title: A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance [RNA-seq]

status: Public on Mar 16 2021

city: La Jolla

first: Stanislav

last: Dikiy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: Scripps Research

summary: STAT5 transcription factor activation downstream of the Interleukin-2 receptor (IL-2R) induces expression of Foxp3, a critical step in the differentiation of regulatory T (Treg) cells. Due to the pleiotropic outputs of IL-2R signaling, it is unclear whether STAT5 acts directly on the Foxp3 locus to promote its expression . Here, we report that IL-2 – STAT5 signaling converged on an enhancer (CNS4) during Foxp3 induction. CNS4 facilitated and sustained the IL-2 dependent CD25+Foxp3– precursor to Treg cell transition in the thymus. Its deficiency resulted in markedly impaired Treg cell generation in neonates, which was partially mitigated with age. While the thymic Treg cell paucity caused by CNS4 deficiency did not result in autoimmunity on its own, it exacerbated autoimmune manifestations caused by disruption of the Aire gene. Thus, CNS4 enhancer activity ensures robust Treg cell differentiation early in postnatal life and cooperatively with other tolerance mechanisms, minimizes autoimmunity.

overall_design: Regulatory T cells sorted from age- and sex-matched male and female CNS4-sufficient and -deficient mice were subjected to RNA sequencing to uncover the differential gene expression.

first: Beisi

last: Xu

first: Jun

last: Li

first: Lu

last: Bai

first: Menglin

last: Jiang

first: Laura

last: Janke

first: Xinying

last: Zong

first: Xiaolei

last: Hao

first: Beatrice

last: Hoyos

first: Zhong-Min

first: Yiping

last: Fan

middle: Y

last: Rudensky

first: Yongqiang

last: Feng


title: A Single-Cell Resolution Atlas of expanding hematopoietic organ in zebrafish

status: Public on Mar 18 2021

city: Shanghai

first: Zhixin

last: Kang

address: 320 Yue Yang Road, Shanghai

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology

type: Expression profiling by high throughput sequencing

summary: To profile the developmental landscape of fetal HSPCs and their local niche, here, by using single-cell RNA-sequencing, we decoded the expanding hematopoietic organ in zebrafish

overall_design: The tails of 3.5 dpf and 4.5 dpf Tg (kdrl:mCherry/CD41:GFP) embryos were collected and digested with 2.5% trypsin for dissociation.The 50,000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting (FACS) for 10× Genomics analysis (CapitalBio Technology Corporation). Please note that the GSE120503 (GSM3402061 55hpf CHT single cell RNA seq data) raw data been re-analyzed in the current study.

last: Xia

first: Yuanyuan

last: Xue

first: Feng

last: Liu


title: A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance [ATAC-Seq]

status: Public on Mar 17 2021

country: USA

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Cells were FACS sorted from male Foxp3GFP mice by the following markers: DN1: CD4–CD8–CD44+CD25–, DN2: CD4–CD8–CD44+CD25+, DN3: CD4–CD8–CD44–CD25+, DN4: CD4–CD8–CD44–CD25–, DP: CD4+CD8+, CD4SP: CD4+CD8–CD44–CD25–, (thymus); Tn: CD4+TCRβ+Foxp3-GFP–CD25–CD44loCD62Lhi, rTreg: CD4+Foxp3-GFP+CD44loCD62Lhi, and aTreg: CD4+Foxp3-GFP+CD44hiCD62Llo (SLOs). There was 1 biological replicate per cell population with 40,000 to 50,000 cells. Immediately after sorting cells were processed to generate ATAC libraries as previously described with minor modifications (Buenrostro et al., 2015).

last: Wang

first: Alexander


title: A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance[TCR-seq]

city: Memphis

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: STAT5 activation downstream of the Interleukin-2 receptor (IL-2R) facilitates Foxp3 expression, which is required for the differentiation and function of regulatory T (Treg) cells. However, due to the pleiotropic roles of IL-2R signaling, it is unclear how STAT5 acts on the Foxp3 locus to promote Treg cell lineage commitment. Here, we report that IL-2–STAT5 signaling converges on an enhancer (CNS4) during early Foxp3 induction. CNS4 facilitates and sustains the IL-2–dependent CD25+Foxp3– precursor to Treg cell transition in the thymus. Its deficiency results in markedly impaired Treg cell generation in neonates, which is partially mitigated with age. While the thymic Treg cell paucity caused by CNS4 deficiency did not result in autoimmunity on its own, it exacerbated autoimmune manifestations caused by disruption of the Aire gene. Thus, CNS4 enhancer activity ensures robust Treg cell differentiation early in postnatal life and, cooperatively with other tolerance mechanisms, minimizes autoimmunity.

overall_design: Regulatory T cells were sorted from Foxp3 enhancer CNS4-floxed and deficient mice. Total RNA was extracted to amplify T cell receptor (TCR) alpha and beta chains to uncover TCR repertoire diversities with high throughput sequencing.

last: Dikiy


title: Predicting the allergenicity of legume proteins using a PBMC gene expression assay

city: Zeist

first: Marjolein

last: Meijerink

state: Utrecht

address: Utrechtseweg 48

department: RAPID

country: Netherlands

institute: TNO

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

overall_design: Refer to individual Series


title: A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance[ChIP-seq][Stat5]

last: Xu

overall_design: Chromatin immunoprecipitation (ChIP) was used to reveal STAT5 binding around the Foxp3 locus.

last: Li

first: Stanislav


title: A distal Foxp3 enhancer enables interleukin-2 dependent thymic Treg cell lineage commitment for robust immune tolerance

overall_design: Treg cells (CD4+Foxp3-GFP+) were sorted from the SLOs of 8-week-old Cd4-cre(tg+)CNS4FL (experimental) and Cd4-cre(tg–)CNS4FL (control) littermates. There were 2 biological replicates per cell population with 40,000 to 50,000 cells. Immediately after sorting cells were processed to generate ATAC libraries as previously described with minor modifications (Buenrostro et al., 2015).

last: Bai

last: Jiang

first: Beisi


title: Predicting the allergenicity of legume proteins using a PBMC gene expression assay_Pilot experiment

summary: Food proteins differ in their allergenic potential. Currently, there is no predictive and validated bio-assay to evaluate the allergenicity of novel food proteins. The objective of this study was to investigate the potential of a human peripheral blood mononuclear cell (PBMC) gene expression assay to identify biomarkers to predict the allergenicity of legume proteins. PBMCs from healthy donors were exposed to weakly and strongly allergenic legume proteins. Possible biomarkers for allergenicity were investigated by exposing PBMCs to a protein pair of weakly (white bean) and strongly allergenic (soybean) 7S globulins in a pilot experiment. Gene expression was measured by RNA-sequencing and differentially expressed genes were selected as biomarkers. 153 genes were identified as having significantly different expression levels to the 7S globulin of white bean compared to soybean.

overall_design: PBMCs from four donors were stimulated with 10 μg/mL or 50 μg/mL 7S globulins from white bean (phaseolin) and soybean (Gly m 5) for 4h in the pilot experiment (five replicates per donor, 2 outlier fastq-files were removed).

first: Mark

last: Smits

first: Thuy

middle: M

last: Le

first: André

last: Knulst

first: Aard

last: de Jong

first: Martinus

middle: P

last: Caspers

first: Everton

last: Souto Lima

first: Lilia

last: Babé

first: Gregory

last: Ladics

first: Scott

last: McClain

first: Geert

last: Houben

first: Kitty

last: Verhoeckx


title: Phenotypically anchored mRNA and miRNA expression profiling in zebrafish reveals flame retardant chemical toxicity networks

city: Corvallis

first: Christopher

middle: Michael

last: Sullivan

state: OR

address: Sinnhuber Aquatic Research Laboratory, 28645 East HWY 34

department: Environmental & Molecular Toxicology

institute: Oregon State University

type: Non-coding RNA profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to examine mRNA and miR networks on exposures to flame retardant chemicals (FRCs), an ubiquitous group of chemicals in the environment
Methods: Four biological replicates were created by pooling eight embryos per replicate from individual wells which were placed into an Eppendorf Safelock Tube and excess solution removed. 0.5 mM zirconium oxide beads were added along with 500 µL of RNAzol (Molecular Research Center, Inc.) and the tubes were immediately placed into a bullet blender (Next Advance), using settings recommended by the manufacturer. The RNA was purified using the Direct-zol MiniPrep kit (Zymo Research), including an optional DNase-1 digestion treatment for 15 minutes. RNA integrity (RIN) was assessed using an Agilent Bioanalyzer (Santa Clara, CA), and RNA samples with RIN values >8 were processed for library preparation and sequencing at the Oregon State University Center for Genome Research and Biocomputing. Total RNA was used as input for both mRNA and miRNA sequencing. For mRNA sequencing, mRNA was poly A selected, libraries were prepared with the PrepX™ mRNA and Illumina sequencing workflow (Wafergen Biosystems). For miRNA seq, the Illumina TruSeq Small RNA library kit was used to generate small RNA libraries from total RNA. For sequencing, an Illumina HiSeq 3000 sequencer (Illumina, San Diego) was used for mRNA and small RNA single-end sequencing at 100 and 50 base pairs, respectively. Bioinformatics analysis of sequencing data was performed on an R platform. Briefly, reads were evaluated by FastQC v0.11.3 to detect major sequencing problems, and then trimmed for quality control with Skewer v0.2.2 .  RNA-seq alignment and quantification proceeded with Bowtie2 v2.2.3  being used to build HISAT2 (Kim et al., 2013) genome index files from the Genome Reference Consortium Zebrafish Build 10 (GRCz10) genome. For miR identification and quantification, a combination of miRDeep2 v2.0.0.8, miRBase release 22 and Bowtie v1.2.1.1 were used. Differential expression between experimental and control samples was determined with functions from the Bioconductor package, edgeR; mRNAs with a log2 fold change ≥1.5 and Benjamini-Hochberg (BH) adjusted p ≤ 0.05 were considered differentially expressed while an adjusted p ≤ 0.05 was applied to miRs without any fold change cutoffs. Heatmap clustering of differentially expressed genes were generated in R based on their log2 fold changes using the ggplot2 package.
Results: We found widespread disruption of mRNA and miR expression. Neurodevelopment was a key disrupted biological process across multiple FRCs and was corroborated by behavioral deficits. Several mRNAs (eg: osbpl2a) and miRs (eg- mir-125b-5p), showed differential expression common to multiple FRCs (10 and 7 respectively). These common miRs were also predicted to regulate a network of differentially expressed genes with diverse functions, including apoptosis, neurodevelopment, lipid regulation and inflammation. Commonly disrupted transcription factors (TFs) such as RXR, RAR and VDR were predicted to regulate a wide network of differentially expressed mRNAs across a majority of the FRCs. Many of the differential mRNA-TF and mRNA-miR pairs were predicted to play important roles in development as well as cancer signaling. Specific comparisons between TBBPA and its derivative TBBPA-DBPE showed contrasting gene expression patterns that corroborated with their phenotypic profiles. The newer generation FRCs such as IPP and TCEP produced distinct gene expression changes compared to the legacy FRC BDE-47.
Conclusions: Our study is the first to establish a mRNA-miR-TF regulatory network across a large group of structurally diverse FRCs and diverse phenotypic responses. The purpose was to discover common and unique biological targets that will help us understand mechanisms of action for these important chemicals.

overall_design: mRNA and miR profiles of zebrafish embryos exposed to 10 FRCs from 6 to 48 h post fertilization (hpf)

first: Subham

last: Dasgupta

first: Cheryl

last: Dunham

first: Lisa

last: Truong

first: Michael

last: Simonich

first: Robyn

last: Tanguay


title: Predicting the allergenicity of legume proteins using a PBMC gene expression assay_Biomarker search study

first: Marjolein

last: Meijerink

summary: Food proteins differ in their allergenic potential. Currently, there is no predictive and validated bio-assay to evaluate the allergenicity of novel food proteins. The objective of this study was to investigate the potential of a human peripheral blood mononuclear cell (PBMC) gene expression assay to identify biomarkers to predict the allergenicity of legume proteins. PBMCs from healthy donors were exposed to weakly and strongly allergenic legume proteins. Inclusion of multiple protein pairs from 2S albumins (lupine and peanut) and 7S globulins (white bean and soybean) in a larger study, led to the selection of CCL2, CCL7, and RASD2 as biomarkers to distinguish weakly from strongly allergenic proteins.

overall_design: PBMCs from five donors were stimulated with 10 μg/mL or 50 μg/mL 2S albumins from lupine (δ-conglutin) and peanut (Ara h 2), and 50 μg/mL 7S globulins from white bean and soybean (five replicates per donor).

first: Mark

last: Smits


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (RNA-seq - Differentiation)

city: Dallas

first: Edward

last: Wakeland

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

summary: Myeloid lineage cells use TLRs to recognize and respond to diverse microbial ligands. Although unique transcription factors dictate the outcome of specific TLR signaling, whether lineage-specific differences exist to further modulate the quality of TLR-induced inflammation remains unclear. Comprehensive analysis of global gene transcription in human monocytes, monocyte-derived macrophages and monocyte-derived dendritic cells stimulated with various TLR ligands identifies multiple lineage-specific, TLR-responsive gene programs. Monocytes are hyperresponsive to TLR7/8 stimulation that correlates with higher expression of the receptors. While macrophages and monocytes express similar levels of TLR4, macrophages, but not monocytes, upregulate Interferon-Stimulated Genes (ISGs) in response to TLR4 stimulation. We find that TLR4 signaling in macrophages uniquely engages transcription factor IRF1, which facilitates opening of ISG loci for transcription. This study provides a critical mechanistic basis for lineage-specific TLR responses and uncovers IRF1 as a master epigenetic regulator for the ISG transcriptional program in human macrophages.

overall_design: RNA-seq anlaysis of transcriptional changes in monocytes, MDMs and MDDCs during differentiation from monocytes to MDMs or MDDCs

first: Ran

last: Song

first: Igor

last: Dozmorov

first: Venkat

last: Malladi

first: Chaoying

last: Liang

first: Carlos

last: Arana

first: Benjamin

first: Chandrashekhar

last: Pasare

middle: K


title: Targeted DamID analyses of neural progenitor cells and immature neurons of kdm5[140] and kdm5 shRNA Drosophila larvae and pupae.

city: Bronx

first: Hayden

middle: A. M.

last: Hatch

state: New York

address: 1300 Morris Park Avenue, Ullmann 809

department: Dominick P. Purpura Department of Neuroscience; Department of Genetics

institute: Albert Einstein College of Medicine

summary: Mutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding their spatiotemporal requirements or neurodevelopmental contributions. Utilizing the mushroom body (MB), a major learning and memory center within the Drosophila brain, we demonstrate that KDM5 is required within ganglion mother cells and immature neurons for proper axogenesis. Moreover, the mechanism by which KDM5 functions in this context is independent of its canonical histone demethylase activity. Using in vivo transcriptional and binding analyses, we identify a network of genes directly regulated by KDM5 that are critical modulators of neurodevelopment. We find that KDM5 directly regulates the expression of prospero, a transcription factor that we demonstrate is essential for MB morphogenesis. Prospero functions downstream of KDM5 and binds to approximately half of KDM5-regulated genes. Together, our data provide evidence for a KDM5-Prospero transcriptional axis that is essential for proper MB development.

overall_design: kdm5[140] analysis: 20 samples with 5 biological replicates for kdm5[140]; R71C09-Gal4 with UAS-dam:polII and UAS-dam and 5 biological replicates for R71C09-Gal4 with UAS-dam:polII and UAS-dam. kdm5 shRNA analysis: 12 samples with 3 biological replicates for tubulin-Gal80[ts]; R71C09-Gal4, kdm5 shRNA with UAS-dam:polII and UAS-dam and 3 biological replicates for tubulin-Gal80[ts]; R71C09-Gal4, scramble shRNA with UAS-dam:polII and UAS-dam.

first: H

middle: A

last: Belalcazar

first: O

middle: J

last: Marshall

first: J

last: Secombe


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (RNA-seq - THP-1 IRF1 KO)

overall_design: RNA-seq anlaysis of transcriptional changes in PMA-differentiated control clonal THP-1 cell line and PMA-differentiated IRF1 deficient clonal THP-1 cell lines unstimulated or stimulated with LPS for 1 or 6 hours


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (ATAC - IRF1 KO THP-1)

overall_design: ATAC-seq anlaysis of epigenomic changes in PMA-differentiated control clonal THP-1 cell line and PMA-differentiated IRF1 deficient clonal THP-1 cell line unstimulated or stimulated with LPS for 1, 3 or 6 hours


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (RNA-seq - THP-1)

overall_design: RNA-seq anlaysis of transcriptional changes in undifferentiated and PMA-differentiated THP-1 cells unstimulated or stimulated with LPS or R848 for 18 hours


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (ATAC - Differentiation)

overall_design: ATAC-seq anlaysis of epigenomic changes in monocytes, MDMs and MDDCs during differentiation from monocytes to MDMs or MDDCs


title: Wildtype (wt) mouse cone transcriptome change with Txnip treatment

status: Public on Mar 15 2021

city: Boston

first: Yunlu

last: Xue

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University

summary:
Purpose: To identifiy mRNA changes in wt cone photoreceptors with Txnip overexpression treatment, which improved retinitis pigmentosa (RP) cone survival and visual acuity.
Methods: two wt mouse strains, BALB/c and C57BL/6J were injected with AAV-Txnip or AAV-H2BGFP control subretinally at P0. Retinas were dissected out at P21 for BALB/c and P35 for C57BL/6J. 1,000 H2BGFP labeled cones per retina sample were FACS sorted out, and subject for RNA-sequencing.
Results: only ~70 genes in P21 BALB/c and 1 genes in C57BL/6J  were found differentially expressed with Txnip treatment. Only 1 genes  (i.e. Txnip) were in commonly upregulated between the two lists.
Conclusions: Txnip seems to be not changing RNA expression much in wt cones. Instead, its major function to rescue RP cones may lay in protein-protein interactions.

overall_design: Cone photoreceptor mRNA profiles of 21-day old BALB/c and 35-day old C57BL/6J mice  with or without AAV-Txnip treatment.

first: Connie

last: Cepko


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (ATAC - Time course)

overall_design: ATAC-seq anlaysis of epigenomic changes in monocytes and MDMs unstimulated or stimulated with LPS for 1, 6 or 18 hours


title: Human first trimester villous cytotrophoblast: 8-10 gestational week vs. 12-14 gestational week

city: PARIS

first: Severine

middle: Aude

last: Degrelle

address: 4 avenue de l'Observatoire

country: France

institute: INSERM UMRS-1139

summary: Physiological oxygen tension rises dramatically in the placenta between 8 and 14 weeks of gestation. Abnormalities in this period can lead to gestational diseases, whose underlying mechanisms remain unclear. We explored the changes at mRNA level by comparing the transcriptomes of human placentas at 8-10 gestational weeks and 12-14 gestational weeks. A total of 20 samples were collected and divided equally into four groups based on sex and age. Cytotrophoblasts were isolated and sequenced using RNAseq. Key genes were identified using two different methods: DESeq2 and weighted gene co-expression network analysis (WGCNA). We also constructed a local database of known targets of hypoxia-inducible factor (HIF) subunits, alpha and beta, to investigate expression patterns likely linked with changes in oxygen. Patterns of gene enrichment in and among the four groups were analyzed based on annotations of gene ontology (GO) and KEGG pathways. We characterized the similarities and differences between the enrichment patterns revealed by the two methods and the two conditions (age and sex), as well as those associated with HIF targets. Our results provide a broad perspective of the processes that are active in cytotrophoblasts during the rise in physiological oxygen, which should benefit efforts to discover possible drug-targeted genes or pathways in the human placenta.

overall_design: A total of 20 cytotrophoblast samples were divided into four groups according to the age (8-10 gestational week vs. 12-14 gestational week) and sex (male vs. female). One microgram of total RNA from each sample preparation was used for the construction of sequencing libraries,

first: Fulin

last: Liu

first: Christelle

last: Simasotchi

first: Françoise

last: Vibert

first: Wencan

last: Zhu

first: Sophie

last: Gil

first: Séverine

first: Thierry

last: Fournier


title: IRF1 governs the differential Interferon-Stimulated Gene responses in human monocytes and macrophages by regulating chromatin accessibility (RNA-seq - Time course)

first: Edward

last: Wakeland

overall_design: RNA-seq anlaysis of transcriptional changes in monocytes and MDMs unstimulated or stimulated with LPS, R837, TL8-506 or R848 for 1, 6 or 18 hours

first: Ran

last: Song

first: Igor

last: Dozmorov

first: Venkat

last: Malladi

first: Chaoying

first: Carlos


title: Dichotomic hippocampal transcriptome after glutamatergic versus GABAergic deletion of the cannabinoid CB1 receptor

city: Mainz

first: Anna

last: Wierczeiko

address: Hanns-Dieter-Hüsch-Weg 15

department: Institute for Human Genetics

country: Germany

institute: University Medical Center, Johannes Gutenberg University Mainz

summary:
Brain homeostasis is the dynamic equilibrium whereby physiological parameters are kept actively within a specific range. The homeostatic range is not fixed and may change throughout the individual’s lifespan, or may be transiently modified in the presence of severe perturbations. The endocannabinoid system has emerged as a safeguard of homeostasis, e.g., it modulates neurotransmission and protects neurons from prolonged or excessively strong activation.
We used genetically engineered mouselines that lack the cannabinoid type-1 receptor (CB1) either in dorsal telencephalic glutamatergic or in forebrain GABAergic neurons to create new allostatic states, resulting from alterations in the excitatory/inhibitory (E/I) balance. Previous studies with these two mouse lines have shown dichotomic results in the context of behavior, neuronal morphology, and electrophysiology.Thus, we aimed at analyzing the transcriptomic profile of the hippocampal CA region from these mice in the basal condition and after a mild behavioral stimulation (open field).
Our results provide insights into the gene networks that compensate chronic E/I imbalances. Among these, there are differentially expressed genes involved in neuronal and synaptic functions, synaptic plasticity,and the regulation of behavior. Interestingly, some of these genes, e.g., Rab3b, Crhbp, and Kcnn2, and related pathways showed a dichotomic expression, i.e., they are up-regulated in one mutant line and down-regulated in the other one. Subsequent interrogation on the source of the alterations in transcript levels were applied using exon-intron split analysis. However, no strong directions towards transcriptional or post-transcriptional regulation comparing both mouse lines were observed.
Altogether, the dichotomic gene expression observed and their involved signaling pathways are of interest because they may act as “switches” to modulate the directionality of neural homeostasis, which then is relevant for pathologies, such as stress-related disorders and epilepsy.

overall_design: Transcriptomic profiles of the hippocampal Cornus Ammonis of glutamatergic and GABAergic CB1 knockout and wild-type mice after open field exposure and under basal condition

first: Diego

last: Cuadrado

first: Charlotte

last: Hewel

first: Susanne

last: Gerber

first: Beat

last: Lutz


title: Targeted transcriptomic analysis of C57BL/6 and BALB/c mice during progressive chronic Toxoplasma gondii infection reveals changes in host and parasitic gene expression relating to neuropathology and resolution [Neuroinflammation]

status: Public on Mar 12 2021

city: Riverside

first: Emma

middle: Harriet

last: Wilson

address: 900 University Avenue

institute: UC Riverside

summary: Toxoplasma gondii is a resilient parasite that infects a multitude of warm-blooded hosts and results in a lifelong chronic infection requiring continuous responses by the host. Chronic infection is characterized by a balanced immune response and neuropathology that are driven by changes in gene expression. Previous research pertaining to these processes has been conducted in various mouse models, and much knowledge of infection-induced gene expression changes has been acquired through the use of high throughput sequencing techniques in different mouse strains and post-mortem human studies. However, lack of infection time course data poses a prominent missing link in the understanding of chronic infection, and there is still much that is unknown regarding changes in genes specifically relating to neuropathology and resulting repair mechanisms as infection progresses throughout the different stages of chronicity.   In this paper, we present a targeted approach to gene expression analysis during T. gondii infection through the use of NanoString nCounter gene expression assays. Wild type C57BL/6 and BALB/c background mice were infected, and transcriptional changes in the brain were evaluated at 14, 28, and 56 days post infection. Results demonstrate a dramatic shift in both previously demonstrated and novel gene expression relating to neuropathology and resolution in C57BL/6 mice. In addition, comparison between BALB/c and C57BL/6 mice demonstrate initial differences in gene expression that evolve over the course of infection and indicate decreased neuropathology and enhanced repair in BALB/c mice. In conclusion, these studies provide a targeted approach to gene expression analysis in the brain during infection and provide elaboration on previously identified transcriptional changes and also offer insights into further understanding the complexities of chronic T. gondii infection.

overall_design: 24 samples were analyzed (12 from C57BL/6 mice and 12 from BALB/c mice), the 12 samples were comprised of 3 biological replicates for Naïve, 14day, 28day, and 56day post infection time points repecetively, Naïve time point was used as reference and control for analysis

first: Kristina

middle: V

last: Bergersen

first: Ashli

last: Barnes

first: Danielle

last: Worth

first: Clement

last: David

middle: H


title: Targeted transcriptomic analysis of C57BL/6 and BALB/c mice during progressive chronic Toxoplasma gondii infection reveals changes in host and parasitic gene expression relating to neuropathology and resolution

platform_organism:
Toxoplasma gondii
Mus musculus

overall_design: Refer to individual Series


title: A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1

city: Liverpool

first: Aditi

last: Kanhere

address: Institute of Systems, Molecular and Integrative Biology

country: United Kingdom

institute: University of Liverpool

summary: DNA methyl-transferase-1 or DNMT1 maintains DNA methylation in the genome and is important for regulating gene expression in cells. Aberrant changes in DNMT1 activity and DNA methylation are commonly observed in cancers and many other diseases. Recently, a number of long intergenic non-protein-coding RNAs or lincRNAs have been shown to play a role in regulating DNMT1 activity. CCDC26 is a nuclear lincRNA which is frequently mutated in cancers and is a hotbed for disease-associated single nucleotide changes.  However, the functional mechanism of CCDC26 is not understood. Here, we show that this lincRNA is concentrated on the nuclear periphery. Strikingly, in the absence of CCDC26 lincRNA, DNMT1 is mis-located in the cytoplasm and the genomic DNA is significantly hypomethylated. This is accompanied by double stranded DNA breaks and increased cell death. These results point to a previously unrecognized mechanism of lincRNA mediated subcellular localization of DNMT1 and regulation of DNA methylation.

overall_design: RNA-seq analysis of Wildtype and two CCDC26-null K562 lines


title: Wnt signaling enhances macrophage responses to IL-4 and promotes resolution of atherosclerosis

status: Public on Mar 11 2021

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: We investigated the response of cultured mouse macrophages to Wnt3a and IL-4.

overall_design: Bone marrow derive macrophages (BMDMs) from C57Bl6J female mice were differentiated from monocytes using mCSF. After 7 days macrophages were treated with 100ng/mL Wnt3a, 100pg/mL IL-4 or their combination for 16 hours. As control, cells were left untreated.

first: Ada

last: Weinstock

first: Kelly

last: Ruggles

first: Edward

last: Fisher


title: Global circadian transcript profile of mouse viceral adipose entrained by inverted feeding

city: Chongqing

first: Min-Dian

last: Li

address: 30 Gaotanyan Main Street

department: Cardiology

institute: Southwest Hospital, Third Military Medical University (Army Medical University)

summary: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain, such as liver, heart, kidney and visceral adipose tissue. Here, we presented global circadian transcript profile of mouse visceral adipose tissue entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.

overall_design: RNA-seq of transcriptome in mouse visceral adipose collected from daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF, reference), totaling 56 samples


title: Mitochondrial Metabolism is Essential for Invariant Natural Killer T Cell Development and Function

city: Chicago

first: Eva

last: Morgun

state: IL

address: 320 N Superior St

department: Department of Microbiology and Immunology

institute: Northwestern University

summary: Conventional T cell fate and function are determined by coordination between cellular signaling and metabolism. Invariant natural killer T (iNKT) cells are a subset of “innate-like” pre-activated T cells whose dependence on mitochondrial metabolism remains elusive.  Here, we showed that mature iNKT cells have reduced mitochondrial respiratory reserve and iNKT cell development was highly sensitive to perturbation of mitochondrial function. Mice with T cell-specific ablation of Rieske Iron-Sulphur protein (T-Uqcrfs1-/-), an essential subunit of mitochondrial complex III, had a dramatic reduction of iNKT cells in the thymus and periphery, but minimal effects on conventional T cell development. Residual iNKT cells in T-Uqcrfs1-/- mice retained ability to proliferate but exhibited increased apoptosis, decreased TCR signaling and impaired responses to TCR and IL-15 stimulation. Furthermore, knocking down RISP in mature iNKT cells diminished their cytokine production, correlating with reduced NFATC2 activity. Collectively, our data demonstrate a critical role for mitochondrial metabolism in iNKT cell development and activation outside of supporting bioenergetic demands.

overall_design: Thymic cells were obtained from 2 Uqcrfs1fl/fl; CD4-Cre+ mice and 2 heterozygous littermate controls. CD4+/CD8+ DP thymocytes were sorted by FACS BD Aria with a purity more than 98%. RNA was extracted with RNAeasy® Mini Kit according to the protocol of the manufacture (Qiagen). Libraries were generated using the Illumina TruSeq preparation kit and sequenced on HiSeq4000 at Northwestern's NUSeq Core. Reads were analyzed through the Ceto pipeline (https://github.com/ebartom/NGSbartom) using STAR (Dobin et al., 2013) for alignment on mm10 mouse genome, HTSeq (Anders et al., 2015) for read counting, and edgeR (Robinson et al., 2010) for differential expression analysis.

first: Xiufang

last: Weng

first: Amrendra

last: Kumar

first: Liang

last: Cao

first: Ying

last: He

first: Lavanya

last: Visvabharathy

first: Jie

last: Zhao

first: Laura

last: Sena

first: Sam

middle: E

last: Weinberg

first: Navdeep

middle: S

last: Chandel

first: Chyung-Ru

last: Wang


title: Preoperative immune landscape predisposes adverse outcomes in hepatocellular carcinoma patients with liver transplantation

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

summary: Immune class in hepatocellular carcinoma (HCC) has been shown to possess immunogenic power; however, how preestablished immune landscapes in premalignant and early HCC stages impact the clinical outcomes of HCC patients remains unexplored. We sequenced bulk transcriptomes for 62 malignant tumor samples from a Korean HCC cohort in which 38 patients underwent total hepatectomy, as well as for 15 normal and 47 adjacent nontumor samples. Using in-silico deconvolution of expression mixtures, 22 immune cell fractions for each sample were inferred, and validated with immune cell counting by immunohistochemistry. Cell type-specific immune signatures dynamically shifted from premalignant stages to the late HCC stage. Total hepatectomy patients displayed elevated immune infiltration and prolonged disease-free survival compared to the partial hepatectomy patients. However, patients who exhibited an infiltration of regulatory T cells (Tregs) during the pretransplantation period displayed a high risk of tumor relapse with suppressed immune responses, and pretreatment was a potential driver of Treg infiltration in the total hepatectomy group. Treg infiltration appeared to be independent of molecular classifications based on transcriptomic data. Our study provides not only comprehensive immune signatures in adjacent nontumor lesions and early malignant HCC stages but also clinical guidance for HCC patients who will undergo liver transplantation.

overall_design: HCC and premalignant samples were collected from HCC or chronic liver disease patients who had undergone surgical resection at Seoul National University Hospital from 2004 to 2009. 15 nontumor samples were collected from patients who received partial hepatectomy for metastatic cancer, cholangiocarcinoma, and polycystic liver disease. Tissue samples were immediately snap-frozen and stored in liquid nitrogen and matched formalin fixed paraffine block were made for histologic diagnosis and immunohistochemical staining. In total, 128 samples (62 malignant tumors, 47 premalignant lesions, 15 nontumor samples and 4 replicates) from 98 patients were collected. Of 54 HCC patients available with clinical information, 35 patients received total hepatectomy for transplantation and remaining 19 patients received partial hepatectomy. All nontumor liver tissues were histologically confirmed to have no evidence of hepatic fibrosis on glass slide and clinical evidence of chronic liver disease, such as viral hepatitis.

first: Sang-Ho

last: Yoon

first: Seo-Won

last: Choi

first: SukWoo

first: KyoungBun

last: Lee


title: R406-Inhibition of Syk-Cn-NFAT Signaling Axis Promotes Chemical Reprogramming via Metabolic Rewiring and H2S Production

status: Public on Mar 14 2021

city: Hangzhou

first: Yunkun

last: Lu

state: Zhejiang

address: 3 Qingchun East Rd.

department: Sir Run-Run Shaw Hospital

institute: Zhejiang University

summary: Small molecules not only are convenient and useful for controlling cell fates, but also can provide better understanding of the molecular mechanisms of cell-fate transitions. Here, we identified that spleen tyrosine kinase (Syk) inhibitor R406 could significantly promote the early stage of mouse chemical reprogramming. Furthermore, R406 alleviated the Syk-calcineurin (Cn)-nuclear factor of activated T cells (NFAT) signaling cascade-mediated suppression of glycine, serine and threonine metabolic genes transcriptionally, which is previously unrecognized. In turn, R406 upregulated metabolites of glycine, serine and threonine metabolism and downstream transsulfuration cysteine biosynthesis pathway and cysteine metabolism. Subsequently, increased cellular hydrogen sulfide (H2S) after R406 treatment downregulated oxidative phosphorylation (OXPHOS) and reactive oxygen species (ROS), modulated redox homeostasis, and significantly enhanced chemical reprogramming. In sum, our studies have not only improved the chemical reprogramming technique, but also identified interesting molecular mechanisms of chemical-induced pluripotent reprogramming, which hold great potentials in regenerative medicine.

overall_design: Compare the differentiation of gene expression between cells treated with DMSO and R406.

first: Weiyun

first: Xi

last: Chen

first: Juanjuan

last: Qu

first: Saiyong

last: Zhu


title: miRNA profile of plasma samples from Plasmodium vivax malaria patients and healthy subjects

city: Belo Horizonte

first: Luzia

middle: Helena

last: Carvalho

state: Minas Gerais

address: Av. Augusto de Lima, 1715

country: Brazil

institute: Instituto René Rachou, FIOCRUZ

summary: Severe thrombocytopenia can be a determinant factor in the morbidity of Plasmodium vivax (Pv), the most widespread human malaria. Although immune mechanisms may drive Pv-induced severe thrombocytopenia (PvST), the current data on the cytokine landscape in PvST is scarce, and often conflicting. The analysis of the bidirectional circuit of inflammatory mediators and miRNAs would lead to a better understanding of the mechanisms underlying PvST.

overall_design: Unique samples from 34 subjects, including Plasmodium vivax malaria patients (n=26) and healthy subjects (n=8) were included in the study.

first: Marina

last: Santos

first: Bernardo

last: Franklin


title: Targeted transcriptomic analysis of C57BL/6 and BALB/c mice during progressive chronic Toxoplasma gondii infection reveals changes in host and parasitic gene expression relating to neuropathology and resolution [Neuropathology]

first: Emma

last: Wilson

first: Kristina

last: Bergersen

first: Ashli

last: Barnes

first: Danielle

last: Worth

first: Clement

last: David


title: Global circadian transcript profile of mouse heart entrained by inverted feeding

first: Min-Dian

last: Li

summary: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain, such as liver, heart, kidney and visceral adipose tissue. Here, we presented global circadian transcript profile of mouse heart entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.

overall_design: RNA-seq of transcriptome in mouse heart collected from daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF, reference), totaling 56 samples


title: Global circadian transcript profile of mouse liver entrained by inverted feeding

summary: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain, such as liver, heart, kidney and visceral adipose tissue. Here, we presented global circadian transcript profile of mouse liver entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.

overall_design: ncRNA-seq of coding and non-coding transcriptome in liver collected from daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF, reference), totaling 280 samples


title: Targeted transcriptomic analysis of C57BL/6 and BALB/c mice during progressive chronic Toxoplasma gondii infection reveals changes in host and parasitic gene expression relating to neuropathology and resolution [InflammationPLUSPanel]


title: Global circadian transcript profile of mouse kidney entrained by inverted feeding

summary: Circadian clocks in peripheral organs are entrained by feeding. Eating in the right time is crucial to maintain metabolic health, whereas eating in the wrong time increases the susceptibility to metabolic diseases. It is unknown how change of mealtime impacts circadian transcriptomes in peripheral organs and brain, such as liver, heart, kidney and visceral adipose tissue. Here, we presented global circadian transcript profile of mouse kidney entrained by inverted feeding to compile an atlas for mechanistic insights into how feed-fast cycle regulates circadian biology.

overall_design: RNA-seq of transcriptome in mouse kidney collected from daytime-restricted feeding (DRF) or nighttime-restricted feeding (NRF, reference), totaling 56 samples


title: miRNA expression data of spent in-vitro culture media condtioned with 2-cell, 8-cell, and blastocyst staged bovine embryos

status: Public on Mar 10 2021

city: Brampton

first: Paul

middle: Nico

last: Del Rio

state: ON

address: 195 Kingswood Drive

department: Reproductive and Biotechnology Laboratory

country: Canada

institute: University of Guelph

summary:
Distinct miRNA populations have been detected in the spent media (SM) of in-vitro cultured embryos. However, profiling has only been conducted in SM cultured with blastocyst-stage embryos.
Therefore, the aim of the study was to globally profile the extracellular microRNA (miRNA) population throughout the pre-implantation period in bovine embryos using a heterologous miRNA microarray

overall_design: Bovine embryos were in-vitro produced in group culture and spent media was collected at the 2-cell, 8-cell, and blastocyst stage of development. Once sufficient media samples were collected from all the conditions, total RNA was extracted and hybridized onto an Affymetrix Genechip miRNA 4.0 array and data was analyzed using Transcriptome Analysis Console.

first: Pavneesh

last: Madan


title: Study of the transcriptional effect of ANO1 knock-down in two head and neck squamous cell carcinoma cell lines by RNA-sequencing of samples cultured in three dimensional collagen type I

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8, Biomedicum 1

country: Finland

institute: University of Helsinki

summary: ANO1 is located in the 11q13 region that is commonly amplified  in head and neck squamous cell carcinoma. However, the exact mechanism of ANO1's involvement in oncogenesis and cancer proliferation remains unclear. In this study, we discovered novel genes which have an interplay in ANO1 cancer signalling pathways and were significantly differentially expressed upon ANO1 knockdown. All cell lines were cultured in three dimensional collagen I, a matrix that closely resembles tumor microenvironment. The aim of this study was to reveal novel mediators and pathways in ANO1 cancer cell signalling, and therefore gain insight on novel molecules that can present potent therapeutic targets.

overall_design: We performed RNA sequencing to identify differentially expressed genes upon ANO1 knockdown in head and neck squamous cell carcinoma (HNSCC) cell lines cultivated in three dimensional collagen type I. HNSCC cell lines used in this study harbor amplification and high expression of ANO1 gene. Each UT-SCC cell line used in the RNA sequencing of this study was transduced using as control three shScramble (shScr) lentiviral transduction replicates, as well as three replicates of shANO1 constructs, including at least once the constructs shANO1 65 and shANO1 66. Transduced cell lines were selected with puromycin. Cells were grown as inert in three dimensional collagen I cultures for up to five days until microscopicaly visible colonies have formed. RNA was extracted and further prosessed for RNA sequencing analysis. Illumina NextSeq1 x 75 bp was used.

first: Artemis

last: Filippou

first: Henna

last: Pehkonen

first: Juho

last: Väänänen

first: Mikko

last: Kivento


title: Cow mammary gland miRNomes before and after food restriction

city: saint-genes-champanelle

first: Pierre-Alexis

last: Billa

address: route de theix

department: UMRH

institute: INRA

summary: Effect of feed restriction in mid lactation Holstein (H) and Montbéliarde (M) cows on mammary glande miRNA profil.

overall_design: Comparison of miRNome of mammary gland obtain by biopsies (one before and one after feed restriction)

first: Christine

last: Leroux

first: Ye

last: Tao


title: DCBLD2 Mediates Epithelial-Mesenchymal Transition-Induced Metastasis by Cisplatin in Lung Adenocarcinoma

status: Public on Mar 09 2021

city: Tianjin

first: Xiaosu

last: Chen

address: 94 Weijin Road

institute: Nankai University

summary: Growing evidence suggests that cisplatin and other chemotherapeutic agents promote tumor me-tastasis while inhibiting tumor growth, which is a critical issue in clinical practices. However, the role of chemotherapeutics in promoting tumor metastasis and the molecular mechanism involved are unclear. Here, we investigated the roles of cisplatin in promoting tumor metastasis in lung adenocarcinoma (LUAD). We demonstrated that cisplatin promoted epithelial-mesenchymal transition (EMT), cell motility, and metastasis in vitro and in vivo. The bioinformatic analysis and molecular biology approaches also indicated that DCBLD2 is a key gene that mediates cispla-tin-induced metastasis. DCBLD2 stabilizes β-catenin by phosphorylating GSK3β and transporting accumulated β-catenin to the nucleus to promote the expression of EMT-related transcriptional factors (TFs), ultimately resulting in tumor metastasis. We also identified that cisplatin aggravated DCBLD2 expression by phosphorylating ERK and hence the AP-1-driven transcription of DCBLD2. Furthermore, DCBLD2-specific siRNAs encapsulated by nanocarriers prominently in-hibits cisplatin-induced metastasis in vivo. Therefore, DCBLD2 plays a key role in cispla-tin-induced metastasis in LUAD and is a potential target for preventing chemotherapy-induced metastasis in vivo.

overall_design: Examination of the difference of gene expression profile between A549 cells over-expressing or down-expressing DCBLD2 and empty vector cells

first: Chongbiao

last: Huang

first: Rong

last: Xiang


title: CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [snATAC-seq]

city: Shenzhen

first: Guipeng

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

summary: We reported a Concanavalin A-based Barcoding Strategy (CASB) for single-cell and single-nucleus sample multiplexing, which could be followed by different single-cell sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. Besides sample multiplexing, the CASB could further improve data quality through doublet identification.

overall_design: plate-base snATAC-seq of HAP1 cells

first: Liang

last: Fang

first: Wei


title: CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [scRNA-seq]

sample_organism:
Drosophila melanogaster
Homo sapiens
Canis lupus familiaris
Cricetulus griseus
Mus musculus
Rattus norvegicus
Chlorocebus sabaeus

overall_design: scRNA-seq of a mixture of 16 celltypes from 7 species


title: MicroRNA signatures of the developing primate fovea

city: Davis

first: Sergi

last: Simo

address: One Shields Avenue, 3402 Tupper Hall

department: Cell Biology and Human Anatomy

institute: University of California Davis

summary: Purpose: Uncover the mRNA and microRNA signatures of  non-human primate retina during development.

overall_design: 1) Comparison of mRNA profiles from nasal versus temporal rhesus macaque retinal punches  at embryonic days (E)50 (n=3), E90 (n=1, pair-end sequencing), andE 150 (n=1, pair-end sequencing), using Illumina NextSeq 500 system (Illumina, San Diego, CA).   2) Comparison of microRNA (miRNA) profiles from nasal versus temporal rhesus macaque retinal punches at embryonic day 50 (n=3), using Illumina NextSeq 500 system (Illumina, San Diego, CA).

first: Elizabeth

last: Fishman

first: Mikaela

last: Louie

first: Adam

last: Miltner

first: Simranjeet

last: Cheema

first: Joanna

last: Wong

first: Nicholas

last: Schlaeger

first: Ala

last: Moshiri

last: Simó

first: Alice

middle: F

last: Tarantal

first: Anna

last: La Torre


title: The spleen as a sanctuary site for residual leukemic cells following ABT-199 monotherapy in ETP-ALL

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

summary: Two mice in which luciferase-positive LOUCY ETP-ALL cells were xenografted were treated with either vehicle or ABT-199 (50 mg/kg) for 11 days. Afterwards, single cells suspensions were made from  bone marrow and spleen of both mice for 10x Genomics scRNA-seq. Following quality control, a total of 13,681 spleen cells and 11,442 bone marrow cells of the  control mouse and 15,955 spleen cells and 9,443 bone marrow cells of the ABT 199 treated mouse were processed for further analysis. Our data show that ABT-199 triggers transcriptional changes in T-cell differentiation genes in leukemic cells obtained from the spleen microenvironment. These results are in line with our previous findings that mature typical T-ALL are resistant to ABT-199.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: 10x Genomics single cell RNA-sequencing of LOUCY cells isolated from the bone marrow and spleen of xenograft mice following 11 days of vehicle or ABT-199 treatment

first: Pieter

last: Van Vlierberghe

first: Triona

last: Ni Chonghaile


title: Transcriptome analysis of MAZR and/or Runx3-deficient cytotoxic T lymphocytes

city: Vienna

first: Shinya

last: Sakaguchi

address: Lazarettgasse 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

summary: We investigated transcriptional changes in MAZR-, Runx3- and MAZR/Runx3-deficient cytotoxic T lymphocytes (CTLs). This analysis revealed that MAZR plays a compensatory role in the Runx3-dependent transcriptional program of CTL differentiation.

overall_design: Total RNA was isolated from in vitro differentiated murine cytotoxic T lymphocytes lacking MAZR and/or Runx3, and was used for transcriptome analysis. Three biological replicates were prepared.

first: Caroline

last: Tizian

first: Willfried

last: Ellmeier

first: Thomas

last: Faux

first: Asta

last: Laiho

first: Laura

middle: L

last: Elo


title: Inhibiting mitochondrial Cytochrome c oxidase downregulates gene transcription after traumatic brain injury in Drosophila

city: Detroit

first: Ekta

last: Shah

state: Michigan

address: 275 E.  Hancock

institute: Wayne State University

summary: Adult male and female w1118 flies were inflicted with traumatic brain injury using high-impact trauma device. Brains were dissected at control, 1, 2 and 4 hours post-TBI and exposed to near-infrared (NIR) light at 750 nm for 2 hours. Total RNA was extracted from fly brains and 3'mRNA-seq was performed to assess gene expression changes in response to TBI and NIR eposure in both sexes. 3 replicates were sequenced for each condition.

overall_design: To investigate sex-differences in gene expression at control, 1, 2 and 4-hours post-TBI in w1118 Drosophila exposed to NIR


title: Genome wide mapping of LSD1 binding sites in NIH/3T3

city: Stuttgart

first: Philipp

last: Rathert

state: Germany

address: Allmandring 31

department: Biochemistry

institute: University Stuttgart

summary: We provide the binding sites of LSD1 in NIH/3T3 cells mapped via ChIP-seq

overall_design: LSD1 ChIP-seq in NIH/3T3 cell line

first: Sabine

last: Pinter


title: Pericardial fluid microRNAs in patients with arrhythmogenic right ventricular cardiomyopathy or ischemic heart disease

city: Saint-Petersburg

first: Aleksandr

last: Khudiakov

address: 2, Akkuratova

department: Institute of molecular biology and genetics

country: Russia

institute: Almazov National Medical Research Centre

summary: Pericardial fluid is enriched by biologically active molecules of cardiovascular origin including microRNAs. Investigation of the disease-specific extracellular microRNAs could shed light on the molecular processes underlying disease development. Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart disease characterized by life-threatening arrhythmias and progressive heart failure development. The current data about the association between microRNAs and ARVC development are limited.  We performed small RNA sequence analysis of microRNAs of pericardial fluid samples obtained during transcutaneous epicardial access for ventricular tachycardia (VT) ablation of six patients with definite ARVC and three post-infarction VT patients. Disease-associated microRNAs of pericardial fluid were identified. Enrichment analysis of differentially expressed microRNAs revealed their close linkage to cardiac diseases.

overall_design: Pericardial fluid microRNA profiling from patients with arrhythmogenic right ventricular cardiomyopathy or ischemic heart disease (control group)

first: Daniil

last: Panshin

first: Yulia

last: Fomicheva

first: Anastasia

last: Knyazeva

first: Ksenia

last: Simonova

first: Dmitry

last: Lebedev

first: Evgeny

last: Mikhaylov

last: Kostareva


title: CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [HAP1]

first: Guipeng

last: Li

overall_design: scRNA-seq of MDA-MB-231 cells; snATAC-seq and scRNA-seq of HAP1 cells

first: Liang

last: Fang

first: Wei

last: Chen


title: CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing

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

platform_organism:
Drosophila melanogaster
Homo sapiens
Canis lupus familiaris
Cricetulus griseus
Mus musculus
Rattus norvegicus
Chlorocebus sabaeus

overall_design: Refer to individual Series


title: CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [mixed Sample of cell lines and organisms]


title: CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing [snATAC]


title: Gene expression analysis of human mortal renal tubular epithelial cells chronically exposed to elevated levels of glucose

status: Public on Mar 07 2021

city: Grand Forks

first: SANDEEP

last: Singhal

state: North Dakota

address: 1301 N Columbia Road Stop 9037

department: Department of Pathology

institute: School of Medicine and Health Sciences, University of North Dakota

summary: This study was designed to simulate the effect of hyperglycemia on the proximal tubule.  This portion of the kidney is responsible for reabsorption of the filtered glucose, and thus, the amount reabsorbed is not regulated by insulin.  A long-term exposure was designed to model aspects of renal demise seen in diabetes.  We utilized mortal cultures of human renal tubule epithelial cells isolated from renal cortical tissue.  Since the majority of these cells express the cell surface marker CD133, these cells can be used as a model for the progenitor cells that repopulate the nephron after a toxic insult.  The outcome of the current study is that the lysosomal genes and mTOR were repressed.

overall_design: Four concentrations of glucose were used: 5.5 mM, representing the normal level, and 7.5, 11, and 16 mM, representing hyperglycemic glucose levels.   Cells were cultured in these concentrations in triplicate.  The cells were continually cultured and passaged three times before total RNA was purified for global gene expression analysis.  Total exposure time was four weeks

first: Scott

last: Garrett

first: Donald

last: Sens

first: Seema

last: Somji

first: Sandeep

first: Swojani

last: Shrestha


title: Characterization of biological pathways regulating acute cold resistance of zebrafish

status: Public on Mar 06 2021

city: Wuhan

first: Yong

last: Long

address: No. 7 Donghu South Rd.

institute: Institute of Hydrobiology, Chinese Academy of Sciences

relation:
SuperSeries of: GSE168355
SuperSeries of: GSE168356


title: MiRNA SIGNATURE FOR ORAL SQUAMOUS CELL CARCINOMA

status: Public on Mar 05 2021

city: Thiruvananthapuram

first: S

last: Kannan

state: Kerala

address: Medical College Campus

department: Cancer Research

country: India

institute: Regional Cancer Centre

summary: The present study is aimed at profiling the miRNA expression pattern in oral squamous cell carcinoma (OSCC) and adjacent oral mucosa to develop a new miRNA signature for oral cancer.  Agilent Human miRNA Microarray v2.0 (G4470B, Agilent Technologies) was used to identify miRNAs differentially expressed in OSCC. MicroRNA processing was carried out according to the manufacturer’s instructions. Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings. Data pre-processing and differential expression analysis were done in R Studio using the Bioconductor AgiMicroRna package.12 The Total Gene Signal provided by the AFE image analysis software was used for data analysis. Data were normalized between arrays using the quantile method. Microarray profiling identified a set of 105 miRNAs to be differentially expressed in OSCC, out of which a subset of 19 most dysregulated miRNAs were considered to formulate the miRNA signature for oral cancer.

overall_design: miRNA microarray was used for miRNA profiling of 30 tumor and 18 normal tissue samples.

first: Christo

last: Rajan

first: VG

last: D Roshan


title: Re-routing of sugar catabolism provides a better insight into fungal flexibility in using plant biomass-derived monomers as substrates

status: Public on Mar 08 2021

city: Utrecht

first: Ronald

last: de Vries

address: Uppsalalaan 8

department: fungal physiology

institute: Centre of fungal biodiversity

summary: The filamentous ascomycete Aspergillus niger has received increasing interest as a cell factory, being able to efficiently degrade plant cell wall polysaccharides as well as having an extensive metabolism to convert the released monosaccharides into value added compounds. The pentoses D-xylose and L-arabinose are the most abundant monosaccharides in plant biomass after D-glucose, being major constituents of xylan, pectin and xyloglucan. In this study, the influence of selected pentose catabolic pathway (PCP) deletion strains on growth on plant biomass and re-routing of sugar catabolism was addressed to gain a better understanding of the flexibility of this fungus in using plant biomass-derived monomers. The transcriptome, metabolome and proteome response of three PCP mutant strains, ΔlarAΔxyrAΔxyrB, ΔladAΔxdhAΔsdhA and ΔxkiA, grown on wheat bran (WB) and sugar beet pulp (SBP), was evaluated. Our results showed that despite the absolute impact of these PCP mutations on pure pentose sugars, they are not as critical for growth of A. niger on more complex biomass substrates, such as WB and SBP. However, significant phenotypic variation was observed between the two biomass substrates, but also between the different PCP mutants. This shows that the high sugar heterogeneity of these substrates in combination with the high complexity and adaptability of the fungal sugar metabolism allow for activation of alternative strategies to support growth.

overall_design: mRNA profiling of five Aspergillus niger strains grown on wheat bran or sugar beet pulp at three time points.

first: Tania

last: Chroumpi

first: Mao

last: Peng

first: Meng

last: Markillie

first: Hugh

middle: D

last: Mitchell

first: Carrie

last: Nicora

first: Chelsea

middle: M

last: Hutchinson

first: Vanessa

last: Paurus

first: Samuel

middle: O

last: Purvine

first: Chaevien

last: Clendinen

first: Galya

last: Orr

last: Baker

first: Miia

middle: R

last: Makela


title: Characterization of biological pathways regulating acute cold resistance of zebrafish - experiment 2

last: Long

summary: This experiment was performed to investigate the functional mechanisms of the critical pathways including ERK, p38 MAPK and the transcription factor Foxo1 in enhancing cold resistance of zebrafish.Specific inhibitors of these pathways were used to treat zebrafish larvae under both normal and low temperatures to investigate the functions of these pathways in regulating cold stress response.

overall_design: Zebrafish larvae were maintained at 28 oC or exposed to 10 oC for 12 h in the presence of inhibitors including AS1842856 (0.5 μM), PD0325901 (5 μM) and SB203580 (50 μM), respectively. An untreated control group (96 hpf) and a vehicle (0.1% DMSO) control were also included.

first: Jing

last: Ren

first: Ran

last: Liu

first: Guili

last: Song

first: Qing

last: Li

first: Zongbin

last: Cui


title: Characterization of biological pathways regulating acute cold resistance of zebrafish - experiment 1

first: Yong

summary: Low temperature stress represents a major threat to the lives of both farmed and wild fish species. However, biological pathways determining the development of cold resistance in fish remain largely unknown. Zebrafish larvae at 96 hpf were exposed to lethal cold stress (10 oC) for different time periods to evaluate the adverse effects at organism, tissue and cell levels. In this study, time series RNA sequencing (RNA-seq) experiments were performed to delineate transcriptomic landscape of zebrafish larvae under cold stress and during the subsequent rewarming phase.

overall_design: This experiment contained four groups of samples. The controls (ctrl) were maintained at 28 oC and collected at developmental stages including 96 hpf, 97 hpf, 98 hpf, 102 hpf, 108 hpf and 132 hpf. The lethal cold stress treated samples (lc) were exposed to 10 oC for 1 h, 2 h, 6 h, 12 h and 24 h. The recovery group (re) were exposed to 10 oC for 12 h and then incubated at 28 oC for 1 h, 2 h, 6 h, 12 h and 24 h. The normal (er_nor) and abnormal (er_ab) ones after 24 h of both cold exposure and recovery were also included in RNA-seq analysis.


title: Safety and Transcriptome Analysis of Brucella Live Attenuated Vaccine Strain S2 on Cynomolgus Monkeys

status: Public on Mar 04 2021

city: Beijing

first: Liangquan

last: Zhu

email: 1367391894@qq.com, sunshijing@dbn.cn

address: No. 8, Zhongguancun South Street, Haidian District

institute: China Institute of Veterinary Drug Control

summary: Brucellosis, caused by Brucella spp, is an important zoonotic disease leading to enormous economic losses in livestock and posing great threat to public health worldwide. The live attenuated Brucella suis (B. suis) strain S2 is a safe and effective vaccine, and it is most widely used in animals in China. However, S2 vaccination in animals may raise debates and concerns in terms of safety to primates, particularly human. In this study, using cynomolgus monkey as an animal model, we evaluated the safety of the S2 vaccine strain on primate, in addition, we performed transcriptome analysis to determine gene expression profiling on cynomolgus monkeys immunized with the S2 vaccine. Our results suggested that the S2 vaccine was safe to cynomolgus monkeys. Transcriptome analysis identified 663 differentially expressed genes (DEGs), of which 348 were significantly up-regulated and 315 were remarkably down-regulated. Gene Ontology (GO) classification and KEGG pathway analysis indicated that these DEGs were involved in various biological processes, including chemokine signaling pathway, actin cytoskeleton regulation, defense response, immune system processing, and type I interferon signaling pathway. The molecular functions of the DEGs mainly comprised of 2'-5'-oligoadenylate synthetase activity, double-stranded RNA binding and actin binding. Moreover, the cellular components of these DEGs included integrin complex, myosin II complex and blood microparticle. Our findings alleviate the concerns in safety of the S2 vaccine on primates and provide genetic basis of mammalian host response and gene regulation after vaccination with the S2 vaccine.

overall_design: mRNA profile of 4 cynomolgus monkeys immunized with Brucella live vaccine S2 strain and 2 cynomolgus monkeys injected with PBS

first: Shijing

last: Sun

first: Hui

last: Jiang

first: Jiabo

last: Ding


title: High dose IFN-𝛽 activates GAF to enhance expression of ISGF3 target genes in epithelial cells

city: Los Angeles

first: Quen

last: Cheng

address: 611 Charles E Young Dr E

institute: UCLA

summary: GAF is transcriptionally inactive in epithelial cells but enhances expression of ISGF3 target genes, thus functioning as a dose-sensitive amplifier of the IFN-𝛽 response.

overall_design: Sequencing data from MLE-12 murine lung epithelial cell line, stimulated with interferon 𝛽 or 𝛾: STAT1 ChIP-seq (19 samples), mRNA-seq (53 samples).

first: Kensei

last: Kishimoto

first: Catera

last: Wilder

first: Justin

last: Buchanan

first: Minh

last: Nguyen

first: Chidera

last: Okeke

first: Alexander

last: Hoffmann


title: single cell RNA sequencing on minipig PBMCs

city: Marcy L'Etoile

first: Emilie

last: Chautard

address: 1541 Avenue Marcel Mérieux

institute: Sanofi

summary: Single cell RNA sequencing was used to explore the long-term maintenance of immune memory cells and their functionality for the first time in this animal model. It revealed an increase in pertussis-specific T cells frequency in DTaP primed minipigs, together with up-regulation of genes involved in antigen presentation and interferon pathways.

overall_design: 6 samples were analyzed including 2 PBMC samples from control minipig, 2 PBMC samples from DTaP/Tdap immunized minipig incubated in vitro with medium, and 2 PBMC samples from DTaP/Tdap immunized minipig incubated in vitro with pertussis antigens pool.

first: Cyril

last: Dégletagne

first: Céline

last: Vaure

first: Stéphanie

last: Husson

first: Virginie

last: Courtois


title: MX2 mediates establishment of interferon response profile, regulates XAF1 and can sensitize melanoma cells to targeted therapy

status: Public on Mar 03 2021

city: Solna

first: Gert-Jan

last: Hendriks

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

summary: The goal of the study was to identify downstream genes affected by overexpresion on MX2 gene in a huma melanoma cell line WM983

overall_design: 3 groups containing 3 independent replicates: Untreated control cells; GFP overexpressing cells; MX2 overexpressing cells;

first: Ana

last: Slipicevic

first: Marina

last: Juraleviciute

first: Jérémie

last: Nsengimana

first: Julia

last: Newton-Bishop

first: Gert


title: EphB6

city: Padova

first: Marco

last: Montagner

state: PD

address: viale G. Colombo, 3

country: Italy

institute: University of Padua


title: Extended Amygdala-Parabrachial Circuits Alter Threat Perception to Control Feeding

status: Public on Mar 02 2021

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Ribosome TRAP (affinity purification) from Glutamaterigc or GABAergic neurons of the Bed Nucleus Stria Terminalis (BNST) expressing Cre, enabling expression of a floxed TRAP reporter delivered by retrofecting AAV injected into the parabrachial nucleus (PBN) of mice.

overall_design: RNA-seq of dissected BNST (whole lysate, "input") and immunoprecipitate fraction ("IP") to determine genes enriched in Glutamatergic or GABAergic neurons of BNST projecting to the PBN.

first: Bernard

last: Mulvey


title: A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis

city: Moscow

first: Anton

last: Kuzmenko

email: dr.ant.kuz@gmail.com, antonk@img.ras.ru

address: Akademika Kurchatova square 2

institute: Institute of Molecular Genetics, Russian Academy of Sciences

summary: Argonaute proteins are programmable nucleases that are found in both eukaryotes and prokaryotes and provide defense against invading genetic elements. Although some prokaryotic Argonautes (pAgos) were shown to recognize RNA targets in vitro, the majority of studied pAgos have strict specificity toward DNA, which limits their practical use in RNA-centric applications. Here, we describe a unique pAgo nuclease, KmAgo, from the mesophilic bacterium Kurthia massiliensis that can be programmed with either DNA or RNA guides and can precisely cleave both DNA and RNA targets. KmAgo binds 16-20 nt long 5’-phosphorylated guide molecules with no strict specificity for their sequence and is active in a wide range of temperatures. In bacterial cells, KmAgo is loaded with small DNAs with no obvious sequence preferences suggesting that it can uniformly target genomic sequences. Mismatches between the guide and target sequences greatly affect the efficiency and precision of target cleavage, depending on the mismatch position and the nature of the reacting nucleic acid. Target RNA cleavage by KmAgo depends on the formation of secondary structure indicating that KmAgo can be used for structural probing of RNA. These properties of KmAgo open the way for its use for highly specific nucleic acid detection and cleavage.

overall_design: Investigation of the pattern, nucleotide bias and length distribution of small DNAs associated with KmAgo

first: Daria

last: Esyunina

first: Ekaterina

last: Kropocheva

first: Alexei

last: Aravin

first: Andrey

last: Kulbachinskiy


title: Promoter-specific changes in initiation, elongation and homeostasis of histone H3 acetylation during CBP/p300 Inhibition

status: Public on Mar 01 2021

first: Arnold

last: Berk

state: CA

address: 611 Charles E. Young Dr.


title: Gene expression profile of AT1-like cells in monoculture or cocultured with control or shEphB6-depleted D2.0R-EGFP cells

summary: We studied how crosstalk with disseminated dormant breast cancer cells affects transcriptome of AT1-like cells and the requirement of EphB6 expression in the cancer cells for this genetic program

overall_design: D2.0R-EGFP-shControl or D2.0R-EGFP-shEphB6 (1,8x105 cells/well) were plated on top of AT1-like cells (1,36x106 cells/sample) in MLNL medium (in 60 mm dish) for three days before separation by Fluorescence-Activated Cell Sorter (FACS) based on EGFP signal. EGFP- cells (AT1-like cells) were subjected to analysis.

first: Erik

last: Sahai


title: Gene expression profile of control or shEphB6-depleted D2.0R-EGFP cells in monoculture or cocultured with AT1-like cells

summary: We studied how crosstalk with AT1-like cells affects transcriptome of disseminated dormant breast cancer cells and the requirement of EphB6 expression in the cancer cells for this genetic program

overall_design: D2.0R-EGFP-shControl or D2.0R-EGFP-shEphB6 (1,8x105 cells/well) were plated on top of AT1-like cells (1,36x106 cells/sample) in MLNL medium (in 60 mm dish) for three days before separation by Fluorescence-Activated Cell Sorter (FACS) based on EGFP signal. EGFP-+cells (D2.0R cells) were subjected to analysis.


title: Medium-dependent gene-expression profiling of the human K562 chronic myeloid leukemia cell line

city: Madison

first: Jason

last: Cantor

state: WI

address: 330 North Orchard Street

institute: Morgridge Institute for Research

summary: Forward genetic screens across hundreds of diverse cancer cell lines have started to define the genetic dependencies of proliferating human cells and how these vary by genotype and lineage. Most screens, however, have been carried out in culture media that poorly resemble metabolite availability in human blood. To explore how medium composition influences gene essentiality, we performed CRISPR-based screens of human cancer cell lines cultured in traditional versus human plasma-like medium (HPLM). Sets of medium-dependent fitness genes span several cellular processes and can vary with both natural cell-intrinsic diversity and the specific combination of basal and serum components that comprise typical culture media. Notably, we traced the causes for each of three conditional CRISPR phenotypes to the availability of metabolites uniquely defined in HPLM versus traditional media. Our findings reveal the profound impact of medium composition on gene essentiality in human cells, and also suggest general strategies for using genetic screens in HPLM to uncover new cancer vulnerabilities and gene-nutrient interactions.

overall_design: RNA sequencing: human K562 cells cultured in either RPMI+dS or HPLM+dS. There were two biological replicates per condition.

first: David

last: Sabatini


title: Small extracellular vesicles derived from interferon-γ pre-conditioned mesenchymal stromal cell(MSC)s effectively treat liver fibrosis (scRNA-seq)

city: Niigata

first: Atsunori

last: Tsuchiya

state: %null%

address: 1-757, Asahimachi-dori, Chuo-ku, Niigata

country: Japan

institute: Niigata University

summary: A new therapeutic approach of IFN-γ-treated mesenchymal stromal cell-produced extracellular vesicles effectively treated a cirrhosis model.

overall_design: Single cell RNA-seq data of liver cells after treatment of MSCs or thieir small extracellular vesicles

first: Suguru

last: Takeuchi

first: Shuji

last: Terai

first: Katsunori

last: Fujiki

first: Katsuhiko

last: Shirahige


title: AP-1 subunits converge promiscuously at enhancers to potentiate transcription

city: Durham

first: Charles

last: Gersbach

state: North Carolina

address: 101 science drive rm 2323

institute: Duke University

summary: The AP-1 transcription factor dimer contributes to many biological processes and environmental responses. The many ways that AP-1 subunits can dimerize has posed a challenge to understanding its regulatory function. To determine patterns of AP-1 dimerization genome-wide, we definitively establish the genome-wide binding patterns and the enhancer function of five AP-1 subunits. We find limited evidence for strong dimerization preferences between specific subunits. In particular, our analysis suggests that canonical AP-1 motifs have the potential to recruit all AP-1 subunits to genomic sites that also have hallmarks of strong enhancer activity. We term those sites AP-1 hotspots. AP-1 hotspots function as a ‘hub' for AP-1 subunit binding that elicits changes in cell-type specific AP-1-mediated gene expression. AP-1 hotspots are more predictive of genomic responses to glucocorticoid signaling than super enhancers, and are particularly enriched in disease-associated genetic variants. Together, these results support a model that promiscuous convergence of many subunits to common genomic locations potentiates AP-1-mediated transcription in a cell-type specific fashion.

overall_design: ap1_flagtag: A549-derived cell lines with a FLAG epitope inserted at the C-terminus of each of seven AP-1 family members: c-FOS, FOSL1, FOSL2, FOSB, c-JUN, JUNB, and JUND. Directed precise insertion of each FLAG sequence via homologous recombination, using CRISPR/Cas9 to introduce a double strand break in the A549 genome and co-delivering a donor plasmid containing the FLAG tag and a puromycin resistance gene. After selecting for edited cells with puromycin, Cre recombinase was delivered to remove the resistance gene

first: Seo

last: Jungkyun

first: D

last: Koçak

first: Luke

middle: C

last: Bartelt

first: Courtney

last: Williams

first: Alejandro

last: Barrera

first: Linda

middle: K

last: Hong

first: Timothy

last: Reddy


title: RNA-seq gene expression profiling determined for five subcellular fractions for protein coding and lncRNA genes from livers of male and female mice, with or without exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand

city: Boston

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

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

overall_design: Refer to individual Series


title: Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells

first: Minjie

last: Zhang

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

summary: RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Direct determination of RNA structures and interactions in living cells remain a major challenge in biology. Crosslinking and proximity-ligation-based approaches, such as PARIS (Psoralen Analysis of RNA Interactions and Structures), offer many advantages, such as the ability to directly capture complex RNA duplexes in cells with single molecule accuracy, near base pair resolution in high throughput and without size limit. Based on a systematic optimization of the photochemistry and enzymology, here we present PARIS2, a re-invented method for capturing RNA duplexes with >3000-fold improved efficiency. PARIS2 captures ribosome small subunit binding sites on mRNAs, thus reporting translation process. PARIS2 also captures the snRNP binding sites on various types of RNA targets. We applied PARIS2 to enterovirus D-68, a re-emerging viral pathogen associated with severe neurological symptoms and discovered dynamic/alternative conformations in the 5’UTR. The new photochemical and enzymological improvements and the PARIS2 method should be widely applicable to basic RNA research and RNA-related diseases.

overall_design: Cells and tissues are crosslinked with AMT/Amotosalen and crosslinked RNA is extracted using new developed TNA method. mRNA and EVD68 viral RNA are enriched using Poly(A)Purist™ MAG Kit (Invitrogen) and antisense oligos respectively. After fragmentation, proximity ligation and reverse crosslinking, RNA are converted into cDNA library for high-throughput sequencing.

first: Zhipeng

last: Lu


title: Methamphetamine Induces Sex-Dependent Changes in Gene Expression in Male and Female Hearts

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: Male and female rats received daily injections of saline or methamphetamine for 10 days.  Changes in gene expression were assessed by RNA sequencing either 24 hours or 30 days following the last injection. Methamphetamine induced changes in the myocardial transcriptome were significantly greater in female hearts than male hearts both in terms of the number of genes affected and the magnitude of the changes. The largest changes in female hearts involved genes that regulate the circadian clock (Dbp, Per3, Per2, BMal1, and Npas2) which is known to impact myocardial sensitivity to ischemia. These genes were unaffected by methamphetamine in male hearts.  All changes in gene expression identified at day 11 returned to baseline by day 30. These data demonstrate that female rats are more sensitive than males to methamphetamine-induced changes in the myocardial transcriptome and that methamphetamine does not induce changes in myocardial transcription that persist long term after exposure to the drug has been discontinued.

overall_design: Gene expression profiling of cardiac tissue of male and female rats following treatment with methamphetamine or saline, with and without 30 days of abstinence following treatment.

first: Hasitha

last: Chavva

first: Sarah

last: Seeley

first: Daniel

last: Brazeau

first: Donald

middle: A

last: Primerano

first: Jun

last: Fan

first: Boyd

last: Rorabaugh


title: Gene expression profile of EphB6-depleted D2.0R-EGFP cells in vivo

first: Marco

last: Montagner

summary: We analysed gene expression profiles of D2.OR-EGFP-shControl and D2.OR-EGFP-shEpB6 cells isolated from lungs

overall_design: D2.0R-EGFP-shControl (1x106 cells/mouse) or a mix of D2.0R-EGFP-shEphB6 cells (shEphB6#31, #34, #35) were injected in the tail vein of nude athymic BALB/c mice. After two weeks, lungs were harvested and digested into a single-cell suspension as described above. CD45-/EGFP+ cells were sorted directly into lysis buffer and total RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s instructions.

first: Erik

last: Sahai


title: RNA-seq gene expression profiling of  protein coding and lncRNA genes in chromatin bound (non-polyA selected) RNA from livers of male and female mice, with or without exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand [G177]

first: David

state: MA

summary: PolyA-selected RNA was isolated from the chromatin bound (non-polyA selected) fraction of  frozen liver tissue from adult male and female ICR/CD1 mice that were treated with 3 mg/kg TCPOBOP disolved in corn oil, or corn oil vehicle, for 27 hr. These samples are part of a study where we characterize global patterns of expression, maturation and localization for both lncRNA and protein coding gene transcripts in mouse liver, and where we identify candidate regulatory lncRNAs that may be important for a variety of hepatic functions, based on their co-localized within topologically associating domains, or their transcription divergent, antisense or intergenic to protein coding genes associated with key pathways linked to hepatic physiology and disease.

overall_design: Chromatin bound (non-polyA selected) liver RNA was isolated from frozen liver tissue from 7-8 week old male and female CD-1 mice treated with TCPOBOP or vehicle control for 27 hr. Each sample was derived from a single liver, with n=3-4 mice per treatment group.

first: Christine

last: Goldfarb

middle: J


title: Effect of vitrification on global gene expression dynamics of bovine elongating embryos

city: Gainesville

first: Zongliang

last: Jiang

state: FL

address: 2033 Mowry Rd

department: Animal Sciences

institute: University of Florida

summary: Embryo vitrification involves exposure to high concentrations of cryoprotectants and osmotic stress during cooling and warming. A multitude of these factors have the potential of affecting gene expression. In this study, in vitro produced bovine embryos at the blastocyst stage were submitted to vitrification. Four recipients each were used for transferring non-vitrified (80) and vitrified (80) embryos. Twelve non-vitrified and nine vitrified viable day-14 (D14) embryos were recovered by uterine flushing. RNA-seq analysis of whole embryo or isolated trophectoderm (TE) from vitrified and fresh recovered D14 embryos revealed a total of 927 genes changed their expression as a result of vitrification, among them 782 and 145 genes were up- and down-regulated, respectively. In TE isolates, vitrification resulted in 4,096 and 280 up- and down-regulated genes, respectively. In addition, we found 671 and 61 genes commonly up- and down-regulated in both vitrified whole embryo and TE. Commonly up-regulated pathways by vitrification included epithelial adherens junctions, sirtuin signaling, germ cell-sertoli cell junction, ATM signaling, NER, and protein ubiquitination pathways. The commonly down-regulated pathways included EIF2 signaling, oxidative phosphorylation, mitochondrial dysfunction, regulation of eIF4 and p70S6K signaling, mTOR signaling, sirtuin singling, and NER pathways. Our analysis identified specific pathways and implicated specific gene expression patterns important to cryopreservation affecting embryo developmental competence.

overall_design: Twelve non-vitrified and nine vitrified viable day-14 (D14) embryos were recovered by uterine flushing. RNA-seq analysis was performed using the whole embryo or isolated trophectoderm (TE) from vitrified and fresh recovered D14 embryos.

first: Emilo

last: Gutierrez

first: Kenneth

last: Bondioli


title: The gene analysis in telaprevir-treated keratinocytes.

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary: Telaprevir is known to cause a high frequency of cutaneous adverse events. In this study, we analyzed the profile fluctuation of gene expression with or without telaprevir treatment.

overall_design: After telaprevir treatment, total RNA was extracted from NHEK cells and examined gene expression by using 3D-Gene (Toray)

first: Yu

last: Sawada

first: Motonobu

last: Nakamura


title: The gene analysis in telaprevir-treated keratinocytes

summary: Trichloroethylene (TCE) is known to cause cutaneous adverse events. In this study, we analyzed the profile fluctuation of gene expression with or without TCE treatment.

overall_design: After telaprevir TCE, total RNA was extracted from NHEK cells and examined gene expression by using 3D-Gene (Toray)


title: Promoter-specific changes in initiation, elongation and homeostasis of histone H3 acetylation during CBP/p300 Inhibition [GRO-Seq]

first: Arnold

last: Berk

summary: Regulation of RNA Polymerase II (Pol2) elongation in the promoter proximal region is an important and ubiquitous control point for gene expression in metazoans. We report that transcription of the adenovirus 5 E4 region is regulated during the release of paused Pol2 into productive elongation by recruitment of the super elongation complex (SEC), dependent on promoter H3K18/27 acetylation by CBP/p300. We also establish that this is a general transcriptional regulatory mechanism that applies to ~6% of expressed protein-coding genes in primary human airway epithelial cells. We observed that a homeostatic mechanism maintains promoter, but not enhancer H3K18/27ac in response to extensive inhibition of CBP/p300 acetyl transferase activity by the highly specific small molecule inhibitor A-485. Further, our results suggest a function for BRD4 association at enhancers in regulating paused Pol2 release at nearby promoters. Taken together, our results uncover processes regulating transcriptional elongation by promoter region histone H3 acetylation and homeostatic maintenance of promoter, but not enhancer, H3K18/27ac in response to inhibition of CBP/p300 acetyl transferase activity.

overall_design: Examination of transcribed nascent RNAs using Global Run-on Sequencing (GRO-seq)

first: Emily

last: Hsu

first: Nathan

last: Zemke


title: KIR Polymorphism is Associated with Primary Resistance to PD-1 Blockade in Lung Cancer

city: Basel

first: Heinz

last: Läubli

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

summary: Adaptive immune escape of tumor cells by upregulation of ligands for programmed death 1 (PD-1) has been identified as an important and targetable pathway in many cancer types. Many clinical trials have demonstrated that targeting PD-1 or its ligand PD-L1 with immune checkpoint inhibitors (ICI) can restore anti-tumor immunity and induce durable remission. In patients with non-small cell lung cancer (NSCLC), several trials have demonstrated a survival benefit with ICI in patients with metastatic and locally advanced NSCLC.Yet, most patients have primary resistance to PD-1 or PD-L1 blockade during treatment: approximately 20% of unselected patients with NSCLC achieve a partial response while 40-50% have progressive disease as best response. Understanding mechanisms of primary resistance to PD-(L)1 blockade is important in the search for potentially targetable pathways and may ultimately allow discrimination between patients that benefit from PD-(L)1 blockade and those requiring combination or other approaches. We collected PBMCs and serum samples  from 35 patients with NSCLC before and during PD-1 blockade treatment with nivolumab. We analyzed differentially expressed genes in CD8+ T cells from the peripheral blood of 5 patients with partial response and 5 patients with primary progressive disease to identify mechanisms of resistance to PD-1 therapy. Cells were collected from samples taken before and after 4 weeks of treatment.

overall_design: Peripheral blood mononuclear cells (PBMCs) were prospectively collected from metastatic NSCLC patients (discovery cohort) just before the first administration (N1) and during treatment (at 4 weeks, N2) with PD-1 blockade. Patiens were classified to either "responder"(partial response PR) or "nonresponder" (progressive disease PD) based on objective radiological response by RECIST by a thoraic radiologist. From 5 responder and 5 nonresponder patients peripheral CD8+ T cells were sorted by fluorescence activated cell sorting using a BD FACS AriaIII and RNA isolated from these cells. We investigated changes in RNA expression upon treatment wit PD-1 blockade associated with clinical response.

first: Marcel

middle: P

last: Trefny

first: Franziska

last: Uhlenbrock

first: Petra

last: Herzig

first: Daniela

last: Thommen

first: Spasenija

last: Savic

first: Stefan

last: Schaub

first: Frank

last: Stenner

first: Sacha

last: Rothschild

first: Alfred

last: Zippelius


title: RNA-seq gene expression profiling of  protein coding and lncRNA genes in cytoplasmic RNA from livers of male and female mice, with or without exposure to TCPOBOP, a CAR (Nr1i3) agonist ligand [G174]

first: David

last: Waxman

country: USA

summary: PolyA-selected RNA was isolated from the cytoplasmic fraction of frozen liver tissue from adult male and female ICR/CD1 mice that were treated with 3 mg/kg TCPOBOP disolved in corn oil, or corn oil vehicle, for 27 hr. These samples are part of a study where we characterize global patterns of expression, maturation and localization for both lncRNA and protein coding gene transcripts in mouse liver, and where we identify candidate regulatory lncRNAs that may be important for a variety of hepatic functions, based on their co-localized within topologically associating domains, or their transcription divergent, antisense or intergenic to protein coding genes associated with key pathways linked to hepatic physiology and disease.

overall_design: Cytoplasmic Liver RNA, polyA-selected, was isolated from frozen liver tissue from 7-8 week old male and female CD-1 mice treated with TCPOBOP or vehicle control for 27 hr. Each sample is derived from a single liver, with n=3-4 mice per treatment group.

first: Christine

last: Goldfarb


title: PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

summary: Radial glia (RG) in the neocortex sequentially generate distinct subtypes of projection neurons, accounting for the diversity and complex assembly of cortical neural circuits. Mechanisms that drive the rapid and precise temporal progression of RG are beginning to be elucidated. Here we reveal that the RG-specific transcriptional regulator PRDM16 promotes the transition of early to late phase of neurogenesis in the mouse neocortex. Loss of Prdm16 delays the timely progression of RG, leading to defective cortical laminar organization. Our genomic analyses demonstrate that PRDM16 regulates a subset of genes that are dynamically expressed between early and late neurogenesis. We show that PRDM16 suppresses target gene expression through limiting chromatin accessibility of permissive enhancers. We further confirm that critical target genes regulated by PRDM16 comprise neuronal specification genes, cell cycle regulators and molecules required for neuronal migration. These findings provide evidences to support that neural progenitors temporally shift gene expression program to achieve neural cell diversity.

overall_design: To study the function of PRDM16 in gene regulation, ChIP-seq, RNA-seq and ATAC-seq datasets were generated to identify its genomic binding sites, gene expression change and chromatin accessibility change in the mutant versus wild-type control.

first: Qi

last: Dai


title: In vivo genome editing restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES


title: Promoter-specific changes in initiation, elongation and homeostasis of histone H3 acetylation during CBP/p300 Inhibition [ChIP-Seq]

first: Arnold

last: Berk

institute: UCLA

overall_design: Examination of Pol2 Ser5-P, Pol2 Ser5-2, CDK9, NELF, AF9, ENL, BRD4, H3K9ac, H3K18ac, H3K27ac by ChIP-seq

first: Emily

last: Hsu


title: RNAseq data from WT and Lbr N-terminal mutant, divided for sex

city: London

first: Andrea

last: Cerase

address: Newark st

institute: QMUL

summary: In this study, we compare the transcriptomic difference between these animals. We report significant differences between WT and KO animals, expecially if divided for sex.

overall_design: We used 2 matched WT and KO, males and females

first: Alex

middle: N

last: Young

first: Nicola

last: Pomella


title: Characterization of C9orf72 haplotypes to evaluate the effects of normal and pathological variations on its expression and splicing

city: Jerusalem

first: Israel

last: Ben-Dor

state: Israel

address: Ein-Kerem

department: Gene Therapy

country: Israel

institute: Hadassah university hospital

summary: Expansion of the hexanucleotide repeat (HR) in the first intron of the chromosome 9 open reading frame 72 (C9orf72) gene is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in Caucasians. All C9orf72 ALS/FTD patients share a common risk (R) haplotype, but its single nucleotide polymorphism (SNP) signature has not been fully characterized. Here, we characterized the C9orf72 haplotypes in Europeans and created a detailed molecular map, including HR length, for each haplotype. By analyzing RNA-seq reads and sequencing chromatograms that overlap with heterozygous SNP sites, we identified allelic differences in C9orf72 expression in normal subjects and ALS patients. In cells from healthy individuals, upstream promoter transcript levels increased with increased HR length. Intron 1 levels were higher in one of the non-R haplotypes due to SNP variation, and in R haplotype with 10 or more HR units. In pathological HR expansion, we observed the highest levels of intron 1 that were accompanied by aberrantly spliced transcripts at cryptic donor sites downstream of the expanded HR. Intron 1 retention was associated with sequential intron 2 retention. The SNP signature of C9orf72 haplotypes described here enables allele-specific analysis of transcriptional products and may pave the way to allele-specific therapeutic strategies.

overall_design: Expression profiling by high throughput sequencing of human primary fibroblasts and iPSCs of control and C9orf72-ALS patients. Three C9orf72-ALS primary fibroblasts samples were compared to two control samples. Three samples from each condition were taken for iPSCs.

first: Crystal

last: Pacut

first: Yuval

last: Nevo

first: Eva

last: Feldman

first: Benjamin

middle: E

last: Reubinoff