title: Loss of DUX causes minor defects in zygotic genome activation and is compatible with mouse development

status: Public on Apr 10 2019

city: Cincinnati

first: Zhiyuan

last: Chen

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: How maternal factors in oocytes trigger zygotic genome activation (ZGA) is a long-standing question in developmental biology.  Recent studies in 2-cell like embryonic stem cells (2C-like cells) implicate that the DUX family transcription factors are key regulators of ZGA in placental mammals.  To characterize the role of DUX in ZGA, we generated Dux cluster knockout (KO) mouse lines. Unexpectedly, we found both Dux zygotic KO (Z-KO) and maternal/zygotic KO (MZ-KO) embryos can survive to adulthood despite showing reduced developmental potential.  Furthermore, transcriptome profiling of the MZ-KO embryos revealed that loss of DUX has minimal effect on ZGA and most DUX targets in 2C-like cells are normally activated in MZ-KO embryos.  Thus, contrary to the key function in inducing 2C-like cells, our data indicate that DUX only has a minor role in ZGA and loss of DUX is compatible with mouse development.

overall_design: To assess the role of Dux in mouse zygotic genome activation, RNA sequencing (RNA-seq) were performed for Dux wildtype (WT) and maternal-zygotic knockout (MZ-KO) 1-cell and 2-cell embryos


title: A large-scale drug screen identifies selective inhibitors of class I HDACs as a potential therapeutic option for SHH medulloblastoma

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

type: Expression profiling by high throughput sequencing

summary: Here we performed a targeted small molecule screen on a stable, SHH-dependent murine MB cell line (SMB21). A subset of the HDAC inhibitors tested significantly inhibit tumor growth of SMB21 cells by preventing SHH pathway activation. Of note, class I HDAC inhibitors were also efficacious in suppressing growth of diverse SMO inhibitor-resistant clones of SMB21 cells. Finally, we show that the novel HDAC inhibitor Quisinostat (JNJ) targets multiple class I HDACs, is well tolerated in mouse models and robustly inhibits growth of SHH MB cells in vivo as well as in vitro. Our data provide strong evidence that Quisinostat (JNJ) or other class I HDAC inhibitors might be therapeutically useful for patients with SHH MB including those resistant to SMO inhibition.

overall_design: RNA sequencing data of SMB21 cells treated with the HDAC inhibitor Quisinostat, or with loss of Hdca1 or Hdac2.

middle: J

first: Rosalind

middle: A

last: Segal


title: Gene expression of wild-type Porphyromnas gingivalis 33277 vs the transposon-mutant, J5-c5.

status: Public on Apr 09 2019

city: Seattle

first: Sumita

last: Jain

state: WA

address: 1959 NE Pacific Street, HSB D-652

department: Periodontics

country: USA

institute: University of Washington

summary: The P. gingivalis 33277 transposon mutant J5-c5, isolated in this study, was demonstrated to exhibit a lipid A deacylase phenotype. The mutant is unable to deacylate lipid A, which confers to it, in stark contrast to wild-type, an inability to evade the powerful TLR4 innate immune response. The mutant was shown to contain five transposons. In order to determine the affected gene responsible for this phenotype, we took the approach of comparing gene expression between wild-type and J5-c5 transposon mutant. RNA was extracted from three separate biological samples of each strain and RNAseq performed using Illumina’s HiSeq sequencing facility at the University of Washington Center for Precision Diagnostics. RNAseq data was analyzed closely following guidance outlined in Law et al (doi:10.12688/f1000research.9005.2).

overall_design: Gene expression in 3 biological replicates of each of two strains are compared.

first: Ana

middle: M

last: Chang

first: Manjot

last: Singh

first: Jeffrey

middle: S

last: McLean

first: Stephen

middle: R

last: Coats

first: Roger

middle: W

last: Kramer

first: Richard

middle: P

last: Darveau


title: Translatome analysis of the ribosomal protein L10 R98S mutation reveals altered serine metabolism in acute lymphoblastic leukemia [supplementaryRNA-seq]

city: Leuven

first: Kim

last: De Keersmaecker

address: Herestraat 49

department: Oncology

country: Belgium

institute: KU Leuven

summary: Somatic ribosomal protein defects have recently been described in cancer, yet their impact on cellular transcription and translation remain poorly understood. Here we integrated mRNA sequencing, ribosome footprinting, polysomal RNA seq and quantitative mass spectrometry datasets obtained from an isogenic mouse lymphoid cell model in order to study the T-cell acute lymphoblastic leukemia (T-ALL) associated R98S mutation in ribosomal protein L10 (RPL10 R98S). RPL10 R98S induced changes in protein levels were to a much larger extent caused by transcriptional then translational changes and RPL10 R98S cells showed a gene signature corresponding to deregulation of hematopoietic transcription factors. Phosphoserine phosphatase (PSPH), a key enzyme in serine biosynthesis, displayed elevated transcription and translation and was one of the proteins showing the strongest upregulation in RPL10 R98S cells. Increased Psph protein levels were confirmed in RPL10 R98S engineered JURKAT cells and in hematopoietic cell cultures derived from Rpl10 R98S knock-in mice. Moreover, elevated serine and glycine biosynthesis in RPL10 R98S cells was supported by metabolic flux analyses. Analysis of PSPH expression levels in T-ALL patient samples revealed that PSPH upregulation is a generalized phenomenon in this disease, associated with elevated circulating serine and glycine levels. Addition of serine and glycine enhanced survival of stromal and myeloid cells, suggesting supportive effects on the hematopoietic niche. Finally, reduction of PSPH expression levels in T-ALL cell lines suppressed their in vitro proliferation and their capacity to expand in T-ALL xenograft models. In conclusion, transcriptome, translatome and proteome analysis of the RPL10 R98S mutation identified RPL10 R98S driven induction of cellular serine biosynthesis. Whereas serine metabolism has been implicated in cancer via PHGDH amplification, this is the first report supporting dependence of ALL cells on the serine biosynthesis enzyme PSPH.

overall_design: 3 biological replicates for each condition (RPL10 R98S, RPL10 WT)

last: Kampen

first: Laura

last: Fancello

first: Tiziana

last: Girardi

first: Fabricio

last: Loayza

first: Benno

last: Verbelen

first: Stijn

last: Vereecke

first: Gianmarco

last: Rinaldi

first: Jelle

last: Verbeeck

first: Joyce

middle: O

last: de Beeck

first: Karin

last: Thevissen

first: Bruno

last: Cammue

first: Pieter

last: Vermeersch

first: David

last: Cassiman

first: Jan

last: Cools

first: Sarah-Maria

last: Fendt

first: Reuven

last: Agami

first: Mark

last: Fiers


title: Translatome analysis of the ribosomal protein L10 R98S mutation reveals altered serine metabolism in acute lymphoblastic leukemia [Ribo-seq]

first: Kim

last: De Keersmaecker

overall_design: Ribosome footprinting and mRNA-Seq libraries from 3 biological replicates for each condition (RPL10 R98S, RPL10 WT). For ribosome footprinting three technical replicates were generated for each biological replicate. The sequencing files of three technical replicates were merged for downstream analyses

last: Kampen


title: Translatome analysis of the ribosomal protein L10 R98S mutation reveals altered serine metabolism in acute lymphoblastic leukemia

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

overall_design: Refer to individual Series


title: Translatome analysis of the ribosomal protein L10 R98S mutation reveals altered serine metabolism in acute lymphoblastic leukemia [PolySeq]

overall_design: For polysomal RNA sequencing: RPL10 R98S samples (8 replicates) versus RPL10 WT samples (6 replicates); for RNA-Seq: RPL10 R98S samples (9 replicates) versus RPL10 WT samples (8 replicates)

first: Laura

last: Fancello

last: Girardi


title: Epigenetic regulation of mammalian Hedgehog signaling to the stroma determines the molecular subtype of human bladder cancer

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

summary: In bladder, loss of mammalian Sonic Hedgehog (Shh) accompanies progression to invasive urothelial carcinoma, but the molecular mechanisms underlying this cancer-initiating event are poorly defined. Here, we show that loss of Shh results from hypermethylation of the CpG shore of the Shh gene, and that inhibition of DNA methylation increases Shh expression to halt the initiation of murine urothelial carcinoma at the early stage of progression. In full-fledged tumors, pharmacologic augmentation of Hedgehog (Hh) pathway activity impedes tumor growth, and this cancer-restraining effect of Hh signaling is mediated by the stromal response to Shh signals, which stimulates subtype conversion of basal to luminal-like urothelial carcinoma. Our findings thus provide a basis to develop subtype-specific strategies for the management of human bladder cancer.

overall_design: RNA-Seq of mouse organoids with various conditions

first: Jae-Seok

first: Kunyoo

last: Shin


title: hnRNP-K targets open chromatin in mouse embryonic stem cells in concert with multiple regulators

city: Saint Petersburg

first: Adel

last: Gazizova

address: Tikhoretsky av., 4

country: Russia

institute: Institute of Cytology RAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The transcription factor Oct4 plays a key regulatory role in the induction and maintenance of cellular pluripotency. With this paper, we show that ubiquitous and multifunctional poly(C) DNA/RNA-binding protein hnRNP-K occupies Oct4 (Pou5f1) enhancers in embryonic stem cells (ESCs) but is dispensable for the initiation, maintenance, and downregulation of Oct4 gene expression. Nevertheless, hnRNP-K has an essential cell-autonomous function in ESCs to maintain their proliferation and viability. To better understand mechanisms of hnRNP-K action in ESCs we have performed ChIP-seq analysis of genome-wide binding of hnRNP-K and identified several thousands of hnRNP-K target sites that are frequently co-occupied by pluripotency-related and common factors (Oct4, TBP, Sox2, Nanog, Otx2, etc.), as well as active histone marks. Furthermore, hnRNP-K localizes exclusively within open chromatin, implying its role in the onset and/or maintenance of this chromatin state.

overall_design: ChIP-Seq of hnRNP-K was performed in E14 mouse embryonic stem cells

first: E

middle: I

last: Bakhmet

first: A

first: N

middle: E

last: Vorobyeva

middle: N

last: Tomilin


title: Autophagy Suppresses CD8+ T cell Anti-tumour Immunity

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

country: Canada

institute: University of British Columbia

summary: Here we demonstrate that inactivation of the essential autophagy genes, Atg5, Atg14, or Atg16L1 results in tumour rejection. Despite a significant reduction in the total number of CD8+ tumour infiltrating lymphocytes (TILs), loss of Atg5 causes a profound shift toward IFNg and TNF producing effector memory cells. Consistent with this, adoptive transfer with Atg5-/- T cells promotes tumour control. Mechanistically, CD8+ T cells lacking autophagy exhibit enhanced glucose metabolism resulting in global changes in histone trimethylation and increased transcriptional activation of effector target genes. Restricting glucose is sufficient to suppress autophagy-dependent increases in effector function and reverse alterations in histone trimethylation. These findings identify autophagy as a cell-autonomous negative regulator of CD8+ T cell anti-tumour immunity with implications on T cell-based immunotherapy.

overall_design: Examination of two different histone modifications in CD8+ tumour-infiltrating lymphocytes from wild-type (WT) and Atg5-/- (KO) mice.

first: Lindsay

last: deVorkin

first: Nils

last: Pavey

first: Gillian

last: Carleton

first: Alexandra

last: Comber

first: Cally

last: Ho

first: Junghyun

last: Lim

first: Erin

last: McNamara

first: Haochu

last: Huang

first: Paul

last: Kim

first: Lauren

middle: G

last: Zacharias

first: Noboru

last: Mizushima

first: Tatsuya

last: Saitoh

first: Shizuo

last: Akira

first: Wayne

last: Beckham

first: Aditya

last: Murthy

first: Alireza

last: Lorzadeh

first: Qi

last: Cao

first: Michelle

last: Moksa

first: Ralph

last: DeBerardinis

first: Julian

last: Lum


title: Transcriptomic analysis of murine splenic basophils in steady-state or on day 14 of Trichuris muris infection

status: Public on Apr 08 2019

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

summary: Whole transcriptome analysis of genes expressed by spleen basophils in response to gasttrointestinal helminth infection, compared to naïve animals, analyzing the role of basophil-intrinsic Notch signaling using a basophil specific inhibition of Notch (Mcpt8Cre-DNMAML)

overall_design: RNAseq analysis of FACS sorted splenic basophils after IL-3-complex treatment

last: Webb

first: Elia

last: Tait Wojno

first: Charles

last: Danko


title: YY1 regulates skeletal muscle regeneration through controlling metabolic reprogramming during adult muscle stem cell activation

city: Guangzhou

first: Jiajian

last: Zhou

state: Guangdong

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

country: China

institute: Southern Medical University

summary: Skeletal muscle satellite cells (SCs) are adult muscle stem cells responsible for muscle regeneration after acute or chronic injuries. The lineage progression of quiescent satellite cells toward activation, proliferation and differentiation during the regeneration is orchestrated by cascades of transcription factors (TFs). Here we elucidate the functional role of a ubiquitously expressed TF, Yin Yang1 (YY1) in muscle regeneration. Muscle-specific deletion of YY1 in embryonic muscle progenitors leads to severe deformity of diaphragm muscle formation thus postnatal death. Inducible deletion of YY1 in satellite cells almost completely blocks the acute damage induced muscle repair and exacerbates the chronic injury induced dystrophic phenotype. Examination of SCs revealed that YY1 loss results in cell autonomous defect in cell activation and proliferation. Mechanistic search through genome-wide profiling of YY1 regulated transcriptome and YY1 binding revealed that YY1 binds and suppresses mitochondrial gene expression. Simultaneously, it also activates Hif1α mediated glycolytic genes to facilitate a metabolic reprogramming toward glycolysis which is needed for SC activation. Altogether our findings have identified YY1 as a key regulator of SC metabolic reprogramming during cell activation through its dual roles in modulating both mitochondrial and glycolytic pathways.

overall_design: 2 ChIP-seq and 4 RNA-seq experiments were performed

first: Huating

last: Wang

first: Hao

last: Sun

first: Fengyuan

last: Chen


title: Effect of High Cholesterol Diet (HCD) on B cell subsets in atheroprone mice with or without myb deficiency

city: Toronto

first: Rickvinder

last: Besla

state: ON

address: 101 college st, MaRS TMDT 3-901

institute: UHN

summary: Splenic B cell subsets (IgM+CD138+ ASC, FO B cells, MZ+B1 B cells) sorted from 8 month LDL-r KO mice with or without c-myb hypomorphism fed a 12 week HCD diet

overall_design: mRNA extracted from sorted cells from Spleens from 3 seperate LDL-R KO and c-myb h/h LDL-R KO Mouse HCD mice (with the exception of group C, only data from two mice available)

first: R

first: C

last: Robbins


title: PFA Ependymoma-associated protein EZHIP inhibits PRC2 through a H3 K27M like mechanism (RNA-seq)

city: Madison

first: Peter

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

summary: To understand the EZHIP-mediated transcriptional profile in mouse embryonic fibroblasts

overall_design: Examination of EZHIP, K27M, and EED knockout in Mouse embryonic fibroblasts

first: Siddhant

middle: U

last: Jain


title: Ependymoma associated protein EZHIP inhibits PRC2 through a H3 K27M like mechanism (ChIP-Seq H2K27me3)

summary: to understand the genome wide alterations in PRC2-mediated K27me3 and PRC1 distribution caused by oncohistone K27M mutation or novel PRC2 inhibitor – EZHIP

overall_design: ChIP-Seq H2K27me3


title: Ependymoma associated protein EZHIP inhibits PRC2 through a H3 K27M like mechanism (ChIP-Seq Ring1b)

overall_design: ChIP-Seq Ring1b


title: Ependymoma associated protein EZHIP inhibits PRC2 through a H3 K27M like mechanism (ChIP-Seq CBX2)

overall_design: ChIP-Seq CBX2


title: Ependymoma associated protein EZHIP inhibits PRC2 through a H3 K27M like mechanism


title: The  telomeric Cdc13-Stn1-Ten1 complex regulates RNA pol II transcription

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

summary: Specialized telomeric proteins have an essential role in maintaining genome stability through chromosome end protection and telomere length regulation. In the yeast Saccharomyces cerevisiae, the evolutionary conserved CST complex, composed of the Cdc13, Stn1 and Ten1 proteins, largely contributes to these functions. Here, we report the existence of genetic interactions between TEN1 and several genes coding for transcription regulators. Molecular assays confirmed this novel function of Ten1 and further established that it regulates the occupancies of RNA polymerase II and the Spt5 elongation factor within transcribed genes. Since Ten1, but also Cdc13 and Stn1, were found to physically associate with Spt5, we propose that Spt5 represents the target of CST in transcription regulation. Moreover, CST physically associated with Hmo1, previously shown to mediate the architecture of S phase-transcribed genes. The fact that, genome-wide, the promoters of genes down-regulated in the ten1-31 mutant are prefentially bound by Hmo1, leads us to propose a potential role for CST in synchronizing transcription with replication fork progression following head-on collisions. The present finding of the existence of extra-telomeric functions for Ten1 in the regulation of RNA polymerase II in cooperation with Stn1 and Cdc13 has profound repercussions on future studies both on telomeric and transcription pathways.

overall_design: 6 RNA-seq samples: 2 conditions with 3 replicates each; 12 ChIP-seq samples: 4 IPs and 2 Inputs, with 2 repliactes each.

first: Olga

last: Calvo

first: Nathalie

last: Grandin

last: Jordán-Pla

first: Esperanza

last: Miñambres

first: Noelia

last: González-Polo

first: José

last: Pérez-Ortín

first: Michel

last: Charbonneau


title: Genome-wide transcriptome analysis of brain region (ventral part of telenchephalon, hypothalamus and pituitary) in medaka [Ribo-Seq]

city: Nagoya

first: Takashi

last: Yoshimura

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

summary: To examine the protein-coding potential of transcripts, we performed ribosomal profiling analysis. We compared the RNA-seq and ribosomal protected fragments profiles (Ribo-seq) in the ventral part of telenchephalon, hypothalamus and pituitary by deep sequencing.

overall_design: Compasison of RNA-seq and Ribo-seq profiles in the ventral part of telenchephalon, hypothalamus and pituitary in medaka.


title: Seasonal regulation of the lncRNA LDAIR modulates self-protective behaviours during the breeding season


title: Genome-wide transcriptome analysis of brain region (ventral part of telenchephalon, hypothalamus and pituitary) in medaka [RNA-seq]

summary: We compared the gene expression of ventral part of telenchephalon, hypothalamus and pituitary using RNA-seq between the two comparison groups, medaka kept under short day and long day.

overall_design: Compasison of gene expression of ventral part of telenchephalon, hypothalamus and pituitary between the two comparison groups, medaka kept under short day and long day.


title: Gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) in wild type and olvl28m13 knockout Medaka fish (Oryzias latipes)

summary: To examine the transcriptome, we compared the gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) between wild type medaka and olvl28m13 knockout medaka.

overall_design: The gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) was measured between wild type medaka and olvl28m13 knockout medaka. Biotinylated cRNAs prepared from pooled ventral part of telenchephalon, hypothalamus and pituitary from three fish (total 9 fish for each genotype) were hybridized to triplicate sets of arrays (n = 3).


title: Seasonal changes of gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) in Medaka fish (Oryzias latipes)

summary: To examine the seasonal adaptaion, we compared the gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) between SD (short-day conditions: 10 h light/14 h dark and 26 °C) and LD (long-day conditions: 14 h light/10 h dark and 26 °C) conditions in Medaka fish (Oryzias latipes).

overall_design: The gene expression of brains (ventral part of telenchephalon, hypothalamus and pituitary) was measured during the transition from SD to LD conditions. For each time point, cRNAs prepared from pooled brains (ventral part of telenchephalon, hypothalamus and pituitary) (n=2) were hybridized to duplicate sets of microarrays.


title: Identification of BSF RNA targets using RIPSeq

status: Public on Apr 06 2019

city: Strasbourg

first: Kamel

last: Hammani

address: 12 Rue du général Zimmer

country: France

institute: IBMP-CNRS

summary: Stroma extracts were isolated from 2-week-old WT plants and incubated with either BSF-specific antibodies or with the pre-immune serum. IgGs were captured with SiMAG-Protein G beads (Chemicell) and recovered RNA was used for generation of libraries with the ScriptSeq v2 RNA-seq Library Preparation Kit (Epicentre). Primary reads were aligned to the Arabidopsis chloroplast genome (accession number NC_000932.1) using CLC Genomics Workbench. BAM files were extracted and sorted in Galaxy . Sorted BAM files were converted into RPKM-normalized bigwig files and displayed in IGB. The differential enrichment of BSF/control of the two replicates was displayed across the entire chloroplast genome to identify the RNA targets of BSF.

overall_design: RNA Immunoprecipitation with BSF-specific antibody and the respective pre-immuneserum as control using WT stroma extract. As BSF represents a soluble chloroplast-localized protein, stroma extract was used for RNA-Immunoprecipitation to identify the plastid RNA targets of the BSF protein. BSF-specific antibodies were produced in Rabbit using recombinant BSF as antigene.

first: Nikolay

last: Manavski

first: Wei

last: Chi

first: Andreas

last: Brachmann


title: The integrative regulatory network of circRNA, microRNA and mRNA in atrial fibrillation

city: Shanghai

first: Ban

last: Liu

address: No. 301 Yanchang Road

institute: Tongji university

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

summary: Atrial fibrillation (AF) is the most common irregular heart rhythm which influence approximately 1–2% of the general population. As a potential factor for ischemic stroke, AF could also cause heart failure. The mechanisms behind AF pathogenesis are complex and remains elusive. As a new category of non-coding RNAs (ncRNAs), circular RNAs (circRNAs) have been known as the key of developmental processes, regulation of cell function, pathogenesis of heart diseases and pathological responses which could provide novel sight into the pathogenesis of AF. circRNAs function as modulators of microRNAs in cardiac disease. To investigate the regulatory mechanism of circRNA in atrial fibrillation, especially the complex interactions among circRNA, microRNA and mRNA, we collected the heart tissues from three AF patients and three healthy controls and profiled their circRNA expressions with circRNA Microarray. The differentially expressed circRNAs were identified and the biological functions of their interaction microRNAs and mRNAs were analyzed. Our results provided novel insights of the circRNA roles in atrial fibrillation and proposed highly possible interaction mechanisms among circRNAs, microRNAs and mRNAs.

overall_design: We collected the heart tissues from three AF patients and three healthy controls.  The circRNA expression profiles of these samples were measured with Arraystar Human circRNA Array V2 (8x15K, Arraystar).

first: Shengyang

last: Jiang

first: Changfa

last: Guo

last: Zhang

first: Wenliang

last: Che

first: Yangyang


title: Analysis of gene expression in colonic epithelial cells following DSS treatment

city: New York

first: Jessica

last: Neil

address: 430 East 29th Street

institute: Skirball Institute, NYU School of Medicine

summary: Mice with and without IFNAR expression were treated with broad-spectrum antibiotics for more than 10 days, either infected with MNV or left uninfected and then treated with 3% DSS in drinking water for 6 days. Intestinal epithelial cells were isolated from the colon and sorted and RNA extracted for RNASeq analysis. We found that mice with IFNAR expression on IEC and infected with MNV had a gene expression signature of DNA repair similar that induced by IL-22 signaling.

overall_design: 3 mice in each group (IFNARf/f ABX, IFNARf/fxVillin-cre ABX, IFNARf/f ABX+CR6 and IFNARf/fxVillin-cre ABX+CR6)

first: Ken

last: Cadwell


title: Efficient neural differentiation of human pluripotent stem cells by extrinsic signals derived from co-cultured neural stem/precursor cells

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

institute: Hanyang University

summary: In this study, we found evidence of neural conversion of human pluripotent stem cells(hPSCs) to neural stem cells(NSCs) when in a co-cultured state. mRNA sequencing was performed to investigate the factors facilitating neural conversion of hPSCs. Candidate genes responsible for neural conversion were drawn out through GO and DEG analysis. The meaning of this study lies on the possibility of the establishment of a new, fast and efficient NSC differentiation protocol with a reproducible manner across hESC and hiPSC lines.

overall_design: mRNA profile of undifferentiated H9 hESC and H9 hESC-derived NPC that was differentiated by co-culturing with MS5 feeder layer cells.

first: Lee

last: Sang-Hun

first: Shim

last: Jae-Won


title: RNA-seq analysis of EBV transformation of primary resting B cells

city: Tampa

first: Mingxiang

last: Teng

state: FL

address: 12902 Magnolia Dr

department: Department of Biostatistics and Bioinformatics

institute: H Lee Moffitt Cancer Center and Research Institute

summary: RNA profile changes in primary resting B cells after EBV infection

overall_design: We infected primary resting B cells with EBV for different time and used RNA-seq to detect RNA profiling changes caused by EBV infection. 3 donors were involved in our experiment

first: Bo

last: Zhao

first: Chong

last: Wang


title: RNA-Seq analysis of the T3SA regulon in Shigella flexneri reveals two new chromosomal genes upregulated in the on-state

city: Ottawa

first: François-Xavier

last: Campbell-Valois

address: 75 rue Laurier est

department: Chemistry and Biomolecular Sciences

institute: University of Ottawa

summary: Transcriptional program of a WT and ipaD strain of Shigella flexneri modeling the off- and on-state of the T3SA in vitro were compared by RNA-Seq

overall_design: RNA-Seq of total RNA obtained from two strains of the human bacterial pathogen Shigella flexeneri whose T3SA is blocked in the off-state and on-state in vitro. The goal of the study was to identify genes that are downregulated or uppregulated during secretion and more precisely to do an exhaustive assessment of the genes composing the T3SA regulon

first: Navoun

last: Silué

first: Endrei

last: Marcantonio

first: Francois Xavier


title: FLT3-N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis

status: Public on Apr 05 2019

city: Lund

first: Axel

last: Hyrenius Wittsten

address: Klinikgatan 28

department: Division of Clinical Genetics

country: Sweden

institute: Lund University

summary: Activating signaling mutations are common in acute leukemia with KMT2A (previously MLL) rearrangements. Herein, we show that co-expression of FLT3-N676K and KMT2A-MLLT3 in human CD34+ cord blood cells primarily cause acute myeloid leukemia (AML) and rarely acute lymphoblastic leukemia (ALL) in immunodeficient mice. By contrast, expression of KMT2A-MLLT3 alone cause ALL, double-positive leukemia (DPL, expressing both CD33 and CD19), or bilineal leukemia (BLL, comprised of distinct myeloid and lymphoid leukemia cells), and rarely AML. Further, AML could only be serially propagated with maintained immunophenotype in secondary recipients when cells co-expressed KMT2A-MLLT3 and FLT3-N676K. Consistent with the idea that activated signaling would allow myeloid cells to engraft and maintain their self-renewal capacity, in a secondary recipient, a de novo KRAS-G13D was identified in myeloid cells previously expressing only KMT2A-MLLT3. Gene expression profiling revealed that KMT2A-MLLT3 DPL had a highly similar gene expression profile to ALL, with both expressing key lymphoid transcription factors and ALL cell surface markers, in line with the DPL cells being ALL cells with aberrant expression of CD33. Taken together, our results highlight the need for constitutive active signaling mutations for driving myeloid leukemia in a human xenograft model of KMT2A-R acute leukemia.

overall_design: mRNA sequencing of various immunophenotypic populations from KMT2A-MLLT3 xenograft leukemias with or without FLT3-N676K generated using Illumina NextSeq 500.

last: Hyrenius-Wittsten

first: Anna

last: Andersson-Hagström


title: Gene expression in BM niche populations

status: Public on Apr 11 2019

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: We report transcriptome profiling of bone marrow niche subsets at the population level. Additionally, we report trascriptional changes in lymphoid -primed multipotential progenitors in the absence of vascular DLL4.

overall_design: Low input RNA-sequencing libraries of rare BM niche and progenitor populations.

first: Anastasia

last: Tikhonova

first: Aristotelis

last: Tsirigos

first: Iannis

last: Aifantis


title: Identification of renal resident macrophages across species [10X]

city: Oklahoma City

first: Kurt

last: Zimmerman

state: Oklahoma

address: 940 Stanton L Young Blvd

department: Internal Medicine

institute: University of Oklahoma Health Sciences Center

summary: We use single cell RNA sequencing to identify an evolutionarily conserved gene expression signature in resident macrophages. Based on our single cell data, we show the presence of a core gene expression signature in a cluster of innate immune cells in mouse, rat, pig, and human kidney tissue. Further, using this gene expression signature, we identify novel candidate markers for resident macrophages that span all 4 species tested.

sample_organism:
Homo sapiens
Sus scrofa
Mus musculus
Rattus norvegicus

overall_design: We performed 10x genomics and fluidigm C1 single cell sequencing on innate immune cells isolated from the kidney of mouse, rat, pig, and human kidney tissue.

first: Melissa

last: Bentley

first: Jeremie

last: Lever

first: Zhang

last: Li

first: David

last: Crossman

first: Cheng

last: Song

first: Shanrun

last: Liu

first: Michael

last: Crowley

first: James

middle: F

last: George

first: Michal

last: Mrug

first: Bradley

last: Yoder


title: Profiling of chromatin accessibility in fibroblasts, iPSCs, iPSC-derived neurons and cells overexpressing Onecut transcription factors (OC1, OC2, OC3)

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Center

summary: Remodeling of chromatin accessibility is necessary for successful reprogramming of fibroblasts to neurons. However, it is still not fully known which transcription factors can induce a neuronal chromatin accessibility profile when overexpressed in fibroblasts. To identify such transcription factors, we here used ATAC-sequencing to generate differential chromatin accessibility profiles between human fibroblasts and iNeurons, an in vitro neuronal model system obtained by overexpression of Neurog2 in induced pluripotent stem cells (iPSCs). We found that the ONECUT transcription factor sequence motif was strongly associated with differential chromatin accessibility between iNeurons and fibroblasts. All three ONECUT transcription factors associated with this motif (ONECUT1, ONECUT2 and ONECUT3) induced neuronal morphology and expression of neuronal genes within two days of overexpression in fibroblasts. We observed widespread remodeling of chromatin accessibility; in particular, we found that chromatin regions that contain the ONECUT motif were in- or lowly accessible in fibroblasts and became accessible after the overexpression of ONECUT1, ONECUT2 or ONECUT3. There was substantial overlap with iNeurons, still, many regions that gained accessibility following ONECUT overexpression were not accessible in iNeurons. Our study highlights the potential of ONECUT transcription factors for direct neuronal reprogramming.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Each ATAC-Seq experiment was performed in duplicate (library constructed from different wells of the same cell line in the same cell culture experiment). Bclxl controls were generated for the overexpression experiments.

first: Jori

last: van der Raadt


title: Immune homeostasis and regulation of the Interferon pathway require myeloid-derived Regnase-3

city: Neuherberg

first: Elke

last: Glasmacher

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum München

summary: The RNase Regnase-1 is a master RNA regulator in macrophages and T cells that degrades cellular and viral RNA upon NF-kB signaling. The roles of the other Regnase family-members remain largely unknown. Here, we analyze Regnase-3 deficient mice, which develop hypertrophic lymph nodes. We used various mice with immune cell specific deletions of Regnase-3 to demonstrate that Regnase-3 acts specifically within myeloid cells. Regnase-3 deficiency systemically increased interferon signaling, which increased the proportion of immature B and innate immune cells and suppressed follicles and germinal center formation. Expression analysis revealed that Regnase-3 and Regnase-1 share protein degradation pathways. Nevertheless, Regnase-3 expression is specifically high in macrophages and transcriptionally controlled by interferon signaling. Although direct targets in macrophages remain unknown, Regnase-3 can bind, degrade and regulate mRNAs, such Zc3h12a encoding Regnase-1, in vitro. These data indicate that Regnase-3, like Regnase-1, is an RNase and essential for immune homeostasis, but has diverged as a key regulator for the interferon pathway in macrophages.

overall_design:
Alveolar macrophages from Regnase-3+/+ and Regnase-3-/- mice were sequenced (n=3/3).
B cells: Lymph nodes were dissected from Regnase-3+/+ and Regnase-3-/- mice and divided into normal sized and enlarged lymph nodes in each Regnase-3-/- mouse (n=3/3/3).

first: Matthias

last: von Gamm

first: Johannes

last: Lichti


title: Identification of renal resident macrophages across species [C1]

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We performed 10x genomics and fluidigm C1 single cell sequencing on innate immune cells isolated from the kidney of mouse, rat, pig, and human kidney tissue. This series includes mouse and human samples.


title: Identification of renal resident macrophages across species

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

platform_organism:
Homo sapiens
Sus scrofa
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Profiling of gene expression using RNA-Seq in fibroblasts, iPSCs, iPSC-derived neurons and cells overexpressing Onecut transcription factors

overall_design: Each RNA-Seq experiment was performed in duplicate (library constructed from different wells of the same cell line in the same cell culture experiment). Bclxl controls were generated for the overexpression. experiments.


title: PAN-INTACT enables isolation of lineage-specific nuclei from fibrous tissues

city: Dallas

first: Samadrita

last: Bhattacharyya

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: PAN-INTACT method can be used to isolate cell type specific nuclei from fibrous mouse organs, which are particularly problematic. It is broadly applicable for profiling the transcriptional and epigenetic landscape of specific cell types.  We envision that our method can be used to systematically probe mechanistic details of cell type-specific functions within individual organs of intact mice.

overall_design: We demonstrate successful isolation of cell type-specific nuclei from mouse heart and kidney. As a proof of generating high quality epigenome maps from specific cell-types in mouse heart, we used nuclei from PAN-INTACT followed by MAN-IP to construct ATAC-Seq libraries in the study.

first: Adwait

last: Sathe

first: Minoti

last: Bhakta

first: Chao

last: Xing

first: Nikhil

middle: V

last: Munshi


title: Mutated H3 Histones Drive Human Pre-Leukemic Hematopoietic Stem Cell Expansion And Promote Leukemic Aggressiveness

city: Montreal

first: Carol

last: Chen

state: QC

address: 1001 Decarie Boulevard, Rm E01.4380

institute: Research Institute of McGill University Hospital Centre

summary: Leukemogenesis is a stepwise progression from mutated, pre-neoplastic hematopoietic stem cells (HSCs) to full-blown leukemia. Our ability to prevent or treat de novo and secondary acute myeloid leukemia (AML) is limited by our incomplete understanding of the epigenetic disruption that is central to this process, including improper histone methylation. We performed a comprehensive analysis of 16 histone H3 genes in 434 primary acute myeloid leukemia (AML) samples and identified mutations in adult and pediatric cases (1.6%), with a higher incidence in secondary AML (s-AML) (9%). These included four novel amino acid substitutions (Q69H, A26P, R2Q and R8H) as well as K27M and K27I in H3.1 and H3.3 genes. These mutations are important early events in leukemogenesis as they were observed in pre-leukemic HSCs in two cases and were in the major clones in every sample. Consistent with a role in pre-leukemic HSC clonal expansion, the mutant histones increased functional human HSC frequency and altered differentiation along the erythroid and myeloid lineages, with activity dependent on the specific mutation (K27M, K27I and Q69H). In established human leukemia, the K27M/I mutant histones amplified leukemic aggressiveness, with increased proliferation, expansion of leukemic progenitor and blast cells, and superior competitiveness in vivo. This was associated with increased expression in genes involved in erythrocyte and myeloid differentiation, correlated with a corresponding decrease in histone H3 K27 tri-methylation and increase in K27 acetylation. While histone mutations can co-occur with alterations in RUNX1, we observed that the functional impact of histone mutations is independent of RUNX1 mutations. Taken together, these data establish the involvement of H3 mutations as early drivers of pre-leukemic HSC expansion and leukemogenesis.

overall_design: TEX cells were transduced with lentiviral particles to overexpress HIST1H3H WT, HIST1H3H K27M, HIST1H3F WT, HIST1H3F K27I and Luc2. Expression profiling comparing between histone mutants to their respective wildtype were performed using high throughput RNA sequencing. Similarly, histone post-translational modification H3K27me3 and H3K27ac were profiled in the histone mutants and their respective wildtypes by high throughput ChIP sequencing.

first: Meaghan

last: Boileau

first: Margret

last: Shirinian

first: Tenzin

last: Gayden

first: Ashot

last: Harutyunyan

middle: C

first: Leonie

last: Mikael

first: Heather

last: Duncan

first: Andrea

middle: L

last: Neumann

first: Patricia

last: Arreba-Tutusaus

first: Nicolas

last: De Jay

first: Michele

last: Zeinieh

first: Jonathan

last: Pratt

first: Hamid

last: Nikbakht

first: Carine

last: Mouawad

first: Radwan

last: Massoud

first: Felice

last: Frey

first: Rihab

last: Nasr

first: Jean

last: El Cheikh

first: Marwan

last: El Sabban

first: Claudia

last: Kleinman

first: Rami

last: Mahfouz

first: Mark

middle: D

last: Minden

first: Nada

last: Jabado

first: Ali

last: Bazarbachi

first: Kolja

last: Eppert


title: Studying the selectivity of a targeted small molecule degrading a hypoxia-associated non-coding RNA

status: Public on Apr 04 2019

city: Jupiter

first: Matthew

last: Costales

address: 130 Scripps Way, A359

institute: The Scripps Research Institute Florida

summary: Small molecule targeted recruitment of nucleases to RNA is a powerful method to affect RNA biology.  Inforna, a sequence-based design approach to target RNA, enables the design of small molecules that bind and cleave RNA in a selective and substoichiometric manner.  Herein, we investigate the ability of RNA targeted degradation to improve the selectivity of small molecules targeting RNA.  The microRNA-210 hairpin precursor (pre-miR-210) is overexpressed in hypoxic cancers.  Previously, a small molecule (Targapremir-210, TGP-210) targeted this RNA in cells, but with only a 5-fold window for DNA binding.  Appendage of a nuclease recruitment module onto TGP-210 locally recruited ribonuclease L onto pre-miR-210, triggering its degradation.  The chimera has enhanced selectivity compared to TGP-210 with nanomolar binding to the pre-miR-210, but no DNA binding, and is broadly selective for affecting RNA function in cells.  Importantly, it cleaved pre-miR-210 substoichiometrically and induced apoptosis in breast cancer cells.

overall_design: Examination of small molecule-treated (TGP-210-RL) or vehicle-treated (DMSO) hypoxic MDA-MB-231 cells in biological triplicates

first: Blessy

last: Suresh

first: Kamalakannan

last: Vishnu

last: Disney


title: MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments

city: La Jolla

first: Miao

last: Yu

state: CA

address: 9500 Gilman Drive

institute: Ludwig Institute for Cancer Research

summary: Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting the information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.

overall_design: PLAC-seq experiment against H3K4me3 and CTCF antibodies in mouse embryonic stem cell (F123); ATAC-seq on F123 cells; H3K4me3 ChIP-seq on F123 cells.

first: Ivan

last: Juric

first: Armen

last: Abnousi

first: Ramya

last: Raviram

first: Rongxin

last: Fang

first: Yuan

last: Zhao

first: Yanxiao

last: Zhang

first: Yunjiang

last: Qiu

first: Yuchen

last: Yang

first: Yun

last: Li

first: Bing

last: Ren

first: Ming

last: Hu


title: Genome-wide occupancy of the CEH-60 and UNC-62 Transcription Factors in Caenorhabditis elegans

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

summary: Animals integrate metabolic, developmental, and environmental information before committing key resources to reproduction.  In C. elegans, adult animals reallocate key fat stores from intestinal cells to the germline via lipoproteins to promote reproduction.  I identified the evolutionarily conserved homeodomain transcription factor CEH-60/PBX as a potent regulator of lipid homeostasis, longevity, and stress response pathways.  To gain a comprehensive view of CEH-60 transcriptional activity, I profiled the transcriptomes of ceh-60 mutants by mRNA-Seq and identified genome-wide CEH-60 binding sites by ChIP-Seq.  These approaches revealed that several homeostatic pathways are directly controlled by the CEH-60 transcription factor.  CEH-60 functions cooperatively with UNC-62/MEIS in the intestine to directly activate lipoprotein genes while simultaneously repressing genes involved in stress responses, including the innate immune and oxidative stress responses.  Thus in wild-type animals, CEH-60 serves as a molecular switch that promotes reproduction (i.e., lipoproteins) while repressing stress response and longevity pathways. This study identifies a new key regulator of fat metabolism, longevity, and stress response pathways during normal C. elegans development.

overall_design: The genome-wide binding sites for CEH-60 and UNC-62 (isoform 7a) were identified by high-throughput sequencing.

middle: H


title: RNA-Seq and protein mass spectrometry in microdissected kidney tubules reveal signaling processes initiating lithium-induced nephrogenic diabetes insipidus

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary:
Purpose: Lithium salts, used for treatment of bipolar disorder, frequently induce nephrogenic diabetes insipidus (NDI), limiting therapeutic success.  NDI is associated with loss of expression of the molecular water channel, aquaporin-2, in the renal collecting duct (CD). Here, we use the methods of systems biology in a well-established rat model of lithium-induced NDI to identify signaling pathways activated at the onset of polyuria.
Methods: We carried out RNA-sequencing in cortical CDs microdissected from rats treated with lithium for 12-72 hours (vs. time controls). Administration of anti-inflammatory doses of dexamethasone to lithium-treated rats countered the loss of aquaporin-2 protein. Protein mass spectrometry in microdissected cortical CDs provided corroborative evidence, but also identified decreased abundance of several anti-oxidant proteins. Cortical thick ascending limbs of Henle were also microdissected for RNA-Seq at 72 hrs. We carried out RNA-Seq for 2-3 CCD sample per rat (1 lithium-treated rat versus 1 control at 12, 24, 36 hrs).
Results and conclusion: Integration of new data with prior data about lithium effects at a molecular level leads to a signaling model in which lithium increases ERK activation leading to induction of NF-κB signaling and an inflammatory-like response that represses Aqp2 gene transcription.

overall_design: We carried out RNA-sequencing and protein mass spectrometry in cortical CDs microdissected from rats treated with lithium. We identified signaling pathways that initiate Lithium-induced NDI using systems biology approaches.

last: Sung

first: Kavee

last: Limbutara

first: Hyun

middle: J

last: Jung

first: Gabrielle

last: Gilmer

first: Chin-Rang

first: Shih-Hua

last: Lin

first: Sookkasem

last: Khositseth

first: Chung-Lin

last: Chou

first: Mark

middle: A

last: Knepper


title: Insulin receptor associates with promoters genome-wide and regulates gene expression [RNA-seq 2]

city: Boston

first: John

last: Flanagan

state: MA

address: 200 Longwood Ave, Building C2, Room 523

department: Cell Biology

institute: Harvard Medical School

summary: RNA-seq analysis identifies transcripts regulated by HCF-1 expression

overall_design: Examination of differentially expressed genes in response to HCF-1 siRNA vs con siRNA in HepG2 cells, using eight biological replicates for each condition (RNA-seq).

first: Melissa

last: Hancock


title: Analysis of the transcription factor CEH-60 in Caenorhabditis elegans development


title: Next Generation Sequencing and Quantitative Analysis of mRNAs in Wild Type and ceh-60 Mutant Caenorhabditis elegans

overall_design: The mRNAs of wild-type and ceh-60 mutant adult animals (day 1 or 4 of adulthood) were profiled by high-throughput sequencing, in triplicate.


title: The interplay between small RNA pathways shapes chromatin landscapes in C. elegans

first: Ekaterina

last: Gushchanskaia

address: 72 East Conconrd, K425

institute: Boston University School of Medicine

summary: The nematode C. elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both “silencing” siRNAs bound by Worm-specific Argonautes (WAGO) and “activating” siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants and describe small RNAs matching enhancers. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to increase in silencing chromatin marks.  Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.

overall_design: Examination of 3 different histone modifications in 3 nematode strains (2 replicates per each sample).

first: Ruben

last: Esse

first: Alla

last: Grishok

first: Qicheng

last: Ma

first: Nelson

last: Lau


title: Insulin receptor associates with promoters genome-wide and regulates gene expression [ChIP-seq]

summary: ChIP-seq analysis demonstrates an association of insulin receptor (IR) and RNA polymerase II on chromatin, with striking enrichment at gene promoters.

overall_design: Examination of IR and RNA Pol II binding in HepG2 and SH-SY5Y cell lines (ChIP-seq).


title: The TOR pathway plays pleiotropic roles in growth and stress responses of the fungal pathogen Cryptococcus neoformans

status: Public on Apr 03 2019

city: Seoul

first: Dong-Gi

last: Lee

address: 50 Yonsei-ro, Seodaemun-gu

institute: Yonsei University

summary: The target of rapamycin (TOR) pathway is an evolutionarily conserved signal transduction system that is activated by varying nutrient and environmental signals and governs a plethora of eukaryotic biological processes, but its role in Cryptococcus neoformans remains elusive. In this study, we investigated the TOR pathway by functionally characterizing two Tor-like kinases, Tor1 and Tlk1, in C. neoformans. We successfully deleted TLK1, but not TOR1. TLK1 deletion did not result in any evident in vitro phenotypes, suggesting that Tlk1 is mainly dispensable for the growth of C. neoformans. We further demonstrated that Tor1, but not Tlk1, is essential and the target of rapamycin by constructing and analyzing conditionally regulated strains and sporulation analysis of heterozygous mutants in the diploid strain background. To analyze the functions of Tor1 in more detail, we constructed constitutive TOR1 overexpression strains. Tor1 negatively regulated thermotolerance and the DNA damage response, which are two important virulence factors of C. neoformans. We also found that TOR1 overexpression reduced Mpk1 phosphorylation, which is required for cell wall integrity and thermoresistance, and Rad53 phosphorylation, which governs the DNA damage response pathway. Tor1 is localized to the cytoplasm but enriched in the vacuole membrane. Phosphoproteomics and transcriptomics revealed that Tor1 regulates a variety of biological processes, including metabolic processes, cytoskeleton organization, ribosome biogenesis, autophagy, and stress response. TOR inhibition by rapamycin caused actin depolarization in a Tor1-dependent manner. Finally, screening rapamycin-sensitive and -resistant kinase and transcription factor mutants revealed that the TOR pathway may crosstalk with a number of signaling pathways, including the Hog1 pathway. In conclusion, our study demonstrates that a single Tor1 kinase plays a variety of roles in the fungal meningitis pathogen C. neoformans.

overall_design: To investigate downstream genes regulated by TOR1, total RNA was isolated from the wild-type (H99), TOR1 overexpression (TOR1oe) mutant, and rapamycin treated wild-type strain. Each strains were incubated in YPD liquid medium overnight at 30°C, subcultured in fresh YPD liquid medium, and then further incubated at 30°C until OD600 was approximately 0.6–0.8. The WT cells were divided in half. One-half was used as a WT control while the other half was treated with rapamycin (3 ng/ml) and further incubated for 3 h at 30°C. The WT, TOR1oe, and rapamycin-treated WT cells were harvested and lyophilized. Three biologically independent cultures were prepared for each strain.

first: Yee-Seul

last: So

first: Yong-Sun

last: Bahn


title: Insulin receptor associates with promoters genome-wide and regulates gene expression


title: TNF promotes SREBP activity to regulate macrophage polarization and tissue repair [RNA-seq]

city: Ulsan

first: Sungho

last: Park

address: 50 UNIST-gil, Eonyang-eup

department: Life Science

institute: Ulsan National Institute of Science and Technology

summary: TNF-mediated macrophage polarization is important for inflammatory disease  pathogenesis, but mechanisms that regulate polarization are not well understood.  Transcriptomic and epigenomic analysis of the TNF response in primary human  macrophages revealed late phase activation of SREBP2, the master regulator of  cholesterol biosynthesis genes. TNF stimulation extended the genomic profile of  SREBP2 occupancy to include binding to and activation of inflammatory and interferon  response genes independently of its functions in sterol metabolism. Genetic ablation of  SREBP function shifted the balance of macrophage polarization from M1 to an M2-like  reparative phenotype in peritonitis and skin wound healing models. Genetic ablation of  SREBP activity in myeloid cells or topical pharmacological inhibition of SREBP  improved skin wound healing under homeostatic and chronic inflammatory conditions.  Our results identify a new function and mechanism of action for SREBP2 in  augmenting TNF-induced M1 macrophage polarization and inflammation, and open  therapeutic avenues for promoting wound repair.

overall_design: Analysis of transcriptional changes in human macrophages stimulated with or without TNF in the presence of various inhibitors (Fatostatin, Atrovastatin, Cholesterol and DMSO)


title: Insulin receptor associates with promoters genome-wide and regulates gene expression [RNA-seq]

summary: RNA-seq analysis identifies transcripts regulated by insulin treatment.

overall_design: Examination of differentially expressed genes in response to insulin treatment in HepG2 cells, using nine biological replicates for each condition (RNA-seq).


title: MTHFD1 links folate metabolism to BRD4-mediated transcriptional regulation

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: The histone acetyl-reader BRD4 is an important regulator of chromatin structure and transcription, yet factors modulating its activity have remained elusive. Here we describe two complementary screens for functional regulators and physical interactors of BRD4, which converge on the folate pathway enzyme MTHFD1. We show that a fraction of MTHFD1 resides in the nucleus, where it is recruited to distinct genomic loci by direct interaction with BRD4. Inhibition of either BRD4 or MTHFD1 results in similar changes in nuclear metabolite composition and gene expression, and pharmacologic inhibitors of the two pathways synergize to impair cancer cell viability in vitro and in vivo. Our finding that MTHFD1 and other metabolic enzymes are chromatin-associated suggests a direct role for nuclear metabolism in the control of gene expression.

overall_design: 35 ChIP-seq samples for BRD4, MTHFD1 and H3K27ac were produced, along with the respective IgG controls in HAP1 cells treated with dBET6 or DMSO. 93 RNA-seq samples for WT, MTHFD1KO or treated cell were produced.

first: Sara

last: Sdelci

first: André

last: Rendeiro

first: Philipp

last: Rathert

first: Gerald

last: Hofstätter

first: Anna

last: Ringler

first: Herwig

middle: P

last: Moll

first: Wanhui

last: You

first: Kristaps

last: Klavins

first: Bettina

last: Gürtl

first: Matthias

last: Farlik

first: Sandra

last: Schick

first: Freya

last: Klepsch

first: Matthew

last: Oldach

first: Pisanu

last: Buphamalai

first: Fiorella

last: Schischlik

first: Peter

last: Májek

first: Katja

last: Parapatics

first: Christian

last: Schmidl

first: Michael

last: Schuster

first: Thomas

last: Penz

first: Dennis

last: Buckley

first: Otto

last: Hudecz

first: Richard

last: Imre

first: Robert

last: Kralovics

first: Keiryn

last: Bennett

first: Andre

last: Müller

first: Karl

last: Mechtler

first: Jörg

last: Menche

first: James

last: Bradner

first: Georg

last: Winter

first: Emilio

last: Casanova

first: Johannes

last: Zuber

first: Stefan

last: Kubicek


title: TNF promotes SREBP activity to regulate macrophage polarization and tissue repair [scRNA-seq]

first: Sungho

last: Park

overall_design: Analysis of transcriptional changes in human macrophages stimulated with or without TNF


title: TNF promotes SREBP activity to regulate macrophage polarization and tissue repair

overall_design: Refer to individual Series


title: TNF promotes SREBP activity to regulate macrophage polarization and tissue repair [ATAC-seq]


title: Increased CP gateway activity under psychological stress leads to recruitment of non-encephalitogenic T cells into the brain

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Knockdown of Glucocorticoid receptor at the choroid plexus in the context of psychological stress leads to the recruitment of T cells into the brain. These T cells show a non-encephalitogenic pattern of T cell associated gene expression.

overall_design: Mice were induced with a knockdown of glucocoritocid receptor on the choroid plexus, followed by exposure to psychological stress using electrical foot-shock. 14 days after exposure to stress, brain parenchyma was collected, sorted for T cells and analyzed for single cell gene expression

first: Alexander

last: Kertser

first: Kuti

last: Baruch

first: Aleksandra

last: Deczkowska

first: Assaf

last: Weiner

first: Tommaso

last: Croese

first: Mor

last: Kenigsbuch

first: Itzik

last: Cooper

last: Tsoory

first: Sefi

last: Ben-Hamo

first: Michal

last: Schwartz


title: Expression data from microglia which were freshly isolated from WT and Lrrc33-/- mice

first: Timothy

last: Springer

address: 3 Blackfan Circle, Room 3103

institute: Harvard University

summary:
We demonstrate that the cell-surface molecule LRRC33 associates with proTGF-β1 and provides a milieu for a restricted subset of TGF-β-dependent functions. We deposit microglia  transcriptional profiles from three Lrrc33+/+ mice and three  Lrrc33-/- mice.
In this dataset, we include the expression data obtained from microglia that were isolated from 3 Lrrc33+/+ mice and 3 Lrrc33-/- mice.

overall_design: 6 Total samples were analyzed using the Affymetrix Murine Exon 1.0 ST platform.

first: Yan

last: Qin

first: Brian

middle: S

last: Garrison

first: Meeta

last: Mistry


title: Comparison of the Damaged Cartilage with the Non-weight Bearing Healthy Cartilage

status: Public on Apr 02 2019

city: ankara

first: mehmet

middle: dogan

last: asik

state: Select Your State or Province

address: kızılcaşar mah mehmetçik cad no 15, gölbaşı

department: School of Medicine

country: Turkey

institute: Ankara Yildirim Beyazit University

summary: The cartilage samples from patient with Internatinaol Cartilage Repair Society's Scoring 3-4 cartilage defects were analysed in order to understand the differences between healthy and damaged cartilage tissues from the knee.

overall_design: Differential Expression profiling by array. Total RNA was isolated from samples collected from patients during the surgery with RNeasy Mini kit. Affymetrix Primeview human Expression kit chips were used following to affimetrix IVT kit. The data analysed with expression console and Trancriptome Analysis Console.

first: Murat

last: Bokzurt

first: Mehmet

last: AŞIK


title: Transcriptome analysis of lung fibroblasts from 5 control and 5 IPF patients with/out TGF-b1 stimulation

city: BATH

first: Marina

last: Hadjicharalambous

address: PHARMACY AND PHARMACOLOGY (5 WEST), CLAVERTON DOWN

country: United Kingdom

institute: University of Bath

summary: Isolated primary human fibroblasts from 5 control and 5 IPF patients were treated with/out 3ng/ml TGF-b1  for 24 hours before cells were lysed for RNA extraction.

overall_design: A total of 20 samples were processed for RNA extraction including  an on-column Dnase treatment. RNA quantity  and quality  were measured (RIN values >8.0) before samples were processed according to  the Affymetrix GeneChip Human Transcriptome Arrays 2.0 user manual.

middle: R

first: Benoit

middle: T

last: Roux

first: Eszter

last: Csomor

first: Carol

last: Feghali-Bostwick

first: Lynne

last: Murray

first: Deborah

last: Clarke

first: Mark

last: Lindsay


title: Glucocorticoid Receptor Quaternary Structure Drives Chromatin Occupancy and Transcriptional Outcome

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

country: Finland

institute: University of Eastern Finland

summary: Most transcription factors, including nuclear receptors, are widely modeled as binding regulatory elements as monomers, homodimers, or heterodimers.  Recent findings in live cells show that the glucocorticoid receptor (GR) forms tetramers on enhancers, due to an allosteric alteration induced by DNA binding, and suggest that higher oligomerization states are important for the gene regulatory responses of GR. Using a variant (GRtetra) that mimics this allosteric transition, we performed genome-wide studies using a GR knock-out cell line with reintroduced wild-type GR or reintroduced GRtetra. GRtetra acts as a super receptor by binding to response elements not accessible to wild-type receptor, and both induces and represses more genes than GRwt. These results argue that DNA binding induces a structural transition to the tetrameric state, forming a transient higher order structure that drives both the activating and repressive actions of glucocorticoids.

overall_design: Genome-wide occupancy profiling of GR and active histone marks by ChIP-seq from mouse mammary adenocarcinoma cell lines (3617) knock-out of endogenous GR (3617-KOGR) and stably integrated with GFP-tagged GR mutants, in biological duplicates, using Illumina NextSeq. GR binding data from the 3617-KOGR cells was used as control for GR and input sample from 3617-KOGR cells were used as controls for the rest. Chromatin accessibility examined by ATAC-seq from GR mutant cell lines, in biological duplicates, using Illumina HiSeq4000. Gene expression profiling from GR mutant cell lines by RNA-seq, in biological triplicates, using Illumina HiSeq2500. Genome-wide occupancy profiling of GR by ChIP-seq from mouse embryonic fibroblast (MEF) cell lines knock-out of endogenous GR (MEF-KOGR) and stably integrated with GFP-tagged GR mutants, in biological duplicates, using Illumina NextSeq. GR binding data from the MEF-KOGR cells was used as control.

first: Thomas

last: Johnson

first: Diego

middle: M

last: Presman

first: Gordon

last: Hager


title: Culture of mature adipocytes under a permeable membrane and comparative analysis with different cell culture models

city: Solna

first: Adil

last: Mardinoglu

address: Tomtebodavägen 23B

department: Systems biology

institute: SciLifeLab, KTH

summary: White adipose tissue (WAT) is a central factor in the development of type 2 diabetes. Despite the epidemiological importance of WAT there is a paucity of translational models to study long term changes in mature adipocytes. Here, we describe a novel method for the culture of mature white adipocytes under a permeable membrane. Compared to existing culture methods such as adipose tissue explants and adipocyte ceiling culture, Membrane mature Adipocyte Aggregate Cultures (MAAC) are superior at maintaining adipogenic gene expression through 2 weeks of culture, do not dedifferentiate, and are under reduced hypoxic stress relative to adipose tissue explants. Unbiased RNA-Sequencing analysis indicates that the gene expression profile of MAAC in culture for 1 or 2 weeks is more similar to starting patient material than cultured adipose tissue explants, floating adipocytes, or in vitro-differentiated precursors from the same donor, with the fewest number of differentially expressed genes and the smallest fold-change in gene expression. Importantly, adipocytes from lean and obese patients can be cultured as MAAC, as can subcutaneous and visceral adipocytes, while maintaining depot-specific gene expression signatures. MAAC remain fully functional after long term culture, with similar responses to insulin and lipolytic stimuli compared to recently isolated cells. In addition, MAAC maintain the ability to crosstalk with other cell types, producing synergistic increases in IL6 and IL8 when co-cultured with macrophages, and respond robustly and predictably to diverse pharmacological agonism. Together, these abilities make MAAC a powerful tool for studying phenotypic changes in mature adipocytes, crosstalk between adipocytes and other cell types, and provide an improved translational model for drug development for the modulation of adipose tissue function.

overall_design:
mRNA profiles of packed D0 cells from patient material, whole fresh tissue, not-differentiated preadipocytes (PA), and cultured cells in 1 and 2 week, such as membrane mature adipocyte aggregate culture (MAAC) cells, floating cells, explant cells, differentiated PA were generated by deep sequencing using Illumina NextSeq.

Submitter declares that raw data will not be submitted due to patient privacy concerns and European Union legislation.

first: Jeremie

last: Boucher

first: Matthew

last: Harms

first: Sunjae

last: Lee


title: Loss of Neurological Disease HSAN-I-Associated  Gene SPTLC2 Impairs CD8+ T Cell Responses to  Infection by Inhibiting T Cell Metabolic Fitness

city: Heidelberg

first: Guoliang

last: Cui

address: Im Neuenheimer Feld 280

country: Germany

institute: German cancer research center (DKFZ)

summary: Hereditary sensory and autonomic neuropathy type I (HSAN-I) is neurological disorder characterized by distal sensory neuron dysfunction, frequent infections, and ulcerative mutilations. It remains unknown if HSAN-I directly dampens protective immunity. Here we report that HSAN-I-causing mutations of serine palmitoyltransferase long chain base subunit 2 (SPTLC2) affect human T cell responses. T cell antigenic stimulation and inflammation induce SPTLC2 expression. Murine T cell-specific ablation of Sptlc2 fundamentally impairs antiviral T cell survival and effector function. Mechanistically, SPTLC2-deficiency reduces sphingolipid biosynthetic flux and causes a prolonged activation of the mechanistic target of rapamycin complex 1 (mTORC1), endoplasmic reticulum (ER) stress and CD8+ T cell death. Antiviral CD8+ T cell responses are restored by supplementing sphingolipids and pharmacologically inhibiting ER stress-induced cell death. Our study reveals that SPTLC2 underpins protective adaptive immunity by translating extracellular stimuli into intracellular anabolic signals and reducing cellular stress to maintain metabolic reprogramming sustainability

overall_design: Triplicates of each group were used for RNA-seq. Four groups were studied: Wild-type and SPTLC2-deficient CD8+ T cells, harvested from either naïve mice (D0) or mice infected with LCMV Armstrong 8 days earlier (D8).


title: TNF promotes SREBP activity to regulate macrophage polarization and tissue repair [ChIP-seq]

first: Sungho

last: Park


title: Circadian transcriptome in mouse skeletal muscle after exercise in the early rest versus active phase

status: Public on Apr 01 2019

city: College Station

first: Shogo

last: Sato

address: 3258 TAMU, Biological Science Building West (BSBW) 309

department: Biology

country: USA

institute: Texas A&M University

summary: We performed the circadian transcriptome analysis using the skeletal muscle from sedentary and exercised mice either in the early rest phase (ZT3) or in the early active phase (ZT15). By the combination with circadian transcriptomic and metabolomic analysis, we revealed time-of-day-dependent remodeling of circadian muscular metabolic pathways involved in glucose and glycerol metabolism after exercise. We found that only exercise in the early active phase elevates the levels of genes encoding glycolytic enzymes followed by the activation of fatty acid oxidation, branched-chain amino acid catabolism and ketogenesis/ketosis. This study demonstrates that time-of-day is a critical factor to modulate the impact of exercise on metabolic pathways within skeletal muscle.

overall_design: Skeletal muscles from sedentary (sham-exercise) mice and mice subjected to acute treadmill exercise either in the early rest phase (ZT3) or in the early active phase (ZT15) were harvested after 0, 4, 8, 12, 16, and 20 hours after exercise or sham-exercise treatment.

first: Paolo

last: Sassone-Corsi


title: Spatially patterned scaffolds enhances vascular organization and functional integration in volumetrc muscle loss

city: Palo Alto

first: Ngan

last: Huang

address: 3801 Miranda Avenue

department: Cardiothoracic Surgery

institute: Stanford University

summary: We report the application of bioengineered skeletal muscle composed of murine skeletal myoblasts interspersed with human vascular endothelial cells (ECs) using spatially patterned scaffolds for the treatment of volumetric muscle loss. To gain insights into the molecular mechanisms by which spatial patterning promoted myo-angiogenesis, we performed mRNA sequencing of engineered muscle and endothelialized engineered muscle on either randomly-oriented or aligned scaffolds. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from four groups: 1) randomly-oriented scaffold seeded with myoblasts; 2) randomly-oriented scaffolds seeded with myoblasts + ECs; 3) aligned scaffold seeded with myoblasts only; 4) aligned scaffold seeded with myoblasts + ECs. Samples were generated in triplicate and the NovaSeq 6000 (Illumina) sequencing platform was utilized. 150-bp paired-end reads were generated (20-30 million reads per sample).  The raw data were checked for quality with FastQC (Version 0.11.7) and results were aggregated with MultiQC and were aligned to the mouse genome (GRCm38) using STAR (Version 2.5.3a) with ENCODE options for long RNA-seq pipeline. The alignment results were assessed using Samtools and aggregated with MultiQC (Version 1.5) and the differential gene expression analysis of the uniquely mapped reads/raw counts wwas performed using the DESeq2 package (Version 1.20.0). Each DE analysis was composed of a pairwise comparison between an experimental group and the control group. Differentially expressed genes were identified after false discovery rate (FDR = 0.05) correction.

overall_design: Examination of differences in transcriptome profiling between 4 different bioengineered skeletal muscle

first: Karina

last: Nakayama


title: Effect of Omomyc treatment on human lung adenocarcinoma cell lines

city: Barcelona

first: Marie-Eve

last: Beaulieu

state: Catalunya

address: Natzaret 115-117

institute: Peptomyc

summary: Analysis of H1975, A549 and H1299 cells treated with 12.8 µM Omomyc or vehicle (PBS) for three days.

overall_design: Samples were prepared at least in triplicates. Control samples were treated with the vehicle

first: Mariano

last: Zacarias-Fluck

first: Laura

last: Soucek


title: Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors [P2A-EGFP control]

city: New York

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Base Editing has been touted the most intelligent and precise application of the CRISPR platform so far, merging the simplicity of RNA-guided nucleases with deaminases that allow for the programmable generation of single base substitutions - without introduction of double-strand breaks. Even though the two-component system has been expected to cause off-target substitutions, studies involving cytosine base editors (CBEs) showed that in most cases, relatively few single base off-targets could be detected on DNA. We introduce the concept of multi-dimensional off-targeting, presenting an extensive amount of RNA cytidines being edited by DNA base editors. Epitranscriptomic off-target effects affected different cell lines and were independent of the guide RNAs used, suggesting Cas9-independent activity of the cytidine deaminase rAPOBEC1 on single-stranded RNA. With the help of protein engineering, we developed CBE variants with massively reduced inadvertent mutation of RNA that preserve and enhance DNA base editing capabilities.

overall_design: HEK293T or HepG2 cells were transfected with P2A-EGFP. Cells were sorted for top 5% GFP based on FITC signal. RNA-seq was performed to measure transcriptional changes associated with different constructs.

first: Julian

last: Grunewald


title: Effect of Omomyc in vivo treatment on lung adenocarcinoma of KRasLSL-G12D/+ transgenic mouse

summary:
Analysis of Kras-driven lung adenocarcinoma of mice intranasally treated with 2.37 mg/kg Omomyc or vehicle (10 mM sodium acetate pH 6.5) for three days.
KRasLSL-G12D/+ mice were treated with Omomyc by intranasal administration sixteen weeks after Adeno-Cre infection. Mice (n=2 for vehicle treated and n=3 for Omomyc treated group) were euthanized three days post-treatment and lung tumors were excised and frozen at -80ºC until processing.

overall_design: Two control (vehicle) samples and three treated (Omomyc) samples were analized.


title: Gene expression of ulcer-associated cell lineage

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

summary: We applied RNA-seq analysis of total RNA isolated from laser capture microdissected intestinal epithelium. The analysis aimed at charactericing the gene expression seen in ulcer-associated cell lineage epithelial cells, and to contrast this with that of healthy control epithelium and epithelium from inflammatory bowel disease-patients with active inflammation.

overall_design:
The epithelial monolayer from six patients with active Crohn's disease (CD) with ulcer-associated cell lineage (UACL) and seven healthy controls were included in the final analysis. Both UACL and non-UACL epithelium was isolated from the CD patients, bringing the total sample pool up to 19.

***Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data.

first: Silje

last: Thorsvik

last: van Beelen Granlund


title: Effect of Omomyc treatment on lung adenocarcinoma of KRasLSL-G12D/+ transgenic mouse and human lung adenocarcinoma cell lines

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


title: The small non-coding RNA landscape of prostate epithelium

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Vitamin D, a hormone that acts through the nuclear vitamin D receptor (VDR), upregulates anti-tumorigenic microRNA in prostate epithelium. This may contribute to the lower levels of aggressive prostate cancer (PCa) in patients with high serum vitamin D. Expression of other small non-coding RNAs (ncRNAs) in prostate epithelium and their potential regulation by vitamin D are uncharacterized. Laser capture microdissection (LCM) followed by small-RNA sequencing was used to identify ncRNA in the prostate epithelium of tissues from a vitamin D-supplementation trial. We compared the expression profiles to small-RNA sequencing data from primary prostate epithelial cells and publically-available benign whole prostate. Application of LCM to isolate epithelium promoted sample homogeneity and captured more diversity in ncRNA species. An abundance of PIWI-interacting RNAs (piRNAs) was detected in normal prostate epithelium, which increased under high vitamin D conditions.

overall_design: Small RNA from benign epithelium of four control prostates and four prostates containing a high concentration of vitamin D was sequenced. Small RNA from one primary prostate epithelial cell line treated with ethanol or 50 nM vitamin D (1,25D) was also sequenced.

first: Giovanni

last: Lugli

first: Bethany

last: Baumann

first: Shang

last: Gao


title: Analysis of the messenger RNAs in Spores of Bacillus subtilis

city: Farmington

first: Peter

last: Setlow

state: CT

address: 263 Farmington Ave.

department: MBB

institute: UConn Health

summary: Using RNA-seq, we cataloged messenger RNAs in highly purified dormant Bacillus subtilis spores prepared either on plates or in liquid. Almost all of the most abundant spore mRNAs are encoded by genes expressed only in the developing spore late in sporulation under control of the forespore-specific RNA polymerase sigma factor, sG. Given the levels of the ~40 most abundant mRNAs in dormant spores, we calculated the great majority of the low abundance mRNAs can be present in only a small fraction of the spore population.

overall_design: Examination of highly purified spores from B. subtilis strain PS533, a laboratory 168 derivative that contains plasmid pUB110. Dormant spores were prepared either on plates or in liquid.

first: George

last: Korza

first: Melissa

last: Caimano


title: MicroRNA expression in IDG-SW3 cells treated with or without E2

city: Bunkyo-ku

first: Mikihito

last: Hayashi

state: Tokyo

address: 1-5-45 Yushima

department: Graduate School of Medical and Dental Sciences

institute: Tokyo Medical and Dental University

summary: We examined a global miRNA expression in E2-treated osteocytic IDG-SW3 cells to identify miRNA(s) involved in Sema3a expression.

overall_design: IDG-SW3 cells were treated with or without 10–7M E2.

first: Tomoki

last: Nakashima

first: Hiroshi

last: Takayanagi


title: Whole transcriptome sequencing of HOPX-depleted neonatal human keratinocytes

city: La Jolla

first: Bryan

last: Sun

address: 9500 Gilman Drive MC 0869

institute: UC San Diego

summary: The goal was to determine genes controlled by HOPX in differentiated human keratinocytes by comparison of HOPX-depleted vs. control keratinocyte transcriptomes

overall_design: Primary keratinocytes were infected with non-targeting short hairpin RNA (shCTRL) or HOPX-targeting short hairpin RNA (shHOPX), then differentiated in culture for 6 days before collection of RNA and sequencing. Each control and HOPX-knockdown was performed in triplicate, for a total of 6 samples.

middle: K

first: Selena

middle: Y

last: Chen


title: Cyp2b-null male mice are susceptible to high-fat diet-induced obesity due to changes in PUFA metabolism and response to hepatic lipids as measured by RNAseq

city: Clemson

first: William

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

summary: To investigate the role of CYP2B in lipid metabolism, a Cyp2b triple knockout mouse lacking Cyp2b9, Cyp2b10, and Cyp2b13 was developed using CRISPER/Cas9. Wildtype (WT) and Cyp2b-null mice were fed a normal diet (ND) or a 60% high-fat diet (HFD) for 10 weeks. RNA was extracted from the livers of male and female mice from all treatment groups and used for RNA seqencing. RNAseq data demonstrated that hepatic gene expression in ND-fed Cyp2b-null male mice is similar to HFD-fed WT mice, indicating that Cyp2b-null male mice are reacting as if they are receiving a HFD even if they are not. Gene ontology and KEGG pathways show perturbations in lipid metabolism pathways, including PUFA metabolism, fatty acid elongation, and glycerophospholipid metabolism.

overall_design: Use RNA-sequencing to investigate the role of Cyp2b in hight-fat diet-induced obesity on a transcriptomic level, by comparing the livers of WT and Cyp2b-null mice fed a HFD for 10 weeks using Illumina technology.

last: Heintz

first: Rooksana

middle: E

last: Noorai


title: Effect of metformin on 24 hour culture of SLE CD4 T cells and Healthy Control CD4 T cells

city: Gainesville

first: Laurence

last: Morel

address: 1395 Center Drive, D6-6

department: Pathology and Immunology

institute: University of Florida

type: Expression profiling by genome tiling array

summary: Investigate the effect of 1.0 mM Metformin on CD4 T cells from Systemic Lupus Patients and compare to Healthy Control CD4 T cells

overall_design: Peripheral blood CD4+ T cells from 5 female Systemic Lupus patients of varying disease activity, and 5 healthy controls were cultured in cRPMI. CD4 T cells were isolated by Rosette Sep (Stem Cell) antibodies and ficoll-paque centrifugation. These antibodies deplete CD8, CD16, CD19, CD36, CD56, CD66b, gamma/delta TCRs. Cells were cultured in 24 well plates for 24 hours in paired conditions for each donor: plate bound CD3 antibody and soluble CD28 for stimulated in complete RPMI media, each donor treated with 1.0mM Metformin or untreated. After culture. cells were lysed in buffer RLT (Qiagen) with 0.1% 2-mercaptoethanol and stored at -80C until further isolation with Qiagen RNeasy mini kit. RNA was quantified with a Biotek Epoch spectrophotometer and 200 ng of each sample was used for fragmenting and labeling synthesized dsCDNA according to Thermo Fisher instructions for HTA 2.0 microarrays. Scanning was performed with GeneChip Scanner 3000 7G, washing and staining with the GeneChip  Fluidics Station 450.

first: Cecilia

last: Lopez

first: Henry

middle: V

last: Baker

first: Anton

last: Titov


title: Maternal Nematode Infection Up-regulates Expression of Genes Associated with Long-Term Potentiation in Brains of Uninfected Pups

city: Sainte Anne de Bellevue

first: Manjurul

last: Haque

state: Quebec

address: Institute of Parasitology, Mac campus

department: Institute of Parasitology

institute: McGill University

summary: Pregnant mice were infected with Heligmosomoides bakeri nematode on gestation day 7, 12 and 17 and on postnatal day 3. Pup brain were collected on postnatal day 2 and 7 and sequenced in illumina HiSeq4000 PE100 sequencing lane

overall_design: Control vs infection in two different time points

first: Kristine

middle: G

last: Koski

first: Marilyn

last: Scott


title: Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)

city: Grenoble

first: Christel

last: Carles

state: Auvergne/Rhone Alpes

address: 17 rue des Martyrs, bât. C2

department: Laboratoire Physiologie Cellulaire Végétale (LPCV)

institute: University Grenoble Alpes

summary: Two methods Fluorescence Activated Cell Sorting (FACS) and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) are combined to analyse the chromatin accessibility of Lateral Organ Founder Cells (LOFCs) in the peripheral zone of the apetala1 cauliflower double mutant Arabidopsis inflorescence meristem. Genome-wide we observed a striking correlation between Transposase Hypersensitive Sites (THS) detected in ATAC-seq and DNase I Hypersensitive Sites (DHS), covering mostly extended regions substructured into several individual THS that correspond to phylogenetically conserved sequence, enhancer elements and binding sites of MADS-box transcription factors. Relative to available RNA-seq data, chromatin configuration changes according to gene activation or repression, i.e. at cellular resolution chromatin regions gain or lose Tn5 transposase accessibility in direct correlation with gene expression levels. A pronounced THS priority immediately upstream of the transcription start and reduced numbers of THSs in the transcription unit are complementary to established H3K4me3 activation or H3K27me3 repressive marks. At this resolution, the FACS/ATAC-seq combination should be widely applicable to detect chromatin changes in course of cell type specification and facilitate the detection of regulatory promoter elements in plant promoters.

overall_design: Examination of chromatin accessibility via ATAC-seq in Lateral organ founder cells and non founder cell neighbours. Three biological replicates were performed for each cell type. Two control samples of sheared DNA from the same tissue were sequenced.

first: Anneke

last: Frerichs

first: Julia

last: Engelhorn

first: Janine

last: Altmueller

first: Jose

last: Gutierrez-Marcos

first: Wolfgang

last: Werr


title: Dengue virus-specific CD8 T cell subsets are associated with specialized gene expression profiles and TCR repertoires

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Accumulating evidence demonstrates that CD8 T cells contribute to protection from severe DENV disease and vaccine efficacy. Nevertheless, the molecular programs associated with DENV-specific CD8 T cell subsets have not been defined. Here, we studied the transcriptomic profiles of human DENV-specific CD8 T cells isolated after stimulation with DENV epitopes from donors that have been infected with DENV multiple times and should therefore associated with significant levels of adaptive immunity. DENV-specific CD8 T cells mainly consist of effector memory subsets, namely Tem and Temra which enact specific gene expression profiles upon stimulation with cognate antigens. DENV-specific CD8 T cell subsets in general, and Temra cells in particular, are fully activated and polyfunctional, yet associated with relatively narrow transcriptional responses and TCR repertoires. This study provides the first transcriptomic definition of DENV-specific activated human CD8 T cell subsets and defines a bench mark profile that vaccine-specific response could aim to reproduce.

overall_design: RNA-sequencing of sorted unstimulated and dengue virus epitopes-stimulated IFN-gamma+ CD8 Tem and Temra cells from cryopreserved PBMC of 6 subjects with secondary dengue infection.

first: Grégory

last: Seumois

first: Shu

last: Liang

first: Rashika

middle: N

last: Tennekoon

first: Aruna

middle: D

last: De Silva

first: Pandurangan

last: Vijayanand

first: Daniela

last: Weiskopf

first: Bjoern

last: Peters

first: Alessandro

last: Sette


title: The RNA helicase UPF1 associates with mRNAs cotranscriptionally

city: Birmingham

first: Anand

middle: Kumar

last: Singh

state: West Midlands

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: UPF1 is an ATP-driven RNA helicase required for efficient nonsense mediated mRNA decay in eukaryotes. Although it is currently understood that UPF1 primarily acts on the 3’UTR of translating mRNAs in the cytoplasm, our data indicates that this is a highly dynamic protein that is rapidly shuttling between nucleus and cytoplasm in Drosophila. Additionally, ChIP-seq analysis in different cell types demonstrates genome-wide association of UPF1 with nascent RNAs at most of the active Pol II transcription sites, and at some specific Pol III genes. Notably, intron recognition appears to interfere with association and translocation of UPF1 on nascent transcripts. Cells depleted of UPF1 show defects in nuclear processes such as mRNA export and transcription site retention. These data, thus redefine UPF1 as a global player in mRNA based processes in the nucleus as well as the cytoplasm.

overall_design: Refer to individual Series


title: Nascent RNA and Poly(A) RNA Seq from S2 cells [RNA-seq]

summary:
Nascent RNA and Poly(A) RNA Seq from S2 cells
UPF1 is an ATP-driven RNA helicase required for efficient nonsense mediated mRNA decay in eukaryotes. Although it is currently understood that UPF1 primarily acts on the 3’UTR of translating mRNAs in the cytoplasm, our data indicates that this is a highly dynamic protein that is rapidly shuttling between nucleus and cytoplasm in Drosophila. Additionally, ChIP-seq analysis in different cell types demonstrates genome-wide association of UPF1 with nascent RNAs at most of the active Pol II transcription sites, and at some specific Pol III genes. Notably, intron recognition appears to interfere with association and translocation of UPF1 on nascent transcripts. Cells depleted of UPF1 show defects in nuclear processes such as mRNA export and transcription site retention. These data, thus redefine UPF1 as a global player in mRNA based processes in the nucleus as well as the cytoplasm.

overall_design: Nascent RNA were isolated from Histone-DNA-Pol II-RNA fraction of S2 cells and poly(A) RNA were isolated from cytoplasmic fraction of S2 Cells. Sequencing was performed using  sequenced by using Illumina HiSeq4000.

first: Saverio

last: Brogna


title: Next Generation Sequencing Facilitates Quantitative Analysis of  E. coli K-12 LE392,  P. putida KT2440, and RP4 plasmid Transcriptomes under triclosan exposure

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

summary: The goals of this study are to use Next-generation sequencing (NGS)to detect bacterial mRNA profiles of  E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid in response to 0, 0.02, 20 and 2000 μg/L triclosan for 2 h, in duplicate, using Illumina HiSeq 2500.The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp. The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.

overall_design: Bacterial mRNA profiles of E. coli K-12 LE392  in response to 0, 0.02, 20 and 2000 μg/L triclosan for 2 h, in duplicate, using Illumina HiSeq 2500

first: Ji

last: Lu

first: Yue

last: Wang

first: Likai

last: Mao


title: Pro-viral miRNAs are detected in BALF extracellular vesicles of patients with influenza virus-induced ARDS

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

institute: Philipps University Marburg

summary: Influenza A virus (IAV) causes severe respiratory infections and alveolar epithelial damage resulting in acute respiratory distress syndrome (ARDS). Extracellular vesicles (EV) have been shown to mediate cellular crosstalk in inflammation by transfer of microRNAs. In this study, we found significant changes in the miRNA composition of EVs in the broncho-alveolar lavage fluid (BALF) from patients with IAV-induced ARDS. Among the nine significantly deregulated microRNAs, miR-17-5p was upregulated in patients` BALF and in EVs of IAV-infected lung epithelial cells (A549). In these cells, transfer of miR-17-5p strongly downregulated expression of the antiviral factor Mx1 and significantly enhanced IAV replication.

overall_design:
A549 cells were routinely cultured in RPMI1640 with 10% FCS. Cells were infected with Influenza H1N1 (A/Memphis/14/96, A/WSN/33) for 12 hours with an MOI of 0.1 and 5. RNA was isolated from biological triplicates by phenol/chloroform extraction. miR-ath-159a was spiked in for later normalization.
400 ng RNA per sample were then reverse transcribed with the Life Technologies miR RT kit with megaplex primers. Reverse transcribed RNA was then loaded on the human Taqman Low Density Array (TLDA) Cards and run according to manufacturer´s recommendations
Uninfected A549 cells were used as control to evaluate the impact of infection. microRNA expression was normalized to spiked-in miR-ath-159a

first: Nicoletta

last: Scheller


title: Systematic identification of human SNPs affecting regulatory element activity

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

institute: Netherlands Cancer Institute

summary: Most of the millions of single-nucleotide polymorphisms (SNPs) in the human genome are non-coding, and many overlap with putative regulatory elements. Genome-wide association studies have linked many of these SNPs to human traits or to gene expression levels, but rarely with sufficient resolution to identify the causal SNPs. Functional screens based on reporter assays have previously been of insufficient throughput to test the vast space of SNPs for possible effects on enhancer and promoter activity. Here, we have leveraged the throughput of the SuRE reporter technology to survey a total of 5.9 million SNPs, including 57% of the known common SNPs world-wide. We identified more than 30 thousand SNPs that alter the activity of putative regulatory elements, often in a cell-type specific manner. These data indicate that a large proportion of human non-coding SNPs may affect gene regulation. Integration of these SuRE data with genome-wide association studies may help to identify causal SNPs.

overall_design: SuRE-seq assays with 8 libraries obtained from four heterozygous genomes from the 1000-genome project, each in 2 biological replicates. Each library is transfected in K562, using 3 biological replicates, and in HepG2 cell-lines, using 2 biological replicates.

first: Joris

last: van Arensbergen

first: Ludo

last: Pagie

first: Marcel

last: de Haas


title: WT and Hira-null undifferentiated mESCs and day15 differentiated cardiomyocytes

city: London

first: Rasha

middle: Noureldin

last: Saleh

address: 30 Guilford street

institute: University College London

summary: Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) resulting from the knockout of Hira in undifferentiated mouse embryonic stem cells (mESCs) and in day 15 differentiated cardiomyocytes.Methods: RNA extraction was done in duplicate from WT and Hira-null mESCs at day0 and day15 using TRIzol reagent. RNAseq was done onIllumina Nextseq500 and processed by the ICH genomics facility, reads were aligned and normalised using BOWTIE and DEseq R2 package. Gene lists were filtered using adjusted p-value ≤ 0.05 and absolute fold change ≥ 2. Results:We identified 1680 transcripts changed in the absence of HIRA in day 15 differentiated cardiomyocytes. GO term cardiovascular system development was the most downregulated gene set(p-value ≤ 0.01 and FDR ≤0.1. Conclusion: this study analysis the role of HIRA in early cardiac mesoderm development usinf an invitro mESCs  model.

overall_design: mRNA profile of WT(control) and Hira-null (KO) undifferentiated mESCs and mESCs- derived cardiomyocytes at day15 were generated by deep sequencing in duplicates using Illumina Nextseq 500 platform.

first: Tony

last: Brooks

first: Ariane

last: Chapgier

first: Peter

last: Scambler