Yombo

first: Nishant

last: Gupta

first: Satish

last: Madala


title: A comparative analysis of reactive Müller glia gene expression after light damage and microRNA-depleted Müller glia – focus on microRNAs [NanoString]

summary:
In order to identify the miRNAs in adult light damaged Muller glia of the the neural retina, we isolated the Müller glia from Rlbp-CreER: Stopf/f-tdTomato by means of fluorescent activated cell sorting and analyzed their miRNAs using NanoStrings Technologies®. We compared the data to that from and Dicer1-CKO Müller glia and wild type glia Müller glia (GSE103098).
We found three miRNAs potentially regulating genes involved in stress response in both data sets.

overall_design: Fluorescence activated cell sorting (FACS) was used to purify adult light damaged Müller glia (pooled from 44 retinas, > postnatal day 21), using an Müller glia specific cre-lox labeling strategy by crossing Rlbp1-CreER with tdTomato mice. The RNA was extracted from purified Müller glia (tdTomato+) and miRNA expression was analysed using NanoString and nCounter Technologies ®.

first: Seoyang


title: Schwann cell plasticity regulates neuroblastic tumor cell differentiation

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

institute: Children's Cancer Research Institute

summary: The remarkable plasticity of Schwann cells (SCs) is essential for nerve regeneration but also contributes to neuropathies and cancer progression. It has not yet been investigated whether the adaptive potential of SCs is manifested in stromal, tumor associated SCs characteristically found within a benign subtype of neuroblastic tumors (NBTs). We here performed transcriptome profiling of human NBTs, rich and poor in SC stroma, as well as human injured nerves, rich in repair SCs, revealing that stromal SCs exhibit a repair SC characteristic gene expression signature. In turn, primary repair SCs had a pro-differentiating and anti-proliferative effect on NBT cell lines after direct and trans-well co-culture. Within the pool of secreted stromal/repair SC factors, we identified EGFL8, a matricellular protein with so far undescribed function, to induce neuronal differentiation of aggressive NBT cells. EGFL8 expression further correlated with favorable tumor stage and increased patient survival. Our findings suggest that stromal SCs exert nerve repair associated functions in the tumor-environment and underline the therapeutic value of SC-derived factors for aggressive, SC stroma-poor NBTs.

overall_design: mRNA of 24 samples were sequenced and analysed. Part of the RNA-Seq data were previously submitted in other GEO Series (GSE94035 and GSE90711).

first: Tamara

last: Weiss

first: Sabine

last: Taschner-Mandl

first: Andrea

last: Bileck

first: Helena

last: Dodig

first: Max

last: Kauer

first: Christian

last: Frech

first: Reinhard

last: Windhager

first: Christopher

last: Gerner

first: Peter

middle: F

last: Ambros

first: Inge


title: Transcriptomic of Beauveria bassiana during in vitro blastospore production

status: Public on Dec 22 2020

last: Dunlap

address: 1815 N. University st

department: Crop Bioprotection Research Unit

summary: Culturing the entomopathogenic fungus Beauveria bassiana under high glucose concentrations coupled with high aeration results in a fungal developmental shift from hyphae growth to mostly blastospores (yeast-like cells). The underlying molecular mechanisms involved in this shift remains elusive. Therefore, this has motivated us to realize a systematic analysis of the differential gene expression to uncover the fungal transcriptomic response to osmotic and oxidative stresses associated with the resulting high blastospores yield. Differential gene expression was compared under moderate glucose concentration (10% w/v) and high glucose concentration (20% w/v) daily for the three-day culturing. The RNAseq-based transcriptomic results underpinned a higher proportion of down- than up-regulated genes when the fungus was grown under 20% glucose than at 10%. A follow-up study explored a broader glucose range (4, 8, 12, 16, 20% w/v) with phenotype assessment and qRT-PCR of selected genes. Antioxidant, calcium transport, conidiation, and osmosensor related genes were highly up-regulated in higher glucose titers (18-20%) than at lower titers. These findings improved the knowledge of the molecular mechanisms during blastospore development and may help the large scale blastospores industrial production.

overall_design: 2 treatments with 3 replicates and sampled at 3 times =18


title: Molecular profiling of insular cortex neurons projecting to the central amygdala

first: Jeffrey

last: Friedman

address: 1230 York Avenue

institute: Rockefeller University

summary: We used the retro-TRAP protocol (Ekstrand et al 2014) to profile insular cortex neurons that project to the central amygdala

overall_design: Phosporylated ribosomes were immunoprecipitated from lateral sepum brain lysates that were dissected following 1 hour of restraint stress.

first: Sarah

last: Stern


title: PBMCs from patients with LS-OCMB characterization

status: Public on Dec 21 2020

city: San Sebastian

first: Maider

last: Muñoz-Culla

address: Paseo Dr.Begiristain s/n

country: Spain

institute: Biodonostia Institute

platform_organism:
Homo sapiens
synthetic construct


title: Whole-transcriptome analysis in peripheral blood mononuclear cells from patients with lipid-specific oligoclonal IgM band characterization reveals two circular RNAs and two linear RNAs as biomarkers of highly active disease

summary: Background: The presence of anti-myelin lipid specific oligoclonal IgM bands (LS-OCMBs) has been defined as an accurate predictor of an aggressive evolution of multiple sclerosis. However, the detection of this biomarker is performed in cerebrospinal fluid, a quite invasive liquid biopsy. In the present study we aimed at studying the expression profile of miRNA, snoRNA, circRNA and linearRNA in PBMCs from patients with lipid-specific oligoclonal IgM band characterization.  Methods: We included a total of 89 MS patients, 47 with negative LS-OCMB status and 42 with positive status. Microarray (miRNA and snoRNA) and RNA-seq (circular and linear RNAs) were used to perform the profiling study in the discovery cohort and candidates were validated by RT-qPCR in the whole cohort. The biomarker potential of the candidates was evaluated by ROC curve analysis.  Results: RNA-seq and RT-qPCR validation revealed that two circular (hsa_circ_0000478 and hsa_circ_0116639) and two linear RNAs (IRF5 and MTRNR2L8) are downregulated in PBMCs from patients with positive LS-OCMBs. Finally, those RNAs show a performance of a 70% accuracy in some of the combinations.  Conclusion: The expression of hsa_circ_0000478, hsa_circ_0116639, IRF5 and MTRNR2L8 might serve as minimally invasive biomarkers of highly active disease.

overall_design: 4 multiple sclerosis patients with positive and 4 patients with negative LS-OCMB status

first: Leire

last: Iparraguirre

first: Danel

last: Olaverri

first: Telmo

last: Blasco

first: Lucía

last: Sepúlveda

last: Castillo-Triviño

first: Mercedes

last: Espiño

first: Lucienne

last: Costa-Frossard

first: Álvaro

last: Prada

first: Luisa

last: Villar

first: David

last: Otaegui


title: Functional network of the long non-coding RNA growth arrest specific transcript 5 (GAS5) and its interacting proteins in senescence

status: Public on Dec 16 2020

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

summary: Increasing studies show that long non-coding RNAs (lncRNAs) play essential roles in various fundamental processes. Long non-coding RNA growth arrest-specific transcript 5 (GAS5) showed differential expressions between young and old mouse brains in our previous RNA-Seq data, suggesting its potential role in senescence and brain aging. Examination using RT-qPCR revealed that GAS5 had a significantly higher expression level in old mouse brain hippocampus region than the young one. Cellular fractionation using hippocampus-derived HT22 cell line confirmed its nucleoplasm and cytoplasm subcellular localization. We then performed overexpression (OE) or knockdown (KD) of GAS5 in HT22 cell line and found that GAS5 inhibits cell cycle progression and promotes cell apoptosis. RNA-Seq analysis of GAS5-knockdown HT22 cell identified differential expressed genes related to cell proliferation (e.g., DNA replication and nucleosome assembly biological processes). RNA pull-down assay using mouse brain hippocampus tissues revealed that potential GAS5 interacting proteins can be enriched into several KEGG pathways and some of them are involved in senescence associated diseases such as Parkinson and Alzheimer's Disease. These results contribute to better understand the underlying functional network of GAS5 and its interacting proteins in senescence at brain tissue and brain-derived cell line levels. Our study may also provide reference for developing diagnostic and clinic biomarkers of GAS5 in senescence and brain aging.

overall_design: RNA-seq of GAS5 knock down in HT22 cells

first: Siqi

last: Wang

first: Shengwei

last: Ke

first: Yueming

last: Wu

first: Duo

last: Zhang

first: Baowei

last: Liu

first: Huawei

last: Mu

first: Xiaoyuan

last: Song


title: Gene expression analysis in canine Vogt-Koyanagi-Harada/uveodermatologic syndrome and vitiligo

status: Public on Dec 17 2020

city: North Grafton

first: Jillian

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

summary: We performed a comparative immunology case study of client-owned dogs to determine if immune and skin gene expression profiles in spontaneous canine VKH and vitiligo mirror those observed in human autoimmune pigmentary diseases.

overall_design: Gene expression was analyzed using 160 custom Nanostring probes to analyze 2 canines with VKH and 1 canine with vitiligo compared to 5 healthy controls (leg margin excisions).

first: Nicholas

last: Robinson


title: miRNA sequence of glioblastoma cells exposed to HMGB1

status: Public on Dec 18 2020

city: Xi'an

first: Xiangyu

last: Gao

address: changle xi

institute: Forth military medical university

summary: Purpose:  The goals of this study are to detect changes in miRNA levels of glioblastoma treated with HMGB1 by miRNA sequence.

overall_design: Methods:glioblastoma cells treated with HMGB1 or control PBS for 48 h were used for miRNA sequencing. RNA was extracted, sequenced, and analyzed by custom service provided by Gene Denovo Biotechnology Co.(Guangzhou,China) using an Illumina NovaSeq


title: KIMAT1 and HIF1A-As2 silencing small RNA-seq

city: Manchester

first: Michela

last: Garofalo

address: Alderley Park

institute: CRUK Manchester Institute

summary: In our study, we valided the important oncogeneic roles of KIMAT1 and HIF1A-As2 in non-small cell lung cancer. We used custom designed GapmeRs to silence the KIMAT1 and HIF1A-As2 in H1299 and performed small RNA-seq. 214 and 233 microRNAs were regulated by KIMAT1 and HIF1A-As2, respectively.

overall_design: GapmeRs targeting control or lncRNAs were tranfected in H1299 cells. Total RNAs were extracted after 48 hours of tranfection.

first: Lei

last: Shi

first: Sudhakar

last: Sahoo

first: Hui-Sun

last: Leong


title: CRISPRi screen of prostate cancer associated risk cis-regulatory elements [Hi-C]

city: Toronto

first: Musaddeque

last: Ahmed

address: 101 College St

institute: University health Network

summary: Prostate cancer (PCa) associated risk SNPs are enriched in cis-regulatory elements (CREs). In this study, we screened 260 CREs that contain at least one PCa risk SNP for essentiality in V16A, 22Rv1 and A549 cells. We tiled the CREs and 14 control regions using 5,873 sgRNAs.

overall_design: Hi-C in V16A and 22Rv1 cells.

first: Housheng

last: He


title: CRISPRi screen of prostate cancer associated risk cis-regulatory elements [ChIP-seq]

overall_design: A pooled library of cells lacking individial CREs or control regions was generated using CRISPR/dCas9-KRAB suppression technique. The regions were targeted using a custom sgRNA library. The cell DNA were extracted at day 0 and day 16, and the abundance of sgRNA was estimated using NGS.


title: Whole-transcriptome in PBMCs from patients with LS-OCMB characterization reveals 4 RNAs as biomarkers of highly active disease

first: Maider

last: Muñoz-Culla

overall_design: 5 multiple sclerosis patients with positive and 6 patients with negative LS-OCMB status

first: Leire

last: Iparraguirre

first: Danel

last: Olaverri

first: Telmo

last: Blasco

first: Lucía

last: Sepúlveda

first: Tamara

last: Castillo-Triviño

first: Mercedes

last: Espiño

first: Lucienne

last: Costa-Frossard

first: Álvaro

last: Prada

first: Luisa

last: Villar

first: David

last: Otaegui


title: CRISPRi screen of prostate cancer associated risk cis-regulatory elements [CRISPRi]


title: CRISPRi screen of prostate cancer associated risk cis-regulatory elements [RNA-seq]


title: Comparative transcriptomic analysis of Crohn's-associated Escherichia coli in laboratory and host environments

city: Hamilton

first: Wael

last: Elhenawy

address: 1200 Main St West

institute: McMaster University

summary: We used next generation sequencing to sequence the transcriptome of AIEC str. NRG857c and identify the genes that are differentially regulated in the gut.

overall_design: RNA was extracted from AIEC populations in vitro and in the ceca of infected hosts. Transcriptomes were sequenced using the Illumina HiSeq 2000 platform and the processed data was used for differential gene expression analysis to map the genes that are differentially regulated in vivo.

first: W

first: S

last: Hordienko

last: Gould

first: A

last: Oberc

first: C

middle: N

last: Tsai

first: T

last: Hubbard

first: M

last: Waldor

first: B

last: Coombes


title: Single cell profilng of hSpS derived from hiPS cells

status: Public on Dec 15 2020

city: Palo Alto

first: Jimena

last: Andersen

state: CA

address: 318 Campus Drive, Clark Center, 2nd floor/W200

institute: Stanford University

summary:
Single cell gene expression profilling of hSpS derived from hiPS cells at day 45 and 53 of differentiation
Raw data not provided due to patient privacy concerns.

overall_design: 5 samples of hiPS cell derived cultures, derived from 4 donors

first: Sergiu

last: Pasca

first: Elisabeth

last: Walczak


title: Ikaros is required for the controled activation of Notch target genes

city: Montréal

first: Eric

last: Milot

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: HMR research center/Université de Montréal

summary: Summary  Purpose: By means of high-throughput data analysis (high-throughput sequencing or next-generation sequencing -NGS-), we addressed the effect of the absence of Ikaros and the Notch pathway activation in mouse fetal liver erythroid cells. Specifically, the goals of this study are (i) to characterize the transcriptome of erythroid cells in the absence of Ikaros, when the Notch pathway is activated or not (by RNA-seq); (ii) to identify patterns in the modification of gene regulation according to the variable conditions; and (iii) to obtain information on mechanisms involved in the variation of gene regulation.    Methods: Erythroid cells obtained from Ikaros wild type (WT) or Ikaros knockout (Null) mouse fetal livers at the embryonic stage e14.5. These cells were co-cultured for 48 h on OP9 or OP9-DL1 cells.  mRNA profiles were generated by NGS, in biological triplicate, using Illumina cBot 2 System. The quality of the raw reads was assessed with FASTQC. Report show no pool imbalance. After examining the quality of the raw reads, no trimming was deemed necessary. The reads were aligned to the GRCm38/mm10 genome with TopHat. The raw alignment counts were calculated with htseq-count. DESeq2 calculates the differential expression of genes directly from the raw alignment counts calculated with htseq-count. The output from DESeq2 includes the raw counts normalized relative to the total number of reads. The log2 fold change is an estimate of the fold change between the conditions, based on the distribution of the reads. qRT-PCR validation was performed using specific primer sets in real-time PCR with SYBR Green.    Results. Based on expression profiles, all samples clustered correctly. The differential expression analysis was perform with all samples. For subsequent analysis, 2452 differentially expressed genes were identified in Ikaros WT vs Ikaros null cells cultured on OP9 cells, using a log2 ≥ 1 and a p value <0.005. Additionally, 2847 differentially expressed genes were identified in Ikaros WT vs Ikaros Null cells cultured on OP9-DL1 cells, using a log2 ≥ 1 and a p value <0.005. Among genes activated by Notch (cells cultured on OP9-DL1), 616 genes were repressed in the absence of Ikaros (Ikaros Null vs WT cells; log2≥ -0.8 and a p value <0.005) and 1558 genes were overexpressed in in the absence of Ikaros (Ikaros Null vs WT cells: log2≥ 0.8 and a p value <0.005), using adjusted p value <0.005. Modified expression or immunoprecipitation of several gene transcripts was confirmed with qRT-PCR.    Conclusions (Summary): The results obtained demonstrate that Ikaros can favour repression of Notch target genes but can also be required for proper activation on Notch targets upon Notch pathway activation.

overall_design: Mouse e14.5 fetal liver erythroid cells mutated or not for Ikaros (Ikaros null allele) were cocultured on OP9 or OP9-DL1 cells for 48hours and used for RNA-sequencing. Biological triplicates were used.


title: CRISPRi screen of prostate cancer associated risk cis-regulatory elements

first: Musaddeque

last: Ahmed

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

overall_design: Refer to individual Series


title: Deficiency in Ybx1 Leads to Postnatal Lethality and IBD-like Disease in Zebrafish

city: Boston

first: Bo

last: Zhu

state: MA

address: 1 Blackfan Circle

department: Biology of Vascular Program

institute: Boston Children's Hospital

summary: Y box-binding protein 1 (Ybx1) is critical for embryogenesis and organogenesis. In zebrafish, we identify Ybx1 is predominantly expressed in the enterocytes of intestine in day5 larvae, whereas its immediately degradation driven by ubiquitination on day6. Here we show the maternal lethality with cardiac edema in ybx1-/- larvae, and postnatal larval lethality exhibited in ybx1-/- larvae within the death window from 10dpf to 20dpf. To study the underlying mechanisms for the ybx1-/- larvae partial lethality, we performed RNA-seq and experimental results showed the increased ROS might be the underlying cause for the postnatal lethality. By ascorbic acid treatment, we found ascorbic acid exposure prevented ybx1-/- larvae from postnatal lethality, while hydrogen peroxide aggravated ybx1-/- larvae postnatal lethality during the death window. By RNA-seq analysis, we also found significantly increased expressions of mmp9 and mmp13a in ybx1-/- larvae, and by inhibition of either MMP9 or MMP13a expression partially rescue the ybx1-/- postnatal lethality during the death window. Later, we further identify the intestinal impairs on 30 dpf and further deteriorated severe intestinal disorder in Ybx1 deficiency zebrafish. By exposure of ybx1-/- zebrafish for 14 days, we discover ascorbic acid partially mend the impaired intestine in ybx1-/-. In this study, we demonstrate that ybx1-/- larvae were ROS-susceptible, and the increased inflammation in ybx1-/- larvae intestine identified enables the ybx1-/- zebrafish as good model for studying of intestinal disease.

overall_design: three different genotypes, day5 WT, day6 WT, and day5 ybx1-/- were used total RNA extraction.

last: ZHU

first: Pardeshi

last: Lakhansing

first: Chen

last: Yingying

first: Wei

last: Ge


status: Public on Dec 14 2020

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

institute: Lund University

summary: mRNA expression data for VPS39-silenced human muscle cells and controls (n=6 per group) were obtained using GeneChip™ Human Gene 2.0 ST Assay (Applied Biosystems)

overall_design: We analyzed mRNA expression in VPS39-silenced human muscle cells and controls (n=6 per group) using GeneChip™ Human Gene 2.0 ST Assay (Applied Biosystems)

first: Cajsa

last: Davegårdh

first: Johanna

last: Säll

first: Camilla

last: Scheele

first: Emma

last: Nilsson


title: expression data for the mouse skeletal muscle from VPS39 ko and WT

summary: mRNA expression data for the mouse muscle (n=6 per sex and genotype, for a total of 24 mice) were obtained using Clariom™ S Assay Mouse (Applied Biosystems) according to the manufacturer’s recommendations.

overall_design: We analysed mRNA expression in the mouse muscle (n=6 per sex and genotype, for a total of 24 mice) using Clariom™ S Assay Mouse (Applied Biosystems) according to the manufacturer’s recommendations.

first: Anna

last: Benrick

first: Jens

middle: U

last: Würthner

first: Elisabet

last: Stener-Victorin

first: Klaus

last: Pfeffer


title: Exosome-mediated radiosensitizing effect on neighboring cancer cells via exosomal microRNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: The precise mechanism of intercellular communication among cancer cells after radiation exposure remains unclear. Exosomes are membrane-enclosed small vesicles constituted by lipid bilayers and are recognized as mediators of intercellular communication that transport a variety of intracellular components, including microRNA (miRNA). Here we identified novel roles of exosomes released from irradiated cells to neighboring cancer cells. To confirm the presence of exosomes in the culture media of the human pancreatic cancer cell line MIAPaCa-2, ultracentrifugation was performed followed by transmission electron microscopy and nanoparticle tracking analysis (NanoSight) using the exosome-specific surface markers CD9 and CD63. Subsequent endocytosis of exosomes was confirmed by fluorescent microscopy. Cell survival after irradiation and following the addition of exosomes was evaluated by a colony-forming assay. Expression of miRNAs in exosomes was then quantified by microarray analysis, while those of Cu/Zn superoxide dismutase (SOD1) and Mn-superoxide dismutase (SOD2) enzymes in MIAPaCa-2 cells were evaluated by western blotting. Results showed that the uptake of irradiated exosomes was significantly higher than that of non-irradiated exosomes. Notably, irradiated exosomes induced higher intracellular levels of ROS and a higher frequency of DNA damage in MIAPaCa-2 cells, as determined by fluorescent microscopy and immunocytochemistry, respectively. Moreover, six upregulated and five downregulated miRNAs were identified in 5 Gy- and 8 Gy-irradiated cells using miRNA microarray analyses. Further analyses using miRNA-mimics and real time reverse transcription PCR identified miR-6823-5p as a possible candidate for SOD1 inhibition, leading to increased intracellular ROS level and DNA damage.  This is the first study to demonstrate that irradiated exosomes can enhance the radiation effect via increased intracellular ROS levels in cancer cells, potentially leading to improved understanding of the bystander effect of neighboring cancer cells.

overall_design: To investigate which exosomal microRNAs are related to radiosensitizing effect, we extracted exomal RNA from non-irradiated cells and irradiated (5 Gy and 8 Gy) cells and compared a total of 2565 microRNAs expressions.

first: Ai

last: Nakaoka

first: Makiko

last: Nakahana

first: Sachiko

last: Inubushi

first: Hiroaki

last: Akasaka

first: Mohammed

last: Salah

first: Yoshiko

last: Fujita

first: Hikaru

last: Kubota

first: Mennaakkah

last: Hassan

first: Ryo

last: Nishikawa

first: Naritoshi

last: Mukumoto

first: Takeaki

last: Ishihara

first: Daisuke

last: Miyawaki

first: Takashi

last: Sasayama

first: Ryohei

last: Sasaki


title: A PRC2-independent function for EZH2 in regulating rRNA 2′-O methylation and IRES-dependent translation

status: Public on Dec 10 2020

first: Yanqiang

last: Li

address: 300 Longwood Ave.

department: Cardiology Department

summary: Overactivated ribosome biogenesis is a common feature of cancer. However, the underlying molecular mechanism remains elusive. Herein, we report enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, could interact with fibrillarin (FBL) directly in the nucleolus. While loss of EZH2 does not impact FBL-mediated histone H2AQ104 methylation (H2AQ104me) and 18S rRNA processing, EZH2 is proved to be involved in rRNA 2′-O methylation in a manner dependent of its interaction with FBL. Mechanistically, EZH2 strengthens the fibrillarin (FBL)-NOP56 interaction by binding to both proteins and thus facilitates the assembly of box C/D small nucleolar ribonucleoprotein (box C/D snoRNP). Strikingly, EZH2 deficiency alters translational efficiency and reduces internal ribosome entry site (IRES) activity of key oncogenes in prostate cancer. In summary, our findings reveal a novel non-methyltransferase role of EZH2 that mediates FBL functions, which may provide more options for the development of EZH2-targeting curative strategies in cancer.

overall_design: Examination of  2'-O-Methylation of the rRNA in the siCTRL(3replicates) and siEZH2(2 and 2 replicates) C4-2 cells using ribo-Meth sequencing methed.

first: Yang

last: Yi

first: Qingshu

last: Meng

first: Wei

last: Zhao

first: Kaifu

last: Chen

first: Qi

last: Cao