title: mTORC1 feedback to AKT modulates MiT/TFE-driven lysosomal biogenesis and EGFR degradation

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

address: 1550 ORLEANS

institute: JOHNS HOPKINS MEDICINE

summary: MiT/TFE transcriptional activity controls lysosomal biogenesis and is negatively regulated by the nutrient sensor mTORC1. Some tumors bypass this regulatory circuit via genetic alterations that drive MiT/TFE expression and activity; however, the mechanisms by which cells with intact or constitutive mTORC1 signaling maintain lysosomal catabolism remain to be elucidated.  Using the murine epidermis as a model system, we find that epidermal Tsc1 deletion results in a wavy hair phenotype due to increased EGFR degradation.  Unexpectedly, constitutive mTORC1 activation increases lysosomal content via up-regulated expression and activity of MiT/TFEs, while genetic or prolonged pharmacologic mTORC1 inactivation has the reverse effect. This paradoxical up-regulation of lysosomal biogenesis by mTORC1 is mediated by feedback inhibition of AKT, and a resulting suppression of AKT-induced MiT/TFE proteasomal degradation. These data suggest that oncogenic feedback loops work to restrain or maintain cellular lysosomal content during chronically inhibited or constitutively active mTORC1 signaling respectively, and reveal a mechanism by which mTORC1 regulates upstream receptor tyrosine kinase signaling.

overall_design: We performed microarray-based differential expression analysis of E18.5 epidermis from wild-type (3 biological replicates) and  Rptor cKO (3 biological replicates) epidermal RNA samples and performed Gene Set Enrichment Analysis, GSEA to evaluate whether a lysosomal gene signature panel (consisting of 360 lysosomal gene transcripts from the Mouse Lysosome Gene Database (mLGDB; http://lysosome.unipg.it/mouse.php) was significantly negatively enriched in Rptor cKO epidermis.

first: Tamara

last: Lotan

first: Kaushal

last: Asrani

first: Akshay

last: Sood

first: Sanjana

last: Murali

first: Chan-Hyun

first: Harsimar

last: Kaur

first: Zoya

last: Khan

first: Brandon

last: Lam

first: Pornima

last: Phatak

first: Michaël

last: Noë

first: Ravi

middle: K

last: Anchoori

first: C

last: Talbot Jr

first: Barbara

last: Smith

first: Michael

last: Skaro


title: Global chromatin occupancy and epigenetic signature analysis reveal new insights into the function of GATA1 N-terminus in erythropoiesis

status: Public on Apr 14 2020

city: Chicago

first: John

last: Crispino

address: 300 Superior St

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mutations in GATA1, which lead to expression of the GATA1s isoform that lacks the GATA1 N-terminus, are seen in patients with Diamond-Blackfan Anemia (DBA). In our efforts to better understand the connection between GATA1s and DBA, we comprehensively studied erythropoiesis in Gata1s mice. Defects in yolks sac and fetal liver hematopoiesis included impaired terminal maturation and reduced numbers of erythroid progenitors. RNA-sequencing revealed that both erythroid and megakaryocytic genes were altered by the loss of the N-terminus, including aberrant up-regulation of Gata2 and Runx1. Mass spectrometry studies demonstrated there was a global increase in H3K27 methylation in the erythroid progenitors. By contrast, chromatin biding assays revealed that, despite similar occupancy of GATA1 and GATA1s, there was a striking reduction of H3K27me3 at regulatory elements of the Gata2 and Runx1 genes. Consistent with the observation that overexpression of GATA2 has been reported to impair erythropoiesis, we found that haploinsufficiency of Gata2 rescued the erythroid defects of Gata1s fetuses. Together, our integrated genomic analysis of transcriptomic and epigenetic signatures reveals that, although Gata1s mice do not precisely model DBA, they provide novel insights into the role of the N-terminus of GATA1 in transcriptional regulation and red blood cell maturation.

overall_design: Fetal liver cells from Gata1s embryos were stained with antibodies against CD71 and Ter119, CD71hiTer119neg/low population (R1/2) and CD71hiTer119hi (R3) population were sorted for analysis comparing with corresponding populations of fetal liver cells from wild type embryos.

first: Te

last: Ling

first: Lihua

last: Zou

first: Nissim

last: Ben-Haim

middle: D


title: Whole-genome gene expression comparison of the chronic myeloid leukemia cell line K562 and its tyrosine kinase inhibitor resistant subclone K562-IR.

city: İzmir

first: Seda

last: Baykal Köse

address: İnciraltı

department: Medical Biology and Genetics

country: Turkey

institute: Dokuz Eylul University

summary: The aim of the analysis is to study the relationship between tyrosine kinase inhibitor (TKI) resistance mechanism and phenotypic plasticity in the TKI-resistant and parental chronic myeloid leukemia K562 cell lines, in the presence and absence of imatinib. Results provide insight into the molecular mechanisms underlying the acquisition of cancer cell plasticity.

overall_design: 4 group of cell lines were studied in triplicate (12 samples) for the microarray analysis. K562 samples were used as reference. K562-IR w/ imatinib cells (suspension) and spindle-shape K562-IR cells (adhering under the suspension cells) were incubated continuously with 10µM imatinib. K562-IR w/o imatinib cells were centrifuged to remove imatinib, and then cultured in complete media during 4 week before collecting for the analysis. K562-IR w/ imatinib cells were collected directly using centrifugation, and spindle-shape K562-IR cells were trypsinized then collected by centrifugation because they grows as monolayer.

first: Ahmet

middle: S

last: Yavuz

first: Uğur

last: Sezerman

first: Zeynep

last: Yüce


title: SF2523: Dual PI3K/BRD4 inhibitor blocks tumor immunosuppression and promotes adaptive immune responses in cancer

city: La Jolla

first: Shweta

last: Joshi

state: CA

address: 3855 Health Sciences Drive, MC 0815

department: Department of Pediatrics

institute: UCSD Moores Cancer Center

summary: Macrophages (MQs) are key immune infiltrates in solid tumors and serve as major drivers behind tumor growth, immune suppression, and inhibition of adaptive immune responses in the tumor microenvironment (TME). Bromodomain and extraterminal (BET) protein, BRD4, which binds to acetylated lysine on histone tails has recently been reported to promote gene transcription of pro-inflammatory cytokines, but has rarely been explored for its role in IL4-driven macrophage transcriptional programming and macrophage-mediated immunosuppression in the TME. Herein, we report that BET bromodomain inhibitor JQ1, blocks association of BRD4 with promoters of arginase and other IL4-driven macrophage genes, which promote immunosuppression in TME. Pharmacological inhibition of BRD4 using JQ1 and/or PI3K using dual PI3K/BRD4 inhibitor SF2523 (previously reported by our group as a potent inhibitor to block tumor growth and metastasis in various cancer models) suppresses tumor growth in syngeneic and spontaneous mice models; reduces infiltration of MDSCs; blocks polarization of immunosuppressive MQs; restores CD8+ T-cell activity and stimulates anti-tumor immune responses. Finally, our results suggest that BRD4 controls the immunosuppressive myeloid tumor microenvironment and provide opportunity to test BET inhibitors and dual PI3K/BRD4 inhibitors to treat cancers driven by the MQ-dependent immunosuppressive TME.

overall_design: Differential Expression of RNA transcripts in LPS and IL4 stimulated macrophages exposed to no treatment, JQ1, and SF2523 dual PI3K/BRD4 inhibitor.

first: Alok

middle: R

last: Singh

first: Kevin

last: Liu

first: Timothy

middle: V

last: Pham

first: Muamera

last: Zulcic

first: Dylan

last: Skola

first: Christopher

last: Glass

first: Donald

middle: L

last: Durden


title: RNA-seq of Schizosaccharomyces pombe nuclear RNA exosome mutants

status: Public on Apr 17 2020

city: Oxford

first: Adrien

last: Birot

address: South Parks Rd

department: Departement of Biochemistry

country: United Kingdom

institute: University of Oxford

summary: Nuclear 3’ to 5’ nuclease RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given the large number of RNA species and intervening RNA processing factors. Here we analysed changes in the poly(A)+ RNA proteins interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. Our data demonstrate a functional connection between Rrp6 and Mtl1 in controlling processing and levels of multiple protein-coding and non-coding transcripts. Furthermore, we show that exosome mutants accumulate components of U1 and U2 snRNPs and show depletion of NTC components from RNA suggesting that the stage prior to the activation of the spliceosome represents a critical quality control step. We have also identified potential new RNA binding factors involved in exosome regulation, including a zinc-finger protein called Mub1 that controls levels of selected transcripts encoding for proteins implicated in stress response. Collectively, our data have provided a global view of RNA metabolism alterations in exosome deficient cells and revealed RNA binding proteins that may act as novel exosome cofactors.

overall_design: 4 samples in two replicates.


title: Gene expression in CD3/CD28 stimulated CD8 vs CD8 with various dosage of Cholesterol treatment

city: Houston

first: xingzhe

last: ma

state: TX

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

summary: gene expression in in vitro diffrerentiated CD8 (CD3/CD28 stimulation ) T cells and CD8 T cells treated with Cholesterol

overall_design: compare gene expression difference in CD8 vs CD8+0.5 Cho or CD8 vs CD8+0.75 Cho cells

first: Xingzhe

last: Ma


title: Regeneration of pulpo-dentinal-like complex by a group of unique multipotent CD24a positive stem cells

status: Public on Apr 15 2020

city: Chengdu

first: Zhonghan

last: Li

state: Sichuan

address: 29 Wangjiang Road

department: College of Life Sciences

country: China

institute: Sichuan University

summary: In this study, through three-dimensional spheroid culture, a group of unique multipotent stem cells were identified from mouse dental papilla, called multipotent dental pulp-regenerative stem cells (MDPSCs). MDPSCs exhibited enhanced osteo/odontogenic differentiation capabilities and could form regenerative dentin and neurovascular-like structures that mimicked the native teeth in vivo. Further analysis revealed that CD24a was the bona fide marker for MDPSCs and their expansion was highly dependent on the expression of a key transcriptional factor Sp7. Finally, CD24a positive cells could be detected in primary dental papilla in mice and human, suggesting MDPSCs resided in their native niches. Together, our study has identified a novel group of multipotent pulpregenerative stem cells with defined molecular markers for the potential treatment of pulpitis and pulp necrosis.

overall_design: Three group of cells (every group in triplicate) including monolayer cells, DPC Spheres and DPC P2  mRNA profiles were  sequenced.

first: Hong

last: Chen

first: Huancheng

last: Fu

first: Xue

last: Wu

first: Yufeng

last: Duan

first: Sicheng

last: Zhang

last: Hu

first: Yuansong

last: Liao

first: Tao

last: Wang

first: Yan

last: Yang

first: Guoqing

first: Weidong

last: Tian


title: RNA-sequencing data of mouse heart in myocardial infarction

city: Gwangju

first: Do Han

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Myocardial infarction (MI) was induced by permanent ligation of the left anterior descending coronary artery (LAD) in 8 weeks C57BL/6 male mice. 1 day (1D), 1 week (1W), 8 weeks (8W) after MI, the mouse left ventricles were used to construct cDNA libraries. For RNA-sequencing, 1 μg of total RNA extracted from pooled mouse LV (left ventricle) of MI or sham animals was used to construct cDNA libraries using the TruSeq RNA library kit (Illumina). For small RNA-sequencing, 1 μg of total RNA from the pooled LV of MI and sham was isolated using a miRNeasy Mini kit (Qiagen) and libraries were prepared using a TruSeq RNA library preparation kit (Illumina). Total RNA and small RNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000 sequencer. The reads from the RNA-seq were aligned to Mus musculus (mm10) using Tophat v2.0.13 which incorporates the Bowtie v2.2.3 algorithm. After aligning the reads to the genome, Cufflinks v2.2.1 was used to assemble aligned reads into transcripts and to estimate their abundance. The reads from small RNA-seq were aligned to Mus musculus matured and precursor miRNAs obtained from miRBase v21 using the miRDeep2 algorithm. qRT–PCR validation was performed using SYBR Green assays. The mean numbers of the total mapped reads by RNA-seq were 33,951,175 and the overall read mapping ratios were 96.84%. For the transcript expression quantification in RNA-seq, the number of reads for the genes were normalized to FPKM. Scatter plots of the normalized read counts of all mRNA (R2 > 0.99) showed high degrees of correlation between biological replicates, indicating their high levels of reproducibility.

overall_design: heart mRNA profiles of 3 different stages of MI (1D, 1W, 8W) were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000.

first: JinOck

first: JeiHyoung

last: Park

first: TaeYoung

first: DoHan


title: CD146+CD45-CD31- pericyte RNA sequencing following an acute bout of electrical stimulation

city: Urbana

first: Marni

last: Boppart

address: 405 N Matthews

department: Kinesiology

institute: University of Illinois at Champaign-Urbana

summary: The objective of this study was to understand the mechanisms by which electrical stimulation in vivo leads to improvements and growth in skeletal muscle post exercise through changing the function of CD146+CD45-CD31- pericytes.  We utilized global gene profiling to identify novel signaling pathways and patterns of gene expression involved in this adaptation process.

overall_design: RNA was extracted from CD146+CD45-CD31- pericytes that were isolated from the gastrocnemius muscles of male mice 3 hours post an acute 10 minute bout of electrical stimulation. Mice that had been electrically stimulated were compared to sham control mice.  Mice were equally distributed among the two groups with n=3/group

first: Svyatoslav

last: Dvoretskiy

first: Koyal

last: Garg

first: Michael

last: Munroe

first: Jenny

last: Drnevich


title: Analysis of gene expression during mouse preimplantation development in vitro, with or without a background of exogenous ovarian stimulation (superovulation)

city: Muenster

first: Michele

last: Boiani

address: Roentgenstrasse 20

country: Germany

institute: Max Planck Institute Muenster

summary:
Among the different procedures of the assisted reproductive technologies (ARTs), the purpose of ovarian stimulation with gonadotropins is to maximize the number of oocytes retrieved, and facilitate scheduling and planning of patient treatment. However, the doses of the gonadotropins required to increase the number of growing ovarian follicles, and, thereby, the number of oocytes, have been found to affect the quality of embryos in the mouse model of human reproduction (PMID 16569317, PMID 22802074, PMID 11387298, PMID 11157810). In order to clarify this issue, we compared the gene expression of mouse embryos with vs without a background of ovarian stimulation with PMSG and hCG.
Pronuclear oocytes were cultured in KSOM(aa) and developmental stages were collected based on morphology. Analysis of transcriptome signal intensities showed similar profiles and produced the expected clustering (one cluster from oocyte to 2-cell stage, another cluster from 4-cell stage to blastocyst) regardless of whether the embryos were produced in stimulated or non-stimulated ovarian cycles; however, the expression levels of some genes were different depending on the ovarian stimulation.

overall_design: Oocytes or embryos were collected in a total of 4 runs with superovulation (n=3096), and 9 runs without superovulation (n=989), during the time from November 2015 to March 2016. The lysates were pooled by developmental stage, keeping the hormonal backgrounds separate. Knowing how many embryos had been accumulated for each stage, we took a subvolume of the total lysate corresponding to 20 oocytes or embryos (of each stage). These subvolumes were subjected to Affymetrix microarray analysis, performed by Anika Witten c/o Institut fuer Humangenetik, Universitaetsklinikum Muenster.

first: Verena

last: Nordhoff


title: Next generation sequencing reveals upregulation of the lncRNA LINC-PINT in the substantia nigra of human Parkinson's disease patients compared to control donors

city: Jerusalem

first: Alon

last: Simchovitz

address: Silberman Building, Safra Campus

country: Israel

institute: Hebrew University of Jerusalem

summary: Parkinson's disease (PD) is the second most common neurodegenerative disease, involving the selecive death of dopaminergic neurons in the substantia nigra pars compacta brain region. Here, we performed next generation sequencing on RNA extracted from human substantia nigra tissue. The samples, acquired from the Netherland's Brain Bank, were taken post-mortem from PD and non-PD control donors. Analysis of the data revealed an upregulation of lncRNA LINC-PINT in PD substantia nigra. LINC-PINT interracts with the Polycomb Repressive Complex 2 (PRC2), inhibiting the tracription of multiple targets. Correspondingly, analysis of the data revealed that targets of PRC2 displayed larger disease-associated differences as compared to other genes, as well as enrichment for downregulation, suggesting that the differential expression of LINC-PINT in PD effects LINC-PINT/PRC2 interaction as well.

overall_design: ribosomal-RNA depleted RNA-Seq libraries were prepared from the substantia nigra of PD and non-PD control donors. Only samples with RIN>6.5 were used for library preperation

first: Mor

last: Hanan

first: Sebastian

last: Kadener

first: Hermona

last: Soreq


title: Distinct Epigenetic Subtypes Are Linked to Disease Progression in Low-Risk MDS

city: Miami

first: Maria

middle: E

last: Figueroa

state: FL

address: 1501 NW 10th Ave

department: Human Genetics

institute: University of Miami

type: Methylation profiling by high throughput sequencing

summary: Myelodysplastic syndromes (MDS) are a heterogeneous group of clonal disorders characterized variably by the presence of peripheral cytopenias, bone marrow hypercellularity and dysplastic changes in the bone marrow. While MDS patients have an increased risk of progression to acute myeloid leukemia (AML), most MDS patients actually succumb to progressive bone marrow failure. Amongst patients classified as low-risk MDS, different clinical evolutions have been observed, with some patients remaining relatively stable for long periods of time (herein, stable MDS), while others show more progressive disease, with worsening cytopenias, and often increased transfusion requirements (herein, progressive MDS). Current risk stratification strategies fail to distinguish these two groups at diagnosis. We report here that these distinct behaviors are encoded at the epigenetic level and that examining DNA methylation profiles of low-risk MDS patients captures underlying differences between the two different groups. In this study, we identified 356 differentially methylated regions (DMRs) between stable and progressive low-risk MDS at the time of diagnosis. The number of DMRs was almost doubled at the time of progression (681 follow-up DMRs), and this was accompanied by an increase in the local variability at specific methylation regions, and an increase in heterogeneity over time. These findings reveal previously unrecognized epigenetic heterogeneity in low-risk MDS patients and opens the possibility for using epigenetic differences to help improve risk-stratification at diagnosis.

overall_design: DNA methylation profiling in peripheral blood (PB) cells from 20 low-risk MDS patients (13 stable vs. 7 progressive low-risk MDS at the time of diagnosis and follow-up; 40 specimens in total), as well as from 4 age-matched healthy donors.

first: Tingting

last: Qin

first: Jason

last: Sotzen

first: Raajit

last: Rampal

first: Franck

middle: T

last: Rapaport

first: Ross

last: Levine

first: Virginia

last: Klimek

first: Stephen

last: Nimer


title: High-throughput sequencing analysis of miRNAs expression profiles in the thoracic ascending aortic aneurysm (TAA) tissues and plasma samples.

city: Vilnius

first: Raimundas

last: Ražanskas

address: Sauletėkio al. 7

department: Institute of Biotechnology, Life Sciences Center

country: Lithuania

institute: Vilnius University

summary:
In the present study, we evaluated miRNA expression profiles of 32 patient aortic aneurysm tissue and plasma samples using Illumina next-generation sequencing platform. A total of 20 miRNA were differentially expressed in tissues, 17 miRNAs - in plasma samples.
Differentially expressed miRNAs determined in the present study could be applied for thoracic ascending aneurysm diagnosis.

overall_design: For the tissue analysis, 8 TAA samples and 6 healthy aortic control samples were collected. The 3 of 7 TAA plasma samples were isolated from the same patients, which were included in the TAA tissue group. Moreover, 4 plasma samples from the same TAA patients 3 months after the surgery were investigated.  A control group of 7 plasma samples was isolated from unrelated healthy patients. All samples were analyzed using Illumina MiSeq v2 miRNA sequencing by Illumina MiSeq system.

first: Stase

last: Gasiule

first: Vaidotas

last: Stankevicius

first: Giedrius

last: Vilkaitis

last: Razanskas


title: The Loss of TBK1 Kinase Activity in Motor Neurons or in All Cell Types Differentially Impacts ALS Disease Progression in SOD1 Mice

status: Public on Apr 13 2020

city: New york

first: Valeria

last: Gerbino

state: Ny

address: 3227 Broadway

department: Zuckerman Mind Brain Behavior Institute

institute: Columbia University

summary:
DNA sequence variants in the TBK1 gene associate with or cause sporadic or familial amyotrophic lateral sclerosis (ALS). Here we show that mice bearing human ALS-associated TBK1 missense loss-of-function mutations, or mice in which the Tbk1 gene is selectively deleted in motor neurons, do not display
a neurodegenerative disease phenotype. However, loss of TBK1 function in motor neurons of the SOD1G93A mouse model of ALS impairs autophagy, increases SOD1 aggregation, and accelerates early disease onset without affecting lifespan. By contrast, point mutations that decrease TBK1 kinase activity in all cells also accelerate disease onset but extend the lifespan of SOD1 mice. This difference correlates with the failure to activate high levels of expression of interferon-inducible genes in glia. We conclude that loss of TBK1 kinase activity impacts ALS disease progression through distinct pathways in different spinal cord cell types and further implicate the importance of glia in neurodegeneration.

overall_design: Dissection of pathways affected by TBK1 loss of function mutations in the ALS spinal cord

first: Tom

last: Maniatis


title: Efficient method for the differentiation of human pluripotent stem cells (hPSCs) into functional brain microvascular endothelial (BME)-like cells

city: Daejeon

first: Na Geum

last: Lee

address: 125 Gwahak-ro, Yuseong-gu

institute: KRIBB

summary: We developed an efficient method for the differentiation of human pluripotent stem cells (hPSCs) into functional brain microvascular endothelial (BME)-like cells. Here, we compared the whole-gene expression pattern of BME-like cells differentiated from hPSCs with primary BMECs (pBMECs). Comparison of expressed genes in the purified BME-like cells and pBMECs indicated a high degree of similarity. Furthermore, brain ECs related gene, including BBB membrane specific proteins, transporters, and channels, showed similar levels between BME-like cells and pBMECs. This study reveals that hPSC-derived BME-like cells have similar character with pBMECs.

overall_design: Gene expression profile of BME-like cells differentiated from hPSCs compared with human primary BMECs (pBMECs)

first: Jeong-Ki

last: Min

middle: G

first: Jongjin

last: Park


title: The Transgenerational Effects of Prenatal Synthetic Glucocorticoids on the Hippocampus Cortex

city: Toronto

last: Matthews

state: Ontario

address: 1 King's College Circle

country: Canada

institute: University of Toronto

summary: First generation animals (F1) were exposed to multiple courses of synthetic glucocorticoids in utero. Animals were then bred to produce second (F2) and third (F3) generation offspring. These animals underwent behavioural assessmenets before sacrifice. In this experiment the prefrontal cortex for F1, F2, and F3 female animals, as well as F1 males (Control and sGC) have been extracted via micro-punch and RNA has been extracted.

overall_design: Methylation Analyses: F1: Control N=6, sGC N=6; F2: Control N=6, sGC N=6; F3: Control N=7, sGC N=5; RNA-Seq Analyses: F1: Control N=6, sGC N=5; F2: Control N=6, sGC N=6; F3: Control N=6, sGC N=7

first: Andrea

last: Constantinof

first: Lisa

last: Boureau

first: Vasilis

last: Moisiadis

first: Moshe

last: Szyf


title: DNA 5-methylcytosine specific profiling with limited input

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

summary: DNA methylation 5mC specific detection has been limited by the mixed signals from traditional bisulfite sequencing or by the severe degradation of input during oxBS-seq pretreatment. Here, we presented a 5mC specific whole genome amplification method (5mC-WGA), with which we achieved whole genome bisulfite sequencing with 5mC retention from limited input down to 10 pg scale without 5hmC signals, presenting DNA 5mC methylome with high producibility and great accuracy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We compared our 5mC-WGA method with well-established TAB-Seq and oxBS-Seq methods.

first: Chang

last: Liu

first: Boxuan

last: Zhao

first: Chuan

last: He


title: C-maf binding to dna in C-maf_ab vs Iso in Mus musculus

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

summary: We report the application of  Chip-seq to study the binding properties of C-maf. We determine the genetic and non genetic regions with the largest Chip-seq peaks in C-maf_ab compared to Isotype control antibody (Iso) samples.

overall_design: Chip-seq peaks of C-maf_ab and Iso from two biological replicates of mouse DNA were compared

first: Min

first: Zan

last: Tong

first: Chuanlin

last: Ding

first: Fengling

last: Luo

first: Shouzhen

last: Wu

first: Sabrin

last: Albeituni

first: Liqing

first: Xiaoling

last: Hu

first: David

last: Tieri

middle: C

first: Michito

last: Hamada

first: Satoru

last: Takahashi

first: Andrew

middle: A

last: Gibb

first: Goetz

last: Kloecker

first: Hang-Ge

last: Zhang

first: Michael

last: Bousamra II

first: Bradford

last: Hill

first: Xiang

first: Jun

last: Yan


title: RNAseq analysis of prostate cancer stem cells

city: Iowa City

first: Songhai

last: Chen

state: IOWA

address: 51 Newton Road, 2-250 BSB

department: Pharmacology

institute: University of Iowa

summary: Prostate cancer stem cells were isolated from PC3 cells by fluorescence activated cell sorting using the SORE6 reporter system. Differential gene expression between cancer stem cells and non-cancer stem cells were determined by RNAseq analysis.

overall_design: mRNA profiles of PC3 cells were determined by deep sequencing, in duplicate, using the BGISEQ-500 platform (BGI). Each sample was sequenced at 100 bp paired-end read and the depth of 30M reads per sample


title: Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [RNA-Seq]

city: Guangzhou

first: Li

last: Zhiwei

address: No.723,Xingke Road

institute: South China Botanical Garden, Chinese Academy of Sciences

summary: Here, we found that the tomato jmjC domain-containing gene SlJMJ6 encodes a histone lysine demethylase that specifically demethylates H3K27 methylation. Overexpression of SlJMJ6 accelerated fruit ripening in tomato, which is associated with the up-regulated expression of a large number of ripening-related genes. Integrated analysis of RNA-seq and ChIP-seq data identified 55 genes that are targeted directly by SlJMJ6 and transcriptionally up-regulated with decreased H3K27m3 in SlJMJ6 overexpressing (SlJMJ6-OE) fruits. A large number of the SlJMJ6-regulated genes are involved in transcription regulation, ethylene biosynthesis, cell wall degradation, pigment biosynthesis, and hormone signaling. Fourteen ripening-related genes including RIN, ACS4, ACO1, PL, TBG4 were confirmed to be directly regulated by SlJMJ6 through removing H3K27me3. Taken together, these results indicated that SlJMJ6 is a ripening prompting H3K27me3 demethylase that activates the expression of the ripening-related genes by modulating H3K27me3, thereby facilitating fruit ripening in tomato. To our knowledge, this is the first report of the involvement of a histone lysine demethylase in the regulation of fruit ripening.

overall_design: Tomato pericarp mRNA profiles of  wild type (WT) and transgenic lines (JMJ6-OE) at 37 days after anthesis were generated by deep sequencing, in triplicate, using Illumina HiSeqTM 2000.

first: Zhiwei

last: Li

first: Guoxiang

last: Jiang

first: Xuncheng

last: Liu

first: Xiaochun

first: Dandan

first: Xiaowan

last: Wang

first: Yijie

last: Zhou

first: Huiling

first: Taotao

first: Keqiang

first: Yueming

first: Xuewu

last: Duan


title: O-GlcNAcylation of human TATA-Box binding protein is required to sustain key metabolic enzyme gene expression

city: Baltimore

first: Gerald

middle: W

last: Hart

state: MD

address: 725 N. Wolfe St.

department: Biological Chemistry

institute: Johns Hopkins School of Medicine

summary: Cellular homeostasis is ensured by myriad cellular processes that integrate environmental changes and maintain stability within the organism. Variation in nutrient availability can be reflected by the post-translational modification of many proteins by the nutrient sensor O-GlcNAcylation. Herein, we describe a molecular mechanism of transcription regulation by O-GlcNAcylation of the TATA-box binding protein (TBP). We show that O-GlcNAcylation regulates its interaction with BTAF1, hence, formation of the B-TFIID complex, and its dynamic cycling on and off of DNA. We mapped three O-GlcNAcylation sites at the N-terminus of TBP and defined T114 as a main regulator of the interaction with BTAF1. CRISPR/Cas9 editing of wild-type TBP replaced by a T114A mutant, leads to profound modification of HeLa cells’ glucose and lipid metabolism and gene expression profile. These data indicate that basal transcription machinery, via O-GlcNAcylation of TBP, can integrate nutrient availability and modulate the transcriptome, resulting in adaptation of cellular metabolism.

overall_design: Endogenous TBP gene was edited using CRISPR/Cas9 technology in HeLa cells. The 3X-FLAG was inserted in phase at the N-terminal of the protein and the T114 O-GlcNAcylation site was replaced by an alanine. RNAs of the parental HeLa cell line as well as HeLa TBP3X-WT and HeLa TBP3X-T114A cell lines were extracted using RNeasy plus kit (QIAGEN) following manufacturer’s instructions. Samples from each cell lines were submitted in triplicate to total RNA deep sequencing. Library preparation, sequencing and data analysis were performed at the Johns Hopkins University Deep Sequencing and Microarray Core Facility. RNA-Seq libraries were constructed using TruSeq stranded Total mRNA library kit (Illumina, Inc.) and 75 cycle runs were performed in multiplex on the NextSeq 500 platform.

first: Stéphan

last: Hardivillé

first: C

last: Talbot Jr


title: Functional heterogeneity exceeds genetic heterogeneity in chronic myelomonocytic leukemia

first: Maria

middle: Eugenia

last: Figueroa

address: 1501 NW 10th Ave, BRB 709A, Locator code C227

institute: University of Miiami

summary: The respective role of genetic and epigenetic heterogeneity in the functional diversity of cells that compose human malignancies remains poorly understood. This question is addressed in chronic myelomonocytic leukemia (CMML), a myeloid neoplasm in which clinical diversity contrasts with a limited genetic heterogeneity. By reprogramming CMML-patient and healthy donor CD34-positive cells, we generated induced pluripotent cell clones (iPSC). In one of the patients, we captured a part of the genetic heterogeneity of the leukemic clone and analyzed five iPSCs with two distinct genetic backgrounds, i.e. with and without KRASG12D mutation. Hematopoietic differentiation of these clones recapitulated the main features of the patient disease, including overproduction of granulomonocytes and dysmegakaryopoiesis. These analyses also disclosed significant discrepancies in the behavior as well as the DNA methylation pattern of hematopoietic cells derived from iPSCs with similar genetic background. Introduction of SRSF2P95H mutation in a KRAS-mutated iPSC partially suppressed the functional and epigenetic gap with the other KRAS-mutated clone. Despite the similar functional behavior of these two clones, only the SRSF2P95H clone responded to low doses of the hypomethylating agent decitabine by restoration of a more balanced production of hematopoietic cells. These analyses unravel additional levels of intraclonal heterogeneity beyond the coding mutations, which may also modulate individual cell response to treatment.

overall_design: Twenty-five ng of high-molecular weight genomic DNA of CD34+ from control or patient A iPS clones were used to perform the ERRBS assay as described (Park et al. 2014) and sequenced on a HiSeq 3000 Illumina sequencer. 11 samples were analyzed, 6 iPS clones derived from a CMML patient and 5 derived from 2 different healthy control individuals.

first: Allan

last: Beke

first: Lucie

last: Laplane

first: Julie

last: Rivière

first: Miguel

last: Torres-Martin

first: Philippe

last: Rameau

first: Véronique

last: Saada

first: Ana

last: Hurtado

first: Cyriane

last: Oeuvray

first: Larissa

last: Lordier

first: Karine

last: Leveque

first: William

last: Vainchenker

first: Nathalie

last: Droin

first: Éric

last: Solary


title: Transcriptome profiling of peripheral blood mononuclear cell subsets

city: Los Angeles

first: Steve

last: Cole

address: 11-934 Factor Bldg, UCLA

department: Medicine

institute: UCLA School of Medicine

summary: Transcriptome profiling was conducted on 2 replicate samples of total peripheral blood mononuclear cells (PBMC) and isolated PBMC subsets.

overall_design: Gene expression profiling was conducted on total PBMC and parallel isolated subsets of CD+/CD4+ T lymphocytes, CD3+/CD8+ T lymphocytes, CD19+ B lymphocytes, CD3-/CD14-/CD56+ NK cells, CD66b+ neutrophils, CD14+ monocytes, CD14+/CD16- classical monocytes, CD14+/CD16+ non-classical monocytes, CD1c+(BDCA1+)/CD19- myeloid dendritic cells (DC1), CD303+(BDCA2+) plasmacytoid dendritic cells (DC2), and CD141+(BDCA3+)/CD14- myeloid dendritic cells (DC3).  Samples of each cell population were isolated from PBMC (derived from ficol gradient centrifugation of buffy coat blood samples).  B, T, and NK cells were isolated from total PBMC by flow cytometry. Neutrophils, monocytes, and DCs were isolated by flow cytometric sorting of PBMC that were pre-depleted of CD3+ and CD19+ cells by immunomagnetic positive selection (MACS microbeads; Miltenyi Biotech).  Flow cytometry indicated > 99% purity of all cell populations.  Two samples of each cell type were pooled to create a total of two independent replicate assay samples for RNA profiling. One replicate set of neutrophil samples yielded sub-optimal RNA and failed post-assay validity checks; that sample has been deleted from the data, so there is only 1 replicate samples of neutrophil data.


title: Defects in mTORC1 Network and mTORC1-STAT3 Pathway Crosstalk Contributes to Noninflammatory Hepatocellular Carcinoma

first: Ting

last: Li

state: Guangdong

address: 253 Gongye Street

department: Department of Hepatobiliary Surgery II, Zhujiang Hospital

institute: Southern Medical University

summary:
mTORC1-driven noninflammatory HCC and provide insight into further development of a protective strategy against noninflammatory HCC.
Background & Aims: Mammalian target of rapamycin complex 1 (mTORC1) is frequently hyperactivated in hepatocellular carcinoma (HCC). Cases of HCC without inflammation and cirrhosis are not rarely seen in clinics. However, the molecular basis of noninflammatory HCC remains unclear.
Methods: Spontaneous noninflammatory HCC in mice was triggered by constitutive elevation of mTORC1 by liver-specific Tsc1 knockout (LTsc1KO). A multi-omics approach was utilized on tumor tissues to better understand the molecular basis for the development of HCC in the LTsc1KO model.
Results: We showed that LTsc1KO in mice triggered spontaneous noninflammatory HCC, with molecular characteristics similar to those of diethylnitrosamine-mediated noncirrhotic HCC. Mitochondrial and autophagy defects, as well as hepatic metabolic disorder were manifested in HCC development by LTsc1KO. mTORC1 activation on its own regulated an oncogenic network (DNA-damage-inducible transcript 4, nuclear protein 1 and fibroblast growth factor 21), and mTORC1–signal transducer and activator of transcription pathway crosstalk that altered specific metabolic pathways contributed to the development of noninflammatory HCC.
Conclusion: Our findings reveal the mechanisms of mTORC1-driven noninflammatory HCC and provide insight into further development of a protective strategy against noninflammatory HCC.

first: Yi

last: Gao


title: Alterations in alternative RNA splicing in hepatocytes from high-fat diet fed C57BL/6 male mice

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

institute: UCSD

summary: C57BL/6J male mice were fed a 60% HFD for 10 weeks, then hepatocytes were isolated, RNA extracted and subjected to RNAseq

overall_design: Comparison of transcriptomes in hepatocytes from obese and lean mice

first: Nicholas

middle: J

last: Webaster

first: Olivia

last: Osborn


title: Expression data from HFL-1 fibroblasts

city: Beijing

first: Dong

last: Leng

address: No.8 Gongti South Road

institute: Beijing Chao-Yang Hospital, Capital Medical University

summary:
Hyaluronidases was reported to be effective in lung fibrosis therapy, and HYAL1 was found to inhibit TGF-β1 mediated cell growth in murine L929 fibroblasts, while the underlying mechanism of HYAL1 in regulating human lung fibroblasts is largely unknown.
We used microarray to detail the gene expression of HYAL1 overexpression HFL-1 fibroblasts, and found significantly downregulated genes.

overall_design: Human fetal lung fibroblasts HFL-1 were infected with HYAL1 overexpression and the control lentiviruses. Total RNAs were extracted from the HYAL1 overexpression and control HFL-1 fibroblasts, and the fragmented biotin-labeled RNAs obtained by in vitro transcription were hybridized to the GeneChip® Prime ViewTM Human Gene Expression Array.


title: Global gene expression profiling of shLUC (control) and shMLL4-1 and shMLL4-3 (MLL4-knockdown) LKR-10 mouse lung cancer cell using RNA sequencing

city: Waltham

first: Ming

last: Tang

state: Massachusetts

address: 21 Hickory Drive, 1

department: Computational biology

institute: Immunitas Therapeutics

summary: Here, we show that the histone H3 lysine (H3K4) methyltransferase MLL4 (a COMPASS/SET1-like enzyme; also called KMT2D) is ranked the most highly inactivated epigenetic modifier in NSCLC tumors lung-specific loss of Mll4 accelerates K-RasG12D-induced lung tumorigenesis in mice while reducing their survival time. Mll4 loss upregulated tumor-promoting programs, such as glycolysis, which is also enriched in human lung tumors with low MLL4 levels or MLL4 inactivation. The inhibition of glycolysis selectively impeded the proliferation and tumorigenic growth of NSCLC cells bearing human MLL4-inactivating mutation. Mll4 loss caused widespread impairment of super-enhancer signals, including super-enhancer associated with the circadian transcriptional repressor gene Per2 which represses glycolysis genes in NSCLC cells.

first: H

last: Alam

first: M

last: Lee


title: Predominant Requirement of Mitochondrial Transcriptional Factor A in Tissue-resident Regulatory T cell Maintenance and Function

city: Gainesville

first: Liang

last: Zhou

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

summary: Regulatory T cells (Tregs) are pivotal for immune suppression. Cellular metabolism is important for Treg homeostasis and function. However, the exact role of mitochondrial respiration in Tregs remains elusive. Mitochondrial transcription factor A (Tfam) is essential for mitochondrial respiration and controls mitochondrial DNA replication, transcription and packaging. Here we show that genetic ablation of Tfam in Tregs impairs Treg maintenance in non-lymphoid tissues at the steady state and in tumor. Tfam-deficient Tregs have reduced proliferation and Foxp3 expression upon glucose deprivation in vitro. Tfam deficiency preferentially affects gene activation in Tregs through regulation of DNA methylation. Tfam-deficient Tregs have enhanced methylation at TSDR of Foxp3 locus. Deletion of Tfam in Tregs affects Treg homing and maintenance, resulting in tissue inflammation in colitis, but enhances tumor rejection. Thus, our work reveals a critical role for Tfam-mediated Treg respiration in regulation of inflammation and anti-tumor immunity.

overall_design: RNA-seq (3 replicates) and ATAC-seq (2 replicates)  analysis of spleen/lymph node regulatory T cells from Tfam cKO and control female mice.

first: Zheng

last: Fu

first: Joseph

last: Dean

first: John

last: Bostick


title: A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

city: Wuhan

first: Zengdong

last: Tan

state: Hubei

address: shizishan street

institute: HZAU

summary: Waterlogging stress (WS) in a dynamic environment seriously limits plant growth, development, and yield. The regulatory mechanism underlying WS conditions at an early stage in maize seedlings is largely unknown. In the present study, the primary root tips of B73 seedlings were sampled before (0 h) and after (2 h, 4 h, 6 h, 8 h, 10 h, and 12 h) WS and then subjected to transcriptome sequencing, resulting in the identification of differentially expressed protein-coding genes (DEpcGs) and long non-coding RNAs (DElncRs) in response to WS. These DEpcGs were classified into nine clusters, which were significantly enriched in several metabolic pathways, such as glycolysis and methionine metabolism. Several Transcription factor families, including AP2-EREBP, bZIP, NAC, bHLH, and MYB, were also significantly enriched. In total, 6099 lncRNAs were identified, of which 3190 were DElncRs. A co-expression analysis revealed lncRNAs to be involved in 11 transcription modules, 10 of which were significantly associated with WS. The DEpcGs in the four modules were enriched in the hypoxia response pathways, including phenylpropanoid biosynthesis, MAPK signaling, and carotenoid biosynthesis, in which 137 DElncRs were also co-expressed. Most of the co-expressed DElncRs were co-localized with previously identified quantitative trait loci associated with waterlogging tolerance. A quantitative RT-PCR analysis of DEpcG and DElncR expression among the 32 maize genotypes after 4 h of WS verified significant expression correlations between them as well as the significant correlation with phenotype of waterlogging tolerance. Moreover, the high proportion of hypoxia response elements in the promoter region increased the reliability of the DElncRs identified in this study. These results provide a comprehensive transcriptome in response to WS at an early stage of maize seedlings and expand our understanding of the regulatory network involved in hypoxia in plants.

first: Feng

last: Yu

first: Tian

last: Fang

first: Kaiyuan

first: Kun

last: Liang

first: Fazhan

last: Qiu


title: Keap1 deficiency results in a genotype-specific dependency on Slc33a1

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: Approximately 20-30% of human lung adenocarcinomas (LUAD) harbor loss-of-function (LOF) mutations in Kelch-like ECH Associated-Protein 1 (KEAP1), which lead to hyperactivation of the antioxidant program downstream from the nuclear factor, erythroid 2-like 2 (NRF2) transcription factor and correlates with poor prognosis1–3. We previously showed that Keap1 mutation accelerates KRAS-driven LUAD and produces a marked dependency on glutaminolysis4.  To extend the investigation of genetic dependencies in the context of Keap1 mutation, we performed a druggable genome CRISPR-Cas9 screen in Keap1-mutant cells. This analysis uncovered a Keap1-mutant-specific dependency on solute carrier family 33 member 1 (Slc33a1), an endomembrane-associated protein with roles in autophagy regulation5, as well as a series of functionally-related genes implicated in the unfolded protein response. Targeted genetic and biochemical experiments using mouse and human Keap1-mutant tumor lines, as well as preclinical genetically-engineered mouse models (GEMMs) of LUAD, validate Slc33a1 as a robust Keap1-mutant-specific dependency. Furthermore, unbiased genome-wide CRISPR screening identified additional genes related to Slc33a1 dependency. Overall, our study provides a strong rationale for stratification of patients harboring KEAP1-mutant or NRF2-hyperactivated tumors as likely responders to targeted SLC33A1 inhibition and underscores the value of integrating functional genetic approaches with GEMMs to identify and validate genotype-specific therapeutic targets.

overall_design: Keap1-mutant (n = 2), WT (n = 2), and WT plus sgSlc33a1 transduced (n = 2) samples were jointly analyzed to derive a murine signature of Slc33a1-mutant gene expression changes

first: Rodrigo

last: Romero

first: Francisco

last: Sánchez-Rivera

first: Peter

middle: M

last: Westcott

first: Kim

last: Mercer

first: Arjun

first: Alexander

last: Muir

first: Tania

last: González-Robles

first: Swanny

last: Lamboy-Rodríguez

first: Laura

middle: Z

last: Liao

first: Sheng

last: Ng

first: Leanne

last: Li

first: Caterina

middle: I

last: Colón

first: Santiago

last: Naranjo

first: Mary

last: Beytagh

first: Caroline

last: Lewis

first: Peggy

middle: P

last: Hsu

first: Roderick

last: Bronson

first: Matthew

last: Vander Heiden

first: Tyler

last: Jacks


title: Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato [ChIP-Seq]

first: Li

last: Zhiwei

overall_design: Tomato histone modification H3K27me3 profiles of  wild type (WT) and transgenic lines (JMJ6-OE) at 37 days after anthesis.

first: Zhiwei

first: Guoxiang

last: Jiang

first: Xuncheng

last: Liu

first: Xiaochun

last: Ding

first: Dandan

last: Zhang

first: Xiaowan

last: Wang

first: Yijie

last: Zhou

first: Huiling

last: Yan

first: Taotao

first: Keqiang

last: Wu

first: Yueming

first: Xuewu

last: Duan


title: Genome-wide transcriptome and alternative splicing changes in pregnant rat uterine arteries

city: Madison

first: Sathish

last: Kumar

state: Wisconsin

address: 2015 Linden drive

department: School of Veterinary Medicine

institute: University of wisconsin Madison

summary: In the current study, we have focused on a whole genome transcriptome and alternative splicing in utrine artery from pregnant and non pregnant Sprague Dawley rats .

overall_design: Determine the functional imapct of pregnancy-induced transcriptome and their splice level changes in rat uterine arteries through whole genome next generation RNA sequencing (NGS)

first: Kathirvel

last: Gopalakrishnan

last: kumar


title: microRNAs from rat muscle derived stem cells treated with lipid factors

city: Torrance

first: Robert

last: Gelfand

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

summary: This is to test whether exposure to lipids has an effect, particularly a damaging effect, on stem cells.

overall_design: Muscle derived stem cells were grown in tissue culture and treated with serum from early or late diabetic animals or with cholesterol or with palmitic acid. Serum from non-obese animals is referred to as LZ serum, while serum from an obese strain of animals is referred to as OZ serum. Cholesterol complexed to cyclodextrin is water soluble and is referred to as cholesterol or water soluble cholesterol. Since the palmitic acid is prepared in the presence of bovine serum albumin, an albumin control is also used. Rat strains referred to as ZL4 and ZF4 refer to animals of non-obese and obese type respectively.

first: Istvan

last: Kovanezc

first: Guiting

last: Lin

first: Tom

last: Lue

first: Nestor

last: Gonzalez-Cadavid


title: Transcriptome analysis profile to understand mechanisms activated by FDA molecules that overcome the ATP7B mediated  resistance to cisplatin in ovarian cancer IGROV-CP20 cells.

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

summary: To understand whether treatments with FDA drugs Trelmisartan, Tranilast or Amphotericin B were able to downregulate pathways important to overcome resistance to cisplatin in ovarian cancer cells IGROV-0CP20 we cemployed  Quant-seq Analysis.Transcriptome of the of IGROV-CP20 cells treated with cisplatin and each of the three FDA molecules were compared with untreated cells.

overall_design: Total RNA was extracted from IGROV-CP20 cells treated with cisplatin (T) or a combination of cisplatin and each of the following drugs: Telmisartan, Tranilast and Amphotericin B; RNA extracted from untreated cells was used as control.

first: A

first: R

last: Polishchuk


title: Histone demethylase SlJMJ6 promotes fruit ripening by removing H3K27 methylation of ripening-related genes in tomato

first: Li

last: Zhiwei

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

overall_design: Refer to individual Series


title: BMAL1 coordinates energy metabolism and differentiation of pluripotent stem cells.

city: Santiago de Compostela

first: Miguel

last: Fidalgo

state: A Coruña

address: Barcelona Avenue s/n-Campus Vida

department: Physiology

country: Spain

institute: Universidade de Santiago de Compostela

summary: In spite of lacking circadian rhythms, several master clock regulators are readily expressed in embryonic stem cells (ESCs). In particular, the role of Brain and Muscle ARNT-Like 1 (Bmal1, also known as Arntl) remains to be addressed. Here, we generated Bmal1 CRISPR/cas9 knock-out ESCs to elucidate the role of BMAL1 in pluripotency maintenance and differentiation. Our findings indicate that although BMAL1 is dispensable for ESC maintenance, it is required for proper differentiation. Moreover, we find that Bmal1 participates in the transcriptional regulation of lineage specification programs during differentiation and gastrulation in vitro. In particular, loss-of-function of Bmal1 changes the metabolic state of ESCs by promoting more oxidation at the expense of glycolysis. Our data points to a circadian clock-independent function of BMAL1 during early developmental stages, and will help in the understanding of the mechanisms that control exit from pluripotency and early cell-fate decisions.

overall_design: RNA profiling  of Mouse Embryonic Stem Cells Wild type and KO (CRISPR-Cas9) for Bmal1 (Arntl) gene.

first: Cristina

last: Ameneiro

first: Tiago

last: Moreira

first: Alejandro

last: Fuentes-Iglesias

first: Alba

last: Coego

first: Vera

last: Garcia-Outeiral

first: Adriana

last: Escudero

first: Daniel

last: Torrecilla

first: Sonia

last: Mulero-Navarro

first: Jose Maria

last: Carvajal-Gonzalez

first: Diana

last: Guallar


title: Alterations in alternative RNA splicing in Srsf3-flox/flox hepatocytes with AAV-CRE mediated deletion of SRSF3 vs hepatocytes with AAV-GFP

first: Nick

last: Webster

summary: Hepatocytes were isolated and infected in vitro, then RNA extracted and subjected to RNAseq

overall_design: Comparison of transcriptomes in SRSF3KO hepatocytes compared to control hepatocytes

first: Nicholas

last: Webaster

first: Deepak

last: Kumar


title: The bacteroides fragilis(BF) in colorectal carcinogenesis

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: To elucidate whether  Enterotoxigenic Bacteroides fragilis (ETBF) plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of  ETBF treated DLD-1 colorectal cancer cell lines.

overall_design: RNA-seq was performed in DLD-1 colorectal cancer cells after ETBF treatment.

first: Yujie

last: Bao


title: The effects of testosterone and corticosterone treatment on gene expression in germinal discs of the laying hen

city: Athens

first: Kristen

middle: Jean

last: Navara

state: GA

address: 203 Poultry Science Building

department: Poultry Science

institute: The University of Georgia

summary: Previous work has suggested that the hormones testosterone and corticosterone influence the process of meiotic segregation in the ovarian follicles of laying hens, ultimately influencing whether the resulting egg produces a male or female chick. We tested whether treatment with testosterone and/or corticosterone stimulated changes in the expression of genes that may influence the process of meiotic segregation as a next step towards understanding the mechanism by which these hormones may play a role in sex ratio adjustment in birds.

overall_design: Five biological replicates were performed. Each replicate contained pooled samples from 8 individual hens. Hens were treated with either corticosterone (1.5mg in 0.5ml peanut oil), testosterone (1.5mg in 0.5ml peanut oil) or control oil (0.5ml peanut oil) at 5h prior to expected ovulation (as predicted according to previous laying cycles). Hens were killed via lethal injection 1.5h after injection (3.5h before ovulation) and germinal discs were collected from F1 follicles to determine whether expression of genes that control chromosome segregation was influenced by either or both of the two treatments.


title: A TFAP2C Gene Signature is Predictive of Outcome in HER2 Breast Cancer

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

institute: Washington University


title: A TFAP2C Gene Signature is Predictive of Outcome in HER2 Breast Cancer (RNA-Seq)

summary:
Abstract: A subset of HER2 breast cancers with amplification of the TFAP2C gene locus becomes addicted to AP-2g.  We sought to define AP-2g-regulated genes that control growth and invasiveness by comparing HER2 cell lines with differential response to TFAP2C knockdown. A set of 68 differentially expressed genes was identified, which included CDH5 and CDKN1A. Pathway analysis implicated the MAPK13/p38δ and retinoic acid regulatory nodes, which were confirmed to display divergent responses. The AP-2g gene signature was highly predictive of outcome in HER2-positive breast cancer patients. We conclude that AP-2g regulates a set of genes in HER2 breast cancer that drive cancer growth and invasiveness and that the AP-2g gene signature can predict outcome of patients with HER2 breast cancer.
Results: Using an optimized data analysis workflow, we mapped about 50-75 million sequence reads per sample to the human genome Human Feb.2009 (GRCh37/hg19) (hg19). By RNA-seq analysis, knockdown of TFAP2C in HCC1954 with siRNA (compared to NT siRNA) identified 364 genes with significantly altered expression. To further create specificity for AP-2gamma-regulated genes, RNA-seq analysis was performed comparing expression in shHCC1954 with shTFAP2C cells vs. shNT; this analysis identified 8,986 genes with significantly altered expression.  The two data sets were subsequently compared to identify a set of genes that were consistently altered with knockdown of TFAP2C by siRNA and shRNA.  This comparison confirmed the identification of 152 AP-2gamma target genes in HCC1954 cells.  Because HCC1954 demonstrated opposite growth regulation and invasiveness with knockdown of TFAP2C compared to SKBR3, we hypothesized that the AP-2gamma target genes responsible for growth and invasion would be differentially regulated with knockdown of TFAP2C in HCC1954 versus SKBR3.  Hence, RNA-seq analysis was performed in SKBR3 after knockdown of TFAP2C with siRNA; in this analysis, a total of 3814 genes were significantly altered. The pattern of expression for the 152 AP-2gamma target genes identified in HCC1954 was subsequently compared to expression changes in SKBR3.  Of note, only 79 of the 152 TFAP2C target genes in HCC1954 were found to change expression significantly in the RNA-seq data set from SKBR-3.
Conclusions:  Knockdown of TFAP2C with co-knockdown of CDH5 in SKBR-3 confirmed no significant effect on invasion, though there was a slight reduction in invasiveness with knockdown of CDH5 that failed to reach statistical significance (p=0.12). These findings support the conclusion that regulation of CDH5 and CDKN1A contribute to alterations of proliferation and invasiveness induced by knockdown of TFAP2C.

overall_design: To identify the key AP-2gamma target genes mediating cell growth and invasiveness, RNA-seq was used to characterize significant changes in gene expression with knockdown of TFAP2C in HER2 positive cell lines, in triplicate.

first: Vincent

last: Wu

first: Boris

last: Kiriazov

first: Kelsey

last: Koch

first: Vivian

last: Gu

first: Anna

last: Beck

last: Borcherding

first: Peter

last: Addo

first: Zarchary

last: Wehrspan

first: Weizhou

last: Zhang

first: Terry

last: Braun

first: Bartlley

last: Brown

first: Vimla

last: Band

first: Hamid

first: Mikhail

last: Kulak

first: Ronald

last: Weigel


title: Abo1 is required for H3K9me2 to H3K9me3 transition in telomeric and centromeric heterochromatin

city: Hudidnge

first: Wenbo

last: Dong

state: Sweden

address: Hälsovägen 7C   Neohuset

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by genome tiling array


title: Of eyes and embryos; subfunctionalization of the CRX homeobox gene in mammalian evolution

city: Oxford

first: Amy

last: Royall

state: Oxfordshire

address: Radcliffe Observatory Quarter

department: Zoology

institute: University of Oxford

summary: We have ectopically expressed two V5-tagged homeobox genes and a control plasmid in mouse embryonic fibroblasts. Following ectopic expression and chemical selection we used whole transcriptome sequencing to reveal any effect of forced missed expression on the MEF transcriptome.

overall_design: Examination and comparison of the roles of 2 homeobox transcription factors

middle: H

first: Stephen

last: Frankenberg

first: Andrew

last: Pask

last: Holland


title: Gene expression analysis of ASPN variant overexpressing WPMY-1 cells [human]

city: Baltimore

first: Robert

last: Hughes

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

overall_design: 9 total samples analyzed, 3 independent samples per group

first: Elana

last: Fertig

first: Paula

last: Hurley


title: Abo1 is required for H3K9me2 to H3K9me3 transition in telomeric and centromeric heterochromatin [ChIP-seq]

summary: Regulation of heterochromatin is critical for genome stability. Different states of methylated H3K9 have been discovered with distinct roles in heterochromatin formation and silencing. However, the control of the transition from H3K9me2 to H3K9me3 is still unclear. Here we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining the global nucleosome organization in fission yeast. We identified several key factors involved in heterochromatin silencing to interact genetically with Abo1: the histone deacetylase Clr3, the H3K9 methyltransferase Clr4, and the HP1 homologue  Swi6. Cells lacking Abo1 display an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin had increased H3K9me2 but decreased H3K9me3 levels compared to wild type. In contrast, facultative heterochromatin regions, show both reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both centromeres and subtelomeres, but not in a subset of heterochromatin islands. Our work uncovers a new role for Abo1 in supporting Clr4 activity and allowing for the transition of H3K9me2 to H3K9me3 in telomeric and centromeric heterochromatin.

overall_design: Total 8 samples: 4 Input files with the corresponding 4 H3K9me2 ChIP samples in wild type and abo1∆ strain (two replicates)

first: Eriko

last: Kawata

first: Mickaël

last: Durand-Dubief


title: Abo1 is required for H3K9me2 to H3K9me3 transition in telomeric and centromeric heterochromatin [gene expression]

summary:
Regulation of heterochromatin is critical for genome stability. Different states of methylated H3K9 have been discovered with distinct roles in heterochromatin formation and silencing. However, the control of the transition from H3K9me2 to H3K9me3 is still unclear. Here we investigate the role of the conserved bromodomain AAA-ATPase, Abo1, involved in maintaining the global nucleosome organization in fission yeast. We identified several key factors involved in heterochromatin silencing to interact genetically with Abo1: the histone deacetylase Clr3, the H3K9 methyltransferase Clr4, and the HP1 homologue  Swi6. Cells lacking Abo1 display an imbalance of H3K9me2 and H3K9me3 in heterochromatin. In abo1∆ cells, the centromeric constitutive heterochromatin had increased H3K9me2 but decreased H3K9me3 levels compared to wild type. In contrast, facultative heterochromatin regions, show both reduced H3K9me2 and H3K9me3 levels in abo1∆. Genome-wide analysis showed that abo1∆ cells have silencing defects in both centromeres and subtelomeres, but not in a subset of heterochromatin islands. Our work uncovers a new role for Abo1 in supporting Clr4 activity and allowing for the transition of H3K9me2 to H3K9me3 in telomeric and centromeric heterochromatin.
We used microarrays to detail the global  gene expression in wilde typ (Hu2185) and abo1∆ (Hu2318) strain with three temperature induction: 25°C (cold stress), 30°C(standard cultivation) and 37°C heat stress. We found silencing defect under in heterochromatin in  abo1∆ deletion in all three conditions.

overall_design: In total 12 samples: 6 wilde type samples and 6 abo1∆ samples with 3 different temperature conditions (with replicates)

first: Punit

last: Prasad


title: Gene Expression Profile of shCTL and shBora -transduced SKOV-3 cells

city: Barcelona

first: Alfonso

last: Parrilla

address: Paseo Vall Hebron (VHIR)

institute: Vall Hebron Research Institute (VHIR)

summary: Gene Expression profile of SK-OV-3 cells transduced with shCTL (control) and shBora (Bora depletion) lentiviral particles for 48h

overall_design: Transcriptome expression profile of triplicate experimental samples for SK-OV-3 shCTL and shBora-infected cells performed using the Affymetrix microarray platform and the Genechip Human Gene 1.0 ST Array.

first: Anna

last: Santamaria


title: Screening key lncRNAs for human rectal adenocarcinoma based on lncRNA-mRNA functional synergistic network

city: Taizhou City

first: Dongguo

last: Wang

state: Zhejiang Province

address: 381 Dong Zhongshan Rd of Jiaojiang district

department: Clinical lab medicine

institute: Taizhou Municipal Hospital

summary: The purpose of this project was to find key long non-coding RNAs  and mRNAs in rectal adenocarcinoma. RNA-sequencing was performed to identify the differentially expressed mRNAs (DEmRNAs) and lncRNAs (DElncRNAs) in rectal adenocarcinoma compared to normal tissue.

overall_design: Total RNA extracted from tissue samples in n=3 rectal adenocarcinoma patients compared to n=3 adjacent normal samples.

first: Xiongwen

last: Zhu

first: Guiyang

last: Wu

first: Shichao

last: Yuan

first: Fubo

last: Ye

first: Qinghao

last: Fan


title: Foxp1 drives striatal projection neuron specification and organization via cell-type specific mechanism

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: The molecular mechanisms that underlie striatal development and organization remain largely unknown. Here, we show that Foxp1, a transcription factor strongly linked to autism and intellectual disability, regulates organizational features of striatal circuitry in a cell-type dependent fashion. Using single-cell RNA-sequencing, we examine the cellular diversity of the early postnatal striatum and demonstrate that Foxp1 specifies a subpopulation of indirect pathway spiny projection neurons (iSPNs) while maintaining the striosome-matrix architecture through molecular mechanisms mediated by direct pathway spiny projection neurons (dSPNs). Functionally, Foxp1 alters striatal projection patterns both cell-autonomously and non-autonomously. We connect these changes in striatal circuitry to distinct behavioral deficits relevant to phenotypes described in patients with FOXP1 loss-of-function mutations. These data reveal novel cell-type specific transcriptional mechanisms underlying distinct features of striatal circuitry and identify Foxp1 as a key regulator of striatal development

overall_design: We used 10X Genomic Chromium technology for single-cell RNA-sequencing of  early post-natal mouse striatum within control mouse samples and mouse samples with deletion of Foxp1 in dopamine receptor 1 (dSPNs) expressing neurons, dopamine receptor 2 (iSPNs) neurons, or both. We used an N=4 per genotype for 16 total samples. 62,778 striatal cells passed quality control filters for the final analysis.

first: Ashley

last: Anderson

first: Ashwinikumar

last: Kulkarni

first: Matthew

last: Harper


title: METTL3 promotes carcinogenesis in colorectal cancer

first: Haoyan

last: Chen

summary: To elucidate whether  METTL3 plays a role in  colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of METTL3-KO and wild-type HCT116 cells.

overall_design: RNA-seq was performed in HCT116  colorectal cancer cells after METTL3 knock out.

first: Shen

last: Chaoqin


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Klf12-/- Lymphocyte Transcriptomes

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

summary: The goal of this study is to determine the role of the transcription factor, Klf12, in mouse NK cells. Transcriptome profiling by RNA-Seq of wild-type and Klf12-deficient mouse CD4+ T cells, CD8+ T cells, B cells, and NK cells. We found that Klf12-deficient mouse NK cells express more transcripts of Btg3 and have a proliferative impairment compared to wild-type mouse NK cells in a competitive setting.

overall_design: Total RNA from 6 week-old Klf12+/+ and Klf12-flox/flox beta-actin Cre- littermate males was isolated from splenic CD3-NK1.1+ NK cells, CD4+TCRβ+CD25- T cells, CD8+TCRβ+CD25- T cells, and B220+IgM+IgD+ B cells following the ImmGen standard protocol (https://www.immgen.org/). One thousand cells (≥ 99% purity) were double-sorted directly into 96-well plates containing TCL buffer (Qiagen) and 1% beta-mercaptoethanol, frozen, and analyzed by the Broad Technology Labs for SmartSeq2 library preparation and NextSeq500 sequencing. Transcripts were quantified using Cuffquant and then normalized using DEseq (Immological Genome Consortium). Three male mice were used per genotype.

first: Viola

last: Lam

first: Lewis

last: Lanier

first: Andrew

last: Rhoads


title: RUNX proteins desensitize multiple myeloma to lenalidomide via protecting IKZFs from degradation

city: Philadelphia

first: Luca

last: Busino

state: PA

address: 421 Curie Blvd, 705 BRB II/III

department: Cancer Biology

institute: Luca Busino

summary: Ikaros family zinc finger protein 1 and 3 (IKZF1 and IKZF3) are transcription factors that promote multiple myeloma (MM) proliferation. The immunomodulatory imide drug (IMiD) lenalidomide promotes myeloma cell death via Cereblon (CRBN)-dependent ubiquitylation and proteasome-dependent degradation of IKZF1 and IKZF3. Although IMiDs have been used as first-line drugs for MM, the overall survival of refractory MM patients remains poor and demands the identification of novel agents to potentiate the therapeutic effect of IMiDs. Using an unbiased screen based on mass spectrometry, we identified the Runt-related transcription factor 1 and 3 (RUNX1 and RUNX3) as interactors of IKZF1 and IKZF3. Interaction with RUNX1 and RUNX3 inhibits CRBN-dependent binding, ubiquitylation and degradation of IKZF1 and IKZF3 upon lenalidomide treatment. Inhibition of RUNXs, via genetic ablation or a small molecule (AI-10-104), results in sensitization of myeloma cell lines and primary tumors to lenalidomide. Thus, RUNX inhibition represents a valuable therapeutic opportunity to potentiate IMiDs therapy for the treatment of multiple myeloma.

overall_design: Gene expression analysis by RNAseq in multiple myeloma cells OPM-1 treated with DMSO,  lenalidomide (LEN), AI-10-104 (RUNXi)  or combination.

last: Zhou


title: Reactivation of mutant p53 by SLMP53-2: a promising therapeutic option against hepatocellular carcinoma

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

summary:
In order to pursue the search for new reactivators of mutant p53, a small library of molecules was synthesized starting from a previously established lead (SLMP53-1). The molecules were tested in various cell-based assays and one, herein referred to as SLMP53-2, displayed a marked reduction of the IC50 values in NCI-H1299 cells expressing the p53 mutants (mutp53) R175H, Y220C, G245S, R248Q, R273C, and R273H. The activity of SLMP53-2 was then investigated using cancer cells lines expressing endogenous mutant p53 and focusing on hepatocellular carcinoma HuH-7 and breast ductal carcinoma HCC1419 cells endogenously expressing mutp53-Y220C.
In HuH-7 cells, SLMP53-2 displayed a concentration-dependent growth inhibitory effect on colony formation, restored wt-like p53 protein conformation and transcriptional activity and displayed in vivo antitumour activity in a xenograft mouse model, with no apparent toxicity for normal tissues. To investigate more deeply the impact of SLMP53-2 treatments on gene expression in HuH-7 cells we performed microarray-based analysis using two different concentrations of the compound, corresponding to 2x and 3x IC50. We also employed the MDM2 inhibitor Nutlin alone or in combination with 2x IC50 SLMP53-2.

overall_design: The treatment were: 2x and 3x IC50 SLMP53-2 (28 and 42 µM), for 24 hours, in quadruplicate.  Cells were processed for RNA extraction and gene expression was assessed by Agilent gene expression microarrays.  Direct comparisons were performed in order to obtain differential gene expression gene lists.

first: Sara

last: Gomes

first: Bartolomeo

last: Bosco

first: Dilara

last: Ayyildiz

first: Michael

last: Pancher

first: Alberto

last: Inga

first: Lucilia

last: Saraiva


title: Early termination of a Phase 1 trial of tenofovir disoproxil fumarate intravaginal ring linked to inflammation

city: Atlanta

first: Gregory

middle: K

last: Tharp

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Objective: To assess safety in women of tenofovir disoproxil fumarate (TDF) polyurethane intravaginal ring (IVR) when used continuously for 3 months by healthy, HIV-uninfected, sexually active women, as compared with a placebo intravaginal ring

overall_design: Women were randomized in a 3:1 ratio to receive either TDF or a placebo IVR which was changed monthly for 3 months

first: Marla

last: Keller

first: Steven

last: Bosinger

first: Lianna

last: Wood

first: James

last: Billingsley

first: Laurie

last: Ray

first: Jessica

last: Goymer

first: Shada

last: Sinclair

first: Hans

last: Spiegel

first: Aileen

last: McGinn

first: Nelly

middle: R

last: Mugo

first: Mark

last: Marzinke

first: Bruce

last: Frank

first: Sujatha

last: Srinivasan

first: Congzhou

last: Liu

last: Atrio

first: Lilia

last: Espinoza

first: Peter

last: Anderson

first: David

middle: N

last: Fredricks

first: Craig

last: Hendrix

first: Jeanne

last: Marrazzo

first: Betsy

last: Herold


title: A TFAP2C Gene Signature is Predictive of Outcome in HER2 Breast Cancer (ChIP-Seq)

first: Tiandao

last: Li

summary: A subset of HER2 breast cancers with amplification of the TFAP2C gene locus becomes addicted to AP-2g.  We sought to define AP-2g-regulated genes that control growth and invasiveness by comparing HER2 cell lines with differential response to TFAP2C knockdown. A set of 68 differentially expressed genes was identified, which included CDH5 and CDKN1A. Pathway analysis implicated the MAPK13/p38δ and retinoic acid regulatory nodes, which were confirmed to display divergent responses. The AP-2g gene signature was highly predictive of outcome in HER2-positive breast cancer patients. We conclude that AP-2g regulates a set of genes in HER2 breast cancer that drive cancer growth and invasiveness and that the AP-2g gene signature can predict outcome of patients with HER2 breast cancer.

overall_design: 2 ChIP-Seq data for TFAP2C in human breast carcinoma cell lines SKBR-3 and HCC1954.

first: Vincent

middle: T

last: Wu

first: Boris

last: Kiriazov

first: Kelsey

middle: E

last: Koch

first: Vivian

last: Gu

first: Anna

last: Beck

first: Nicholas

last: Borcherding

last: Addo

first: Zarchary

last: Wehrspan

first: Weizhou

last: Zhang

first: Terry

last: Braun

first: Bartlley

last: Brown

first: Vimla

last: Band

first: Hamid

first: Mikhail

middle: V

last: Kulak

first: Ronald

last: Weigel


title: MicroRNA-138: A Diagnostic Biomarker and Therapeutic Target for the Aggressive Basal-like subtype of Breast Cancer

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

summary:
This study identifies miR-138 as a prognostic biomarker for basal breast carcinoma.
Identification of differentially regulated genes upon miR-138 knockdown (AntagomiR-138) in basal breast cancer cell lines MDA-MB-231

overall_design: Total RNA was extracted from MDA-MB-231 cells treated with scramble control and antimiR-138 expressing lentivirus

first: Srikanth

last: Nama

first: Manish

last: Muhuri


title: Comparison of different therapeutic regimens in an INI1-deficient proximal-type epithelioid sarcoma patient-derived xenograft highlights the antitumor activity of the EZH2 inhibitor EPZ-011989 and suggests autophagy as a possible cytoprotective mechanism

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

summary: We report that differential gene expression analysis of epithelioid sarcoma samples removed from EPZ-011989-treated and untreated mice revealed that, among the 5521 genes with a significant differential expression (according to FDR<0.05), 62% were up-regulated and 38% down-regulated respectively, thus indicating a generally increased transcriptional activity in treated tumors, consistent with EZH2 inhibition. Interestingly, among the top 15 up-regulated genes in the EPZ-011989-treated samples, 8 are involved in cell survival pathways, including autophagy. The induction of autophagy as a fail-safe mechanism against EZH2 inhibition was further validated in the PDX-derived ES-1 cell line by evaluating the effect of autophagy inhibition on drug-induced activity.

overall_design: PDX mRNA profiles of untreated and EPZ-011989 treated mice were generated by deep sequencing, in duplicate using Illumina NextSeq 500 Sequencing System

first: Valentina

last: Indio


title: Gene expression analysis of Aspn+/+ and Aspn-/- fetal MSCs [mouse]

first: Robert

last: Hughes

state: MD

overall_design: 6 total samples analyzed, 3 Aspn+/+ and 3 Aspn-/- fetal MSC biologic replicates (independently isolated and cultured cell lines)

first: Elana

last: Fertig

first: Paula

last: Hurley


title: Programmable RNA-guided RNA effector proteins built from human parts

city: Chicago

first: Bryan

middle: C

last: Dickinson

state: IL

department: Chemistry

institute: The University of Chicago

summary: Epitranscriptomic regulation controls information flow through the central dogma and provides new opportunities to control the cellular outputs at the RNA level. However, both basic science and translational applications are limited by a lack of methods to target RNA specifically. Here we present a novel protein engineering approach to  construct probgrammable RNA regulatory systems from human parts: CRISPR/Cas-Inspired RNA Targeting System (CIRTS).

overall_design: RNA-seq experiments were performed on mRNA extracted from HEK-293T cells with three biological replicates; each condition includes three replicates containing a non-targeting (NT) gRNA and three replicates containing a on-target gRNA

first: Simone

last: Rauch


title: Gene expression analysis of Aspn+/+ and Aspn-/- fetal MSCs, and PC-3 cells exposed to conditioned media +/- ASPN variants

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

overall_design: Refer to individual Series


title: CD47 in the tumor microenvironment and CD47 antibody blockade regulate natural killer cell recruitment and activation

city: Bethesda

last: Marenco

address: Building 10, Room 4N306

institute: National Institute of Mental Health

summary: Elevated CD47 expression in some cancers is associated with decreased survival and limits phagocytic clearance by engaging its counter-receptor SIRPα, but elevated CD47 mRNA expression in human melanomas is associated with improved survival. Gene expression data suggested that recruitment of natural killer (NK) cells, which highly express CD47, into the tumor microenvironment contribute to this correlation. The CD47 ligand thrombospondin-1 inhibited wildtype but not Cd47-/- murine NK cell proliferation and granzyme B and interferon-γ expression in vitro. Cd47-/- NK cells correspondingly showed augmented effector phenotypes. Although, wildtype and Cd47-/- NK cells were equally effective for killing B16 melanoma cells in vitro, Cd47-/- mice exhibited enhanced B16 tumor growth in vivo. Consistent with the human data, tumor-bearing Cd47-/- mice had decreased splenic NK numbers with impaired effector protein expression and elevated exhaustion markers. A pro-apoptotic signature in Cd47-/- NK cells was associated with stress-mediated elevation of mitochondrial proton leak, increased reactive oxygen species and apoptosis. Gene expression profiling identified CD47-dependent transcriptional responses in in NK cells from tumor-bearing mice that regulate systemic NK activation and exhaustion. Treating wildtype mice with a CD47 antibody that blocks thrombospondin-1 binding delayed tumor growth and was associated with increased NK recruitment and increased granzyme B- and interferon-γ levels in intratumoral NK but not CD8+ T cells. Therefore, CD47 in the tumor microenvironment regulates NK-mediated tumor immunity, and therapeutic blockade enhances NK immune function.

overall_design: Examining natural killer (NK) cell intrinsic role of CD47 in the tumor microenvironment.

first: Pulak

last: Nath

first: Dipasmita

last: Pal-Nath

first: Ajeet

last: Mandal

first: Margaret

last: Cam

first: David

middle: D

last: Roberts


title: Farnesoid X Receptor alters adipose tissue architecture in mice and limits its storage capacity leading to metabolic derangements

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary: The bile acid-activated nuclear receptor Farnesoid X receptor (FXR, NR1H4) has been implicated in the control of lipid and energy metabolism, but its role in fat tissue, where it is moderately expressed, is not understood. In view of the recent development of FXR-targeting therapeutics for treatment of human metabolic diseases, understanding the tissue-specific actions of FXR is essential. We show that transgenic mice expressing human FXR specifically in adipose tissue (aP2-hFXR) have markedly enlarged adipocytes and show extensive extracellular matrix remodelling. Ageing and exposure to obesogenic conditions revealed a strongly limited capacity for adipose expansion and development of fibrosis in adipose tissues of aP2-hFXR transgenic mice. This was associated with impaired lipid storage capacity, leading to elevated plasma free fatty acids, ectopic fat deposition in liver and muscle as well as whole-body insulin resistance. These studies establish that adipose FXR is a determinant of adipose tissue architecture and contributes to whole-body lipid homeostasis.

overall_design: Total RNA optained from 10 BAT and 8 WAT samples, where compaired in 2 by 2 different groups, consisting of biological replicates n=4,5

first: J

last: Stroeve

first: V

middle: W

last: Bloks

first: H

last: Roelofsen

first: N

last: Huijkman

first: T

last: van Zutphen

last: van Dijk

first: A

last: Jurdzinski

last: van Deursen

last: Yang

first: R

last: Vonk

first: B

last: Staels

last: Groen

first: F

last: Kuipers


title: Blood flow-restricted resistance exercise (BFRE) alters the surface profile, miRNA cargo and functional impact of circulating extracellular vesicles

status: Public on Apr 12 2020

city: Aarhus N

first: Jesper

last: Just

address: Palle Juul-Jensens boulevard 99

department: Clinical Medicine

institute: Aarhus University

summary: In this study, we provide evidence that ischemic exercise, conducted as blood flow-restricted resistance exercise, promote changes in the micro-RNA cargo of circulating extracellular vesicles in healthy volunteers.

overall_design: Examination of miRNA changes in circulating extracellular vesicles before and 1 hour after blood flow restricted exercise.

first: Yan

last: Yan

first: Jørgen

last: Kjems

first: Morten

last: Venø

first: Kim

last: Drasbek

first: Mette

last: Sloth


title: microRNA expression profile in human Triple-Negative Breast Cancer stem cells

city: Nanjing

first: Yongmei

last: Yin

address: No.300 Guangzhou Rd

institute: Nanjing Medical University

summary: We reported the distinc expression pattern of TNBC-CSC-related microRNAs, which might be potential biomarkers and targeted therapy for TNBC.

overall_design:
Examination of microRNAs expression pattern in 2 cell types.

contributor: KangChen Bio-tech


title: Expression data from ovarian cancer SKOV3 human cell line

first: Anna

last: Santamaria

address: Pg/Vall Hebron 119-129

institute: Vall Hebron Institut de REcerca

summary:
CDCP1 and PLAGL2 have been shown to act as oncogenes in several cancer types but little is known about the molecular signalling underlying these processes in ovarian cancer cells. In this study we aim to find the downstream signalling upon their individual silencing in the human ovarian cancer cell line SKOV3.
We used microarrays to detail the global programme of gene expression underlying CDCP1 and PLAGL2 signalling in the human ovarian cancer cell line SKOV3

overall_design: Triplicates of the SKOV3 siControl (siLamin A), SKOV3-siCDCP1 and SKOV3- siPLAGL2 were used to carry out the microarray analysis. Human ClariomTM S assay (Affymetrix, Thermo Fisher Scientific) was used to analyze gene-level whole- transcriptome expression profiling, which accurately detects more than 20,000 well- annotated genes, with more than 200,000 probes.

first: Blanca

last: Majem


title: Circular RNA expression profile in human thoracic aortic dissection

city: Guangzhou

first: zou

middle: mei

last: sheng

address: 1838 N Guangzhou Ave

institute: Nanfang Hospital, Southern Medical University

summary: To assess the circular RNAs (circRNAs) expression profile and explore the potential functions in human thoracic aortic dissection (TAD).The differentially expressed circRNAs profiles of the aortic segments between human type A TAD patients (n=3) and age-matched normal donors (NA; n=3) were analyzed using the Arraystar human circRNAs microarray. Quantitative real-time PCR was used to validate the expression pattern of circRNAs, parental genes, and hsa-miR-320a; Western blotting confirmed MMP9 expression with additional samples. Bioinformatic tools including network analysis, Gene ontology, and KEGG pathway analysis were utilized.

overall_design: Aortic specimens were collected from type A TAD patients undergoing aortic replacement in the intimal tear position at the hospital in 2015. Normal thoracic aortas (NA) were obtained from six age- and gender-matched organ donors without aortic diseases.

first: Meisheng

last: Zou

first: Chixiong

last: Huang

first: Xinzhong

last: Li

first: Xiang

last: He

first: Yanmei

last: Chen

first: Wangjun

last: Liao

first: Yulin

first: Jie

last: Sun

first: Ze

last: Liu

first: Lintao

last: Zhong

first: Jianping

last: Bin


title: Plasma circulating miRNA profiling in polymicrobial sepsis by high throughput sequencing

first: Sheng

last: Wang

address: 660 W Redwood Street, Howard Hall 564

department: Anesthesiology

institute: University of Maryland Baltimore

summary:
Aim: To explore the potentially important role of circulating miRNAs in systemic inflammation during sepsis.
Method: 8 to 10-week old C57BL/6 mice underwent cecal ligation and puncture (CLP) or laparotomy (Sham). Plasma RNA was isolated using Trizol LS reagent 24h post-surgery. NGS cDNA libraries were prepared using Norgen Biotek Small RNA Library Prep Kit. Library quality was validated prior to sequencing on an Illumina NextSeq 500 platform.

overall_design: In this study, we profiled extracellular miRNAs from platelet-free plasma. Total 15 samples, including 6 sham and 9 CLP, were analyzed.

first: Wei

last: Chao


title: Cutaneous T cell lymphoma (CTCL) treated with antibiotics and followed over time

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

institute: University of Copenhagen

summary: It is unknown why cutaneous T cell lymphoma (CTCL) progress from a relative indolent skin condition to severe cancer with a poor prognosis. Staphylococcus aureus (SA) has been suspected to play a role, because antibiotics have an inhibitory effect on the tumor burden in some patients. As these patients often display skin colonization by SA, it was hypothesized, but never proven, that SA generate a pro-oncogenic milieu in lesional skin. Here, we study the effect of short-term aggressive antibiotic treatment on tumor cells, the microenvironment, and disease activity in treatment-refractory, advanced stage CTCL. We report that advanced stage CTCL patients experienced significant decrease in clinical and patient-self-reported symptoms in response to aggressive 4-week antibiotic therapy, which eradicated SA. Notably, the clinical improvement lasted for more than 8 months in some patients. Global mRNA expression and cell-signaling pathway analysis indicated a decrease in IL-2 signaling, inflammation, and mitosis in skin lesions after antibiotic therapy. In accordance, IL-2 receptor  chain (IL2R-) expression, STAT3 activation, and mitotic activity were decreased in lesional skin following antibiotic treatment. Conversely, SA toxins triggered IL2R- expression, STAT3 activation, and enhanced proliferation ex vivo in primary malignant T cells derived from untreated patients.   In conclusion, we demonstrate that transient, aggressive antibiotic treatment inhibits tumor cells, partly normalizes the microenvironment, and decreases disease activity in lesional skin. Thus, we provide a first mechanistic link between antibiotics, skin inflammation, and tumor burden and therefore a novel rationale for treatment of SA in advanced CTCL.

overall_design: 8 CTCL patients were followed over time 0, 10 days, 1 month and 2 months. Six healthy controls were used for comparison.

first: Lise

last: Lindahl

first: Lars

last: Iversen

first: Niels

last: Ødum


title: CsBRC1 inhibits axillary bud outgrowth by repressing auxin efflux carriers CsPIN1b and CsPIN3 and in response to shade in cucumber

city: Shanghai

first: Renyi

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology

summary: Shoot branching is an important agronomic trait that directly determines plant architecture and affects crop productivity. To promote crop yield and quality, axillary branches need to be manually removed during cucumber production for fresh market and thus are undesirable. Auxin is well known as the primary signal imposing for apical dominance and acts as a repressor for branching outside of the lateral buds. The TEOSINTE BRANCHED1/CYCLOIDEA /PCF (TCP) family gene BRANCHED1 (BRC1) has been shown to be the central integrator for multiple environmental and developmental factors that functions locally to inhibit shoot branching. However, no direct link has been reported between auxin and BRC1. Here, we find that cucumber BRANCHED1 (CsBRC1) is expressed in the axillary buds and displays higher expression level in cultivated cucumber than its wild ancestor. Knockdown of CsBRC1 by RNAi leads to increased bud outgrowth and reduced auxin accumulation in buds. We further show that CsBRC1 directly binds to two auxin efflux carriers PIN-FORMED (CsPIN1b and CsPIN3) and negatively regulates their expression. Ectopic expression of CsPIN1b or CsPIN3 driven by CsBRC1 promoter results in increased shoot branching. Moreover, shade induces the expression of CsBRC1 in cultivated cucumber, but not in wild ancestor, which may be partly due to the addition of two light response elements in the CsBRC1 promoter of cultivated cucumber. Therefore, our data suggest the formation of a regulatory pathway of shade-CsBRC1-auxin transport in suppressing lateral bud outgrowth during cucumber domestication.

overall_design: Sequencing data of axillary buds in wild-type and CsBRC1-RNAi lines cucumber.

first: Junjun

last: Shen


title: Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California Current System

city: Santa Cruz

first: Jonathan

middle: David

last: Magasin

state: CA

address: 1156 High Street

department: Ocean Sciences

institute: UC Santa Cruz

summary: In summer 2014, we conducted experiments to determine the effects of different N substrates on phytoplankton communities in the North Pacific Ocean and in the transition zone of the California Current and gyre (Shilova, Mills et al., 2017). Samples were incubated with nitrate, ammonium, urea, and filtered deep water (FDW) for 48 hours (T48). Two treatments added iron, alone (Fe) or with a mix of N substrates (N+Fe), to determine the effects of Fe on the utilization of N substrates. All treatments resulted in changes in phytoplankton cell abundances and photosynthetic activity at both locations, with differences between phytoplankton groups. Prochlorococcus had large increases in biomass in response to ammonium and urea, while both eukaryotic phytoplankton and Synechococcus had only modest biomass increases in response to N+Fe and FDW. Moreover, distinct physiological responses were observed within sub-populations of Prochlorococcus and Synechococcus. In order to understand the variable responses to N substrates among phytoplankton groups and sub-populations in the California Current transition zone, the present work examines transcriptional changes that occurred 24 h after the substrates were added. Specifically, we hypothesize that transcription changes at 24 h indicate which phytoplankton taxa are N-limited, and thus help explain changes in cell abundances and photosynthetic activity by individual phytoplankton groups observed at 48 h. Furthermore, we hypothesize that the diversity in physiological responses within Prochlorococcus and Synechococcus are evident in the transcriptional responses measured at sub-population resolution.

overall_design:
Transcription changes by surface sea water microbial communities in response to added nitrogen and/or iron substrates were assessed using MicroTOOLs microarrays (version 2.0; GEO platform GPL24371).  On 24 August 2014, samples were collected from 25 m depth at Station 38 in the California Current System, during the NEMO Cruise NH1417.  Samples were handled using trace-metal clean techniques, with all treatments and nucleic acid collection occurring before dawn (Shilova et al. 2017). Replicate samples (n=2 or 3) were treated with different nitrate, ammonium, urea, iron, nitrate with iron, or filtered deep water (600 m), and incubated on deck.  After 24 h incubation, mRNA was collected for the present work, however incubations continued for another 24 h.  At 24 h and 48 h, bulk physiological measurements were made, and DNA was extracted for community composition analysis, described in Shilova et al. 2017.  The present work examines which community members responded to the different treatments by 24 h in order to understand their nutrient statuses and possible contributions to the physiological changes observed by Shilova et al. 2017.  Metatranscriptomes from the six treatments (as represented by MicroTOOLs) at 24 h were compared to control metatranscriptomes at 24 h.  Comparisons were also made between control metatranscriptomes at 24 h and 0 h.  Microarray data was processed using the MicroTOOLs software pipeline (www.jzehrlab.com), and transcription changes were examined using the pipeline as well as an Ensemble of Gene Set Enrichment Analyses (Alhamdoosh et al. 2017) and Whole Genome Correlation Network Analysis (Langfelder and Horvath, 2008).

CCS = California Current System

control samples: Control_T0_id_64220, Control_T0_id_64221, Control_T0_id_64222, Control_T24_id_60949, Control_T24_id_60950, Control_T24_id_60951
treated samples: Fe_T24_id_60964, Fe_T24_id_60965, Fe_T24_id_60966, Urea_T24_id_60958, Urea_T24_id_60959, Urea_T24_id_60960, NO3_T24_id_60955, NO3_T24_id_60956, NO3_T24_id_60957, NH4_T24_id_60952, NH4_T24_id_60954, N+Fe_T24_id_60967, N+Fe_T24_id_60968, N+Fe_T24_id_60969, FDW_T24_id_60961, FDW_T24_id_60962, FDW_T24_id_60963

first: Irina

last: Shilova

first: Matthew

last: Mills

first: Julie

last: Robidart

first: Kendra

middle: A

last: Turk-Kubo

last: Zehr


title: Biological sex influences susceptibility to Acinetobacter baumannii pneumonia in mice

status: Public on Apr 11 2020

city: Newark

first: Dane

last: Parker

state: NJ

address: 205 South Organge Ave, G-1208

department: Pathology, Immunology and Laboratory Medicine

institute: Rutgers New Jersey Medical School

summary: Through our studies using a murine model of acute pneumonia with A. baumannii, we observed that female mice were more susceptible to infection. Likewise, treatment of male mice with estradiol increased their susceptibility to infection. Analysis of the airway compartment revealed enhanced inflammation and reduced neutrophil and alveolar macrophage numbers compared to male mice. Depletion of either neutrophils or alveolar macrophages was important for bacterial clearance however, depletion of alveolar macrophages further exacerbated female susceptibility due to severe alterations in metabolic homoeostasis.

overall_design: RNA was extracted from lung homogenates of female and male mice depleted of alveolar macrophages following a 4 h infection with Acinetobacter baumannii

first: Silvia

last: Pires