title: Hippo Pathway Regulates Microarchitecture of Fibroblastic Reticular Cells in Lymph Node

city: Irvine

first: Hosung

last: Bae

address: 839 Health Sciences Road Sprague Hall, Room 150

institute: UC Irvine

summary: To unveil the role of Hippo signaling in regulating the maintenance and integrity of FRCs in LNs.

overall_design:
FRCs were sorted from models deleting Yap/Taz to inhibit hippo pathway, and deleting Lats1,2 to activate hippo pathway in FRC specific manner.
We generated [1] FRC-driven Lats1/2 depleted mouse by crossing the PDGFRβ-Cre-ERT2 mouse with Lats1(flox/flox)/Lats2(flox/flox) mouse [2] FRC-driven Yap/Taz depleted mouse by crossing the FRC-specific CCL19-Cre mouse and the double Yap(flox/flox)/Taz (flox/flox) mouse.
Lgr5+ stem cells in dermis were FACS-purified and used for ATAC-seq to explore Yap/Taz driven changes in chromatin accessibility

first: Goh

middle: Y

last: Koh

first: Myung Jin

first: Da-Hye

last: Lee


title: Time-course transcriptomic analysis of Arabidopsis response to high light stress

status: Public on Dec 17 2019

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Biology Laboratory

country: USA

institute: Salk Institute for Biological Studies

type: Expression profiling by high throughput sequencing

summary: Analysis of transcriptome profile response to short-, middle- and long-term high light stress, as well as the transcriptome profile of recovery from high light stress.

overall_design: Total RNA samples were isolated from 7-day old whole seedlings with or without high light treatment for 0.5h, 6h, 12h, 24h, 48h and 72h. Recovery samples were collected after 14 h recovery in growth light condition following 72 h high light treatment. Each time course has duplicates. mRNA expression profiles were generated by deep sequencing using Illumina HiSeq 2500.

first: Jianyan

last: Huang

first: Xiaobo

last: Zhao


title: Transcriptional analysis of tendons from rat

status: Public on Dec 18 2019

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

summary: We report RNA sequencing data from the Achilles, patellar, supraspinatus, and forepaw flexor tendons of adult male rats in the Sprague-Dawley

overall_design: Differential expression of mRNAs were evaluated between each of the 4 different tendons


title: Transcriptomic, epigenetic and functional analyses implicate neutrophil diversity in the pathogenesis of systemic lupus erythematosus [scRNA-seq]

status: Public on Dec 13 2019

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Two subpopulations of low density granulocytes (LGDs) were defined in terms of different gene expression patterns, transcriptional and epigenetic features as well as functions.  This study provides insights into the mechanism of immune dysregulation and the vascular damage characteristic of lupus.

overall_design: This dataset includes 3 scRNA samples, which belong to the super series GSE139360. Transcriptomics and epigenetic assessment of lupus PBMCs, LDGs, autologous normal-density neutrophils (NDN) and healthy control (HC) neutrophils was performed by mRNA sequencing, single cell RNAseq and assay for transposase-accessible chromatin sequencing. NET formation, chemotaxis, phagocytosis, degranulation, induction of endothelial dysfunction and release of oxidized nucleic acids were compared among subsets.

first: P

last: Mistry

first: S

last: Nakabo

first: L

last: O’Neil

first: R

middle: R

last: Goel

first: K

last: Jiang

last: Gupta

last: Dell’Orso

first: G

last: Gutierrez-Cruz

first: H

middle: W

first: M

middle: J

last: Kaplan


title: Expression data from control or conditional Oc-deficient embryonic motor neurons

city: Brussels

first: Frederic

last: Clotman

address: avenue Hippocrate, 55 boxB1.55.11

department: Institute of Neuroscience

country: Belgium

institute: UCLouvain

summary: In the embryonic spinal cord, motor neurons diversify into different subsets characterized by distinct molecular identity, localization and connectivity. However, the factors that control MN diversification remain poorly known. To identify genes downstream of Onecut transcription factors in motor neurons that may contribute to motor neuron diversification, we performed a RNA-sequencing comparison of control and of OC-deficient motor neuron transcriptome at embryonic day 10.5.

overall_design: 5 control and 5 Oc-deficient embryonic motor neurons

first: Mathilde

last: Toch

first: Frédéric


title: PDGFRA Defines the Mesenchymal Stem Cell Kaposi’s Sarcoma Progenitors by Enabling KSHV Oncogenesis in an Angiogenic Environment

status: Public on Dec 12 2019

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: PDGFRA Defines the Mesenchymal Stem Cell Kaposi’s Sarcoma Progenitors by Enabling KSHV Oncogenesis in an Angiogenic Environment [RNA-seq]

summary: Kaposi’s sarcoma (KS) is an AIDS-defining cancer caused by the KS-associated herpesvirus (KSHV). Unanswered questions regarding KS are its cellular ontology and the conditions conducive to viral oncogenesis. We identify PDGFRA(+)/SCA-1(+) bone marrow-derived mesenchymal stem cells (Pα(+)S MSCs) as KS spindle-cell progenitors and found that pro-angiogenic environmental conditions typical of KS are critical for KSHV sarcomagenesis. This is because growth in KS-like conditions generates a de-repressed KSHV epigenome allowing oncogenic KSHV gene expression in infected Pα(+)S MSCs. Furthermore, these growth conditions allow KSHV-infected Pα(+)S MSCs to overcome KSHV-driven oncogene-induced senescence and cell cycle arrest via a PDGFRA-signaling mechanism; thus identifying PDGFRA not only as a phenotypic determinant for KS-progenitors but also as a critical enabler for viral oncogenesis.

overall_design: We designed a novel model of “de novo” KSHV oncogenesis based on infection of PDGFRA-positive mesenchymal stem cell progenitors cultured in pro-angiogenic/vasculogenic KS-like growth conditions. This system serves as a unique and robust platform to identify KSHV oncogenic-pathways and their relationship with cellular lineages and extracellular growth environments. Additionally, it can further be exploited to genetically dissect and elucidate viral, host-cell and environmental features of KS pathobiology.

first: E

middle: A

last: Mesri

first: J

last: Naipauer

middle: C


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism: Liver RNA profiles of mice injected with control, Mafg and LncIRS2 LNA.

city: Odense

first: Jan

middle: Wilhelm

last: Kornfeld

address: Campusbej 50

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

summary: Obesity and type 2 diabetes mellitus are global emergencies and long noncoding RNAs (lncRNAs) are regulatory transcrips with elusive functions in metabolism. Here we report that an unexpectedly high fraction of lncRNAs, but not protein-coding mRNAs, is repressed during diet-induced obesity (DIO) and refeeding, whilst nutrient deprivation specifically induced lncRNAs in mouse liver. Similarly, lncRNAs were lost in diabetic humans. LncRNA promoter analyses, global cistrome and gain-of-function analyses confirmed that increased MAFG signaling during DIO curbs lncRNA expression. Silencing Mafg in primary hepatocytes and in vivo elicited a fasting-like expression profile, improved glucose metabolism, derepressed lncRNAs and prevented mammalian target of rapamycin (mTOR)-driven protein translation. We found that obesity-repressed lincIRS2 is controlled by MAFG and observed that genetic and RNAi-mediated lincIRS2 loss causes hyperglycemia, insulin resistance and aberrant glucose output in lean mice. Taken together, we identify a novel MAFG-lncRNA axis controlling hepatic glucose metabolism in health and metabolic disease.

overall_design: Liver RNA profiles of 18-week-old mice injected with control, Mafg and LncIRS2 LNA respectively, were generated by deep sequencing, in four replicates on Illumina HiSeq 4000.

first: Marta

last: Pradas-Juni

first: Nils

last: Hansmeier

first: Jenny

last: Link

first: Elena

last: Schmidt

first: Paul

last: Klemm

first: Eduardo

last: Fernandez-Rebollo

first: Rute

last: Loureiro

first: Ines

last: Dhouadi

first: Christoph

last: Kiefer

first: Bjørk

middle: D

last: Larsen

first: Robin

last: Schwarzer

first: Sajjad

last: Khani

first: Matteo

last: Oliverio

first: Hande

last: Topel

first: Motoharu

last: Awazawa

first: Peter

last: Frommolt

first: Jörg

last: Heeren

first: Ludger

last: Scheja

last: Dieterich

first: Hildegard

last: Büning

first: Ling

last: Yang

first: Haiming

last: Cao

first: Dario

middle: F

last: De Jesus

first: Rohit

middle: N

last: Kulkarni

first: Branko

last: Zevnik

first: Simon

middle: E

last: Tröder

first: Uwe

last: Knippschild

last: Edwards

first: Richard

middle: G

last: Lee

first: Masayuki

last: Yamamoto

first: Thomas

middle: Q

last: de Aguiar Vallim

first: Jan-Wilhelm


title: Studying the selectivity of a small molecule Synucleozid on transcriptome

status: Public on Dec 11 2019

city: JUPITER

first: Peiyuan

last: Zhang

state: FL

address: 110 Scripps Way

institute: TSRI

summary: One strategy to drugging undruggable proteins is to directly target the mRNA that encodes them, thereby inhibit translation and reducing protein levels. Inforna, a sequence-based design approach to target RNA, enables the design of a small molecule Synucleozid that binds SNCA mRNA which encodes alpha-synuclein.  Herein, we investigate the selectivity of Synucleozid on the whole transcriptome. Based on mechanistic studies, Synucleozid targets IRE locates in 5' UTR of SNCA mRNA and reduces alpha-synuclein protein levels by decreasing the amount of SNCA mRNA loaded into polysomes. Different from alpha-synuclein siRNA, Synucleozid binds mRNA and affect its function without regulating mRNA expression.

overall_design: Examination of small molecule-treated (Synucleozid) vs vehicle-treated (DMSO Vehicle) and alpha-synuclein siRNA-treated vs Scramble siRNA-treated SH-SY5Y cells in biological triplicates.

first: Hye-Jin

last: Park

first: Jie

first: Eunsung

last: Junn

first: Ryan

last: Andrews

first: Sai Pradeep

last: Velagapudi

first: Daniel

last: Abegg

first: Kamalakannan

last: Vishnu

first: Matthew

last: Costales

first: Jessica

last: Childs-Disney

first: Alexander

last: Adibekian

first: Walter

last: Moss

first: Maral

middle: M

last: Mouradian

last: Disney


title: Single-cell molecular and cellular architecture of neurohypophyseal cell types in adult mouse

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: The neurohypophysis (NH), located at the posterior lobe of the pituitary, is a major neuroendocrine tissue, which mediates osmotic balance, blood pressure, reproduction, and lactation by means of releasing the neurohormones oxytocin and arginine-vasopressin from the brain into the peripheral blood circulation. The major cellular components of the NH are hypothalamic axonal termini, fenestrated endothelia and pituicytes, the resident astroglia. However, despite the physiological importance of the NH, the exact molecular signature defining neurohypophyseal cell types and in particular the pituicytes, remains unclear. Using single cell RNA sequencing, we captured seven distinct cell types in the NH and intermediate lobe (IL) of adult male mouse. We revealed novel pituicyte markers showing higher specificity than previously reported markers. Multiplexing single molecule in situ hybridization revealed spatial organization of the major cell types implying intercellular communications. We present a comprehensive molecular and cellular characterization of neurohypophyseal cell-types serving as a valuable resource for further functional research.

overall_design: 2 pools of 5 dissected neurohypophyses from 3-month-old male C57/BL6 mice were prepared for 10x Chromium single-cell RNA-Seq

first: Qiyu

last: Chen

first: Janna

last: Blechman

first: Gil

last: Levkowitz


title: JAK inhibition differentially affects NK cell and ILC1 homeostasis

first: Stephen

last: Brooks

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: We report the application of single-molecule-based RNA sequencing technology for comparing the transcriptome profile in splenic NK and hepatic ILC1 sorted from mice treated or not via oral gavage for 1 week with tofacitinib

overall_design: samples: sorted splenic NK and liver ILC1 cells from mice treated or not with tofacitinib

first: Laura

last: Vian

first: Massimo

last: Gadina


title: RNA sequencing of sorted immune cells from WT and CD4Cre-Yapfloxed mice from tumors and tumor-draining lymph nodes

city: Baltimore

first: Gregory

middle: Lee

last: Szeto

address: 1000 Hilltop Circle, ILSB room 415

institute: UMBC

summary: We report the effect of T cell lineage-specific Yap deletion on tumor immunity in the B16F10 melanoma mouse model.

overall_design: Differential expression analysis of genes from 3 immune cell subsets in 2 tissue sites in WT or CD4Cre Yap flox mice.

first: Xaralabos

last: Varelas

first: Elena

last: Stampougoulou


title: RNA-seq analysis of human WI-38 fibroblast cell line treated with a chalcone that promotes resistance to oxidative stress

status: Public on Dec 10 2019

city: South San Francisco

first: Peichuan

last: Zhang

address: 1070 Veterans Blvd

institute: Calico Life Sciences

summary: We have identified through high-throughput screen a number of small molecules that promote resistance of human WI-38 cells to hydrogen peroxide.  To look into potential mechanism of action for a chalcone hit, we analyzed transcriptional profile by RNA-seq for WI-38 cells treated with this molecule.

overall_design: WI-38 cells were treated with 10uM chalcone (namely, Gr-4D from two different vendors, CB=ChemBridge, MP=MolPort) for 24 hours.  Total RNA was isolated using the RNeasy kit (Qiagen) and used to prepare library (TruSeq Stranded mRNA poly A) for RNA-seq analysis (HiSeq 4000).

first: Cynthia

last: Kenyon


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism:  Liver RNA seq profiles of mice fed different feeding regimes.

first: Jan

last: Kornfeld

overall_design: Liver RNA profiles of 17-week-old mice fed different feeding regimes were generated by deep sequencing, in four replicates on Illumina HiSeq 4000.

first: Marta

last: Pradas-Juni

first: Nils

last: Hansmeier

first: Jenny

last: Link

last: Schmidt

first: Paul

last: Klemm

first: Eduardo

last: Fernandez-Rebollo

first: Rute

last: Loureiro

first: Ines

last: Dhouadi

first: Christoph

last: Kiefer

first: Bjørk

last: Larsen

first: Robin

last: Schwarzer

first: Sajjad

last: Khani

first: Matteo

last: Oliverio

first: Hande

last: Topel

first: Motoharu

last: Awazawa

first: Peter

last: Frommolt

first: Jörg

last: Heeren

first: Ludger

last: Scheja

last: Dieterich

first: Hildegard

last: Büning

first: Ling

last: Yang

first: Haiming

last: Cao

first: Dario

last: De Jesus

first: Rohit

last: Kulkarni

first: Branko

last: Zevnik

first: Simon

last: Tröder

first: Uwe

last: Knippschild

last: Edwards

first: Richard

last: Lee

first: Masayuki

last: Yamamoto

first: Thomas

last: de Aguiar Vallim

first: Jan-Wilhelm


title: Transcriptional analysis effect of excess sugar and lipid on the growth and development of Caenorhabditis elegan

city: Beijing

first: Xiong

last: Wang

address: No. 17, Qinghua East Road, Haidian District, Beijing

department: College of Food Science and Nutritional Engineering

country: China

institute: China Agricultural University

summary:
Purpose：We used transcriptome sequencing to study the mechanism of sugar and lipid excesses on nematode growth and development.
Methods：Nematodes grew to L4 phase and collected nematodes from different treatment groups, including control group without any treatment, 400 mM sucrose, 500 ug/ml stearic acid, co-treatment with sucrose and stearic acid, and co-treatment with resveratrol-sucrose-stearic acid, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data
Results:Reads were obtained for each sample using Illumina Hiseq X Ten sequencing. After discarding the low-quality reads, corresponding to 48 million clean reads obtained from sequencing were mapped on the reference genome of C. elegans (GCF_000002985.6). High Pearson's correlation coefficients of FPKM distribution between the three biological replicates for each sample were detected (R2 = 0.93-0.99, P < 0.001) , reflecting the robustness of our library preparation from nematodes’ RNA samples.Compared with control group, there were 905 DEGs in the sucrose group , of which 387 genes were upregulated and 518 genes were downregulated. Similarly, there were 698 DEGs in the stearic acid group , including 367 upregulated and 331 downregulated DEGs.  Compared with control group, there were 1014 DEGs in group SUC-STE, including 476 upregulated DEGs, and 538 downregulated DEGs. Moreover, in contrast to the sucrose-stearic acid group, there were 10 DEGs after treated with resveratrol, including 5 upregulated DEGs and 5 downregulated DEGs.

overall_design: Deep-sequencing using Illumina, in triplicate, yielded L4 stage nematode mRNA expression profiles without treatment, sugar and lipid treatment alone, sugar and lipid co-treatment, and resveratrol-sugar-lipid co-treatment.

first: Lin

last: Zhang


title: AKAP8 inhibits tumor metastasis by antagonizing EMT-associated RNA alternative splicing

city: Houston

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: Tumor metastasis is the most lethal attribute of breast cancer, and the epithelial-mesenchymal transition (EMT) plays an important role in this process. Alternative splicing has been shown to causally contribute to EMT; however, the scope of critical splicing events and the regulatory network of splicing factors that govern them remain largely unexplored. Here we report the identification of A-Kinase Anchor Protein (AKAP8) as an EMT splicing regulatory factor that impedes EMT and breast cancer metastasis. AKAP8 not only is capable of inhibiting splicing activity of the EMT-promoting splicing regulator hnRNPM through protein-protein interaction, it also binds to RNA directly and alters splicing outcomes. Genome-wide analysis revealed that AKAP8-mediated splicing events, specifically in epithelial cells, are reversely regulated during EMT, suggesting that AKAP8 maintains an epithelial cell-state splicing program. Experimental manipulation of a newly identified AKAP8 splicing target calsyntenin-1 (CLSTN1) revealed that splice isoform switching of CLSTN1 is crucial for EMT. Mining breast cancer patient data supports the experimental findings and AKAP8 expression and the alternative splicing of CLSTN1 predict patient survival. Our work demonstrates the essentiality of RNA metabolism that impinges on metastatic breast cancer.

overall_design: PolyA-RNA-sequencing of control and AKAP8  knockdown cell lines. Single end enhanced crosslinking and immunoprecipitation sequencing libraries for AKAP8 and input samples

first: Chonghui

last: Cheng

first: Rong

last: Zheng


title: Small RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants (sRNA-Seq)

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

type: Non-coding RNA profiling by high throughput sequencing

summary: PIWI-interacting RNAs (piRNAs) promote fertility in many animals. Yet, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets, but rather mediated by the epigenetic silencing of all the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway restores histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that the sRNA-mediated silencing of histone genes impairs fertility of piRNA mutants and may serve to maintain piRNAs across evolution.

overall_design: 25 samples were analyzed by sRNA-seq, including replicates in some cases (sample name contains 'rep'). For the experiments using worms at different generation time independent CRISPR-Cas9 lines were analyzed as replicates (sample name contains 'line')

first: Giorgia

last: Barucci

first: Eric

last: Cornes

first: Meetali

last: Singh

first: Blaise

last: Li

first: Martino

last: Ugolini

first: Aleksei

last: Samolygo

first: Celine

last: Didier

first: Florent

last: Dingli

first: Damarys

last: Loew

first: Piergiuseppe

last: Quarato


title: Small RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants (RNA-Seq)

overall_design: 18 samples were analyzed by RNA-seq using two replicates. For the experiment using worms at different generation time two independent CRISPR-Cas9 lines were analyzed as replicates.


title: Small RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants (sRNA-Seq IP)

overall_design: 2 IP-input paired samples were analyzed by sRNA-seq.


title: Small RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants


title: A MAFG-lncRNA axis links systemic nutrient abundance to hepatic glucose metabolism.

first: Jan

last: Kornfeld

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Cell-to-cell variation in defective virus expression and effect on host response during influenza virus infection

first: Chang

last: Wang

address: 12 Waverly Place

department: Biology

institute: New York University

summary: Virus and host factors contribute to cell-to-cell variation in viral infection and determine the outcome of the overall infection. However, the extent of the variability at the single cell level and how it impacts virus-host interactions at a systems level are not well understood. To characterize the dynamics of viral transcription and host responses, we used single-cell RNA sequencing to quantify at multiple time points the host and viral transcriptomes of human A549 cells and primary bronchial epithelial cells infected with influenza A virus. We observed substantial variability of viral transcription between cells, including the accumulation of defective viral genomes (DVGs) that impact viral replication. We show a correlation between DVGs and viral-induced variation of the host transcriptional program and an association between differential induction of innate immune response genes and attenuated viral transcription in subpopulations of cells. These observations at the single cell level improve our understanding of the complex virus-host interplay during influenza infection.

sample_organism: Influenza A virus (A/Puerto Rico/8/1934(H1N1))

overall_design: Dataset consists of 12 single-cell RNA-seq datasets generated from 10X Genomics Chromium 3' platform with v2 chemistry, 20 conventional bulk RNA-seq datasets generated with NEBNext Ultra II RNA library prep kit and poly(A) mRNA magnetic isolation module, and one viral genome sequencing dataset generated from multi-segment reverse-transcription PCR (M-RT-PCR) products followed by library preparation with Nextera DNA library prep kit.

first: Christian

middle: V

last: Forst

first: Tsui-wen

last: Chou

first: Adam

last: Geber

first: Minghui

first: Wissam

last: Hamou

first: Melissa

last: Smith

first: Robert

last: Sebra

first: Bin

last: Zhou

first: Elodie

last: Ghedin


title: Deep transcriptomic analysis of human vascular cells identifies novel risk genes for common vascular diseases

city: Philadelphia

first: Sylvia

middle: T

last: Nurnberg

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania

summary: Several genome-wide association studies have to date been carried out to identify genetic risk loci associated with vascular diseases. Many of the established common variants likely perturb the expression of disease-relevant genes within the vascular tissue itself. To identify such genes on a genome-wide level, we analyzed the transcriptome of human coronary artery smooth muscle and endothelial cells for Allele-Specific Expression (ASE).

overall_design: observation of mRNA expression in 2 different cell types from paired donor samples

first: Christopher

last: Brown

first: Thomas

last: Quertermous

first: Daniel

last: Rader


title: Expression data of Bone Marrow Derived Macrophages (BMDM) from WT and Nos2-/- mice proinflammatory activated in vitro

city: Frederick

first: Erika

last: Palmieri

address: 1050 Boyles Street BG 560 RM 31-45

institute: National Cancer Institute, NIH

summary:
Proinlfammatory stimulation of murine macrophages elicits profound metabolic changes. iNOS-derived Nitric oxide is both necessary and sufficient for the repression of OXPHOS during M1 polarization. Macrophages derived from mice lacking NOS2 display intact metabolic pathway and fail to rewire carbon fluxes. Since inflammation results in a very controlled genetic programme where specific sets of genes are up-regulated we aim to understand how this is affected in absence of this important endogenous gas responsible of the metabolic phenotype.
We used microarrays to detail the global programme of gene expression underlying proinflammatory stimulation and identified distinct classes of differentially regulated genes during this process in absence of NOS2

overall_design: WT and Nos2-/- BMDM were differentiated for 7 days and then treated with vehicle (PBS) or LPS and IFNγ for 8 hours. Total RNA was extracted from 3 different biological replicates for each group and Affymetrix Mouse Genome 430 2.0 Array was performed,

first: Marieli

last: Gonzalez-Cotto

middle: W

last: McVicar


title: Small RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants (GRO-Seq)

first: Germano

last: Cecere

overall_design: 4 samples were analyzed by GRO-seq using two replicates.

first: Giorgia

last: Barucci

first: Eric

last: Cornes

first: Meetali

last: Singh

first: Blaise

last: Li

first: Martino

last: Ugolini

first: Aleksei

last: Samolygo

first: Celine

last: Didier

first: Florent

last: Dingli

first: Damarys

last: Loew

first: Piergiuseppe

last: Quarato


title: AQP5-Expressing Cells Serve as Stem Cells and Cancer Origins in the Distal Stomach

status: Public on Dec 09 2019

city: Singapore

first: Si Hui

last: Tan

address: 8A Biomedical Grove #06-06 Immunos

country: Singapore

institute: Institute of Medical Biology

summary: Isolating adult stem cells from human stomach epithelia has proven challenging due to a lack of surface markers that are amenable to antibody-based sorting approaches. Here, through comparative expression profiling of mouse Lgr5+ adult stem cells along the gastrointestinal tract, we identify novel pylorus-specific stem cell markers, including the membrane protein Aqp5. FACS-based isolation of endogenous AQP5+ cells from healthy human pyloric stomach revealed their stem cell identity in organoid assays. Using new  Aqp5-driven CreERT2 mouse models to selectively target conditional mutations to the pyloric stem cell compartment in vivo, we establish pyloric stem cells as a major source of Wnt-driven invasive gastric cancer. The new stem cell markers and mouse models described here will be an invaluable resource for deciphering early gastric cancer formation and for isolating and characterizing human stomach stem cells as a prerequisite to potentially exploiting their regenerative medicine potential in the clinic.

overall_design: 8 paired samples of AQP5+ and AQP5- populations were collected from healthy human gastric pylori

first: Nicholas

last: Barker

first: Si

middle: H

first: Yada

last: Swathi

first: Denil

middle: S

last: Johannes


title: Spen regulates X chromosome inactivation (HiC in NPC)

first: samuel

last: Collombet

address: 46 rue d'Ulm

institute: Ecole Normale Superieure

summary: HiC on Spen-degron TX1072 clones of neural progenitor cells (NPCs). HiC in 2 biological replicates before and after. 24h of auxin treatment.

overall_design: We performed HiC in Neural progenitor cells before and after depletion of Spen.

first: Francois

last: Dossin

first: Samuel

first: Job

last: Dekker

first: Edith

last: Heard


title: PDGFRA Defines the Mesenchymal Stem Cell Kaposi’s Sarcoma Progenitors by Enabling KSHV Oncogenesis in an Angiogenic Environment [ChIP-seq]

first: Martin

middle: Carlos

last: Abba

overall_design: We designed a novel model of “de novo” KSHV oncogenesis based on infection of PDGFRA-positive mesenchymal stem cell progenitors cultured in pro-angiogenic/vasculogenic KS-like growth conditions. This system serves as a unique and robust platform to identify KSHV oncogenic-pathways and their relationship with cellular lineages and extracellular growth environments. Additionally, it can further be exploited to genetically dissect and elucidate viral, host-cell and environmental features of KS pathobiology.

first: E

middle: A

last: Mesri

first: J

last: Naipauer

first: H

middle: L

last: Chan


title: Spen regulates X chromosome inactivation (RNAseq in SPEN KO embryos)

status: Public on Dec 08 2019

summary: RNAseq on Spen KO hybrid embryos.

overall_design: We performed RNAseq in single embryos Spen KO.

first: Jan

last: Zylicz


title: Spen regulates X chromosome inactivation (RNAseq in NPC)

summary: RNAseq on Spen-degron TX1072 clones of neural progenitor cells (NPCs). RNAseq in 2 biological replicates at 3 different times of auxin treatment (0h aux, 24h aux, 48h aux).

overall_design: We performed RNAseq in Neural progenitor cells before and after depletion of Spen.


title: RNA sequencing of Schizosaccharomyces pombe cells with the replaced fatty acid synthase complex from Schizosaccharomyces japonicus

status: Public on Dec 07 2019

city: Birmingham

first: Maria

last: Makarova

address: Egbaston 32

country: United Kingdom

institute: University of Birmingham

summary: We have identified that these two organisms have quite distinct phospholipid structures - S. pombe phospholipids display canonical symmetric long acyl chains (18 and/ or 16 carbon atoms), and in S. japonicus significant fraction of phospholipids are asymmetrical  - one acyl chain is 18 carbon atoms and second one is short - only 10 carbon atoms. Medium chain fatty acid like C10:0 are critical for S. japonicus physiology and are synthesised by the cytosolic fatty acid synthase (FAS) complex.  Such findings lead us to address the functional role of these asymmetric lipids and we exchanged FAS between the two fission yeast species. We observed that in S. pombe expressing solely japonicus FAS, the membrane is functionally impaired in a  number of ways (e.g. endocytosis, mitosis etc etc) and moreover, it seems that at lower temperatures (such as 24C) the phenotype is more severe compared to the higher temperatures like 30 and 36. We believe that comparative transcriptomic analysis will shed light on what is going on in S. pombe cells with exchanged FAS and therefore displaying an altered lipidome.

overall_design: Wild type and mutant cells were grown overnight at two temperature conditions 24C and 30C until reaching exponential growth phase and subjected to RNA extraction

first: Snezhana

last: Oliferenko


title: Environmental Arginine Controls Multinuclear Giant Cell Metabolism and Formation

status: Public on Dec 06 2019

city: Vienna

first: Loan

last: Vulliard

address: Lazarettgasse 14, AKH BT25.3

country: Austria

institute: CeMM

summary: Multinucleated giant cells (MGCs) are implicated in many diseases including schistosomiasis, sarcoidosis and arthritis. Formation of MGCs is energy intensive to enforce membrane fusion and cytoplasmic expansion. Here we used receptor activator of nuclear factor kappa-Β ligand (RANKL) induced osteoclastogenesis to model MGC formation. We found amino acid (AA) scarcity controls MGC formation and reveal specific requirements for extracellular arginine in RANKL cellular programming. Systemic arginine restriction improved outcome in multiple murine arthritis models and its removal induced preosteoclast metabolic quiescence, associated with impaired tricarboxylic acid (TCA) cycle function and metabolite induction. Effects of arginine deprivation on osteoclastogenesis were independent of mTORC1 activity or global transcriptional and translational inhibition. Arginine scarcity also dampened generation of IL-4 induced polykaryons, another form of MGCs. Strikingly, in the absence of extracellular arginine, both cell types displayed flexibility as their formation could be restored with select arginine precursors. These data establish how environmental amino acids control the metabolic fate of polykaryons and suggest metabolic ways to manipulate MGC-associated pathologies and bone remodelling.

overall_design: Analysis was performed of 28 samples (7 conditions including 4 biological replicates)

first: Julia

last: Brunner

first: Gernot

last: Schabbauer

first: Stephan

last: Blüml

first: Yohai

last: Mikami

first: John

middle: J

last: O'Shea


title: Spen regulates X chromosome inactivation (RNAseq in ESCs )

first: samuel

last: Collombet

overall_design: We performed RNAseq in ESCs, before and after induction of Xist, with/without deletion of SPEN (auxin treatment).

first: Francois


title: Spen regulates X chromosome inactivation (CUT&RUN)

summary: CUT&RUN on Spen-degron TX1072 mESCs was performed in 2 biological replicates. Cells were treated with doxycycline (1ug/mL) for 0h, 4h, 8h, 24h and 8h doxycycline and auxin (500uM).

overall_design: We performed CUT&RUN against SPEN in ES after induction of Xist.

last: Dossin

first: Samuel


title: Coordination of UPR-related gene expression in early plasma cells by mTORC1

status: Public on Dec 05 2019

first: Brian

middle: Thomas

last: Gaudette

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

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

overall_design: Refer to individual Series


title: Single cell ATAC sequencing profile of quiescent mesenchymal progenitors

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

summary: After tissue injury mesenchymal progenitor subsets undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. Some of these subsets contribute enduring populations to connective tissue structures adjacent to muscle. To gain insights into gene accessibility to complement the single cell RNA seq expression data previously obtained and to uncover the lineage potential of MPs in this context, tdTomato positive cells were profiled by single cell ATAC sequencing.

overall_design: Single cell ATAC-seq analyses of enriched quiescent mesenchymal progenitors from skeletal muscle.

first: R

last: Scott

first: T


title: Transcriptomic analysis of in-vitro plasma cell generation from follicular B cells lacking Xbp1 [Xbp1_PC_stim]

summary: During plasma cell differentiation there is activation of UPR gene expression that has been termed the physiological UPR of plasma cell differentiation.  This is canonically thought to be downstream of Blimp1-mediated increases in immunoglobulin gene production and activation of the Xbp1 transcription factor by the RNA splicing activity of the ER-stress sensor IRE1α.  Having observed UPR-affiliated gene expression prior to upregulation of Blimp1 as reported in the companion linked series, we endeavored to determine the necessity of Xbp1 activity in the early remodeling of the ER in nascent plasma cells.  To this end, we mated mice harboring a floxed exon 2 of the Xbp1 gene (Xbp1flox) to mice expressing a tamoxifen-inducible cre recombinase under the control of the human CD20 promoter (hCD20-TamCre).  These mice and their hCD20-TamCre-Xbp1wt litermates were fed oral tamoxifen in their diet for two weeks and follicular B cells were prepared for in-vitro plasma cell differentiation studies.  We report here that prior to plasma cell differentiation as measured by CD138 expression, which coincides temporally with Blimp1 expression, there is no defect in UPR-affiliated gene expression in cells lacking Xbp1.

overall_design: Samples are follicular B cells from Xbp1-floxed (n=5) and Xbp1-wildtype (n=3) mice expressing tamoxifen inducible Cre under the CD20 promoter after tamoxinen treatment, stimulated in culture to produce plasma cells.  cDNA was prepared from RNA with 3' polyA capture method.  Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.

first: David

last: Allman


title: Transcriptomic analysis of in-vitro plasma cell generation from follicular B cells lacking Raptor [Raptor_PC_stim]

summary: Early UPR-affiliated gene expression occurs before Blimp1 upregulation and independent of canonical ER-stress activated Xbp1.  In linked companion studies we detailed how Xbp1-independent activation of early plasma cell specific UPR-affiliated gene expression occurs prior to Blimp1 upregulation.  Having observed that these genes overlapped with canonical mTORC1 signature genes and that PC-poised marginal zone B cells have higher base line mTORC1 signaling we designed this experiment to assess the dependence of early ER-remodeling on mTORC1 signaling in plasma cell differentiation.  To this end we mated mice harboring a floxed allele for the mTORC1 adapter Raptor (B6.Rptor-flox) to mice expressing a tamoxifen-inducible cre recombinase under the control of the human CD20 promoter (B6.hCD20-TamCre). These mice and their hCD20-TamCre-Rptor-wt litermates were fed oral tamoxifen in their diet for two weeks and follicular B cells were prepared for in-vitro plasma cell differentiation studies.  We report here that as early as 24 hours of stimulation in culture we see a marked defect in the ability of Rptor null B cells to upregulate UPR-affiliated genes associated with plasma cell differentiation.

overall_design: Samples are follicular B cells from Rptor-floxed (n=3) and Rptor-wildtype (n=3) mice expressing tamoxifen inducible Cre under the CD20 promoter after tamoxinen treatment, stimulated in culture to produce plasma cells.  cDNA was prepared from RNA with 3' polyA capture method.  Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.


title: TRPS1 acts as a context-dependent regulator of mammary epithelial cell growth/differentiation and breast cancer development [ChIP-Seq]

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

summary: The GATA-type zinc-finger transcription factor TRPS1 has been implicated in breast cancer. However, its precise role remains unclear, as both amplifications and inactivating mutations in TRPS1 have been reported. Here, we used in vitro and in vivo loss-of-function approaches to dissect the role of TRPS1 in mammary gland development and invasive lobular breast carcinoma, which is hallmarked by functional loss of E-cadherin. We show that TRPS1 is essential in mammary epithelial cells, since TRPS1-mediated suppression of interferon signaling promotes in vitro proliferation and lactogenic differentiation. Similarly, TRPS1 expression is indispensable for proliferation of mammary organoids and in vivo survival of luminal epithelial cells during mammary gland development. However, the consequences of TRPS1 loss are dependent on E-cadherin status, as combined inactivation of E-cadherin and TRPS1 causes persistent proliferation of mammary organoids and accelerated mammary tumor formation in mice. Together, our results demonstrate that TRPS1 can function as a context-dependent tumor suppressor in breast cancer, whilst being essential for growth and differentiation of normal mammary epithelial cells.

overall_design: Binding of TRPS1 and/or GATA3 in mouse or human breast cancer cells profiled by ChIP-seq (Chromatin Immunoprecipitation followed by deep sequencing).

first: Anne

middle: P

last: Drenth

first: Eline

last: van der Burg

first: Roebi

last: de Bruijn

first: Wilbert

last: Zwart

first: Jos

last: Jonkers


title: TRPS1 acts as a context-dependent regulator of mammary epithelial cell growth/differentiation and breast cancer development


title: RNA-seq profiling of adult skeletal muscle after long term conditional knockout of Hic1 [TA RNA-seq]

summary: To determine the effects of long term deletion of the transcriptional repressor Hypermethylated in cancer 1 (Hic1) on skeletal muscle, samples were collected of both wild type mice and those conditionally deleted for Hic1 and profiled by RNA sequencing. Aspects of muscle homeostasis were negatively impacted, highlighting cell and non cell autonomous roles for Hic1 in maintaining functional MPs and muscle tissue.

overall_design: Transcriptome wide profiling of skeletal muscle of aged wild type and Hic1-/- mice, n > 7.


title: Single cell RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury

summary: After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the MP function in regeneration, a muscle-injury model was employed to activate MPs and follow their contribution to tissue regeneration. To compliment the population RNA seq profile previously obtained and to uncover the suspected heterogeneity of MPs in this context, tdTomato positive cells from selected timepoints were profiled by single cell RNA sequencing.

overall_design: Single cell RNA-seq analyes of enriched mesenchymal progenitors at selected timepoints during skeletal muscle regeneration.


title: Transcript sequencing of mononuclear fractions from dissociated murine skeletal muscle

summary: The important role of mesenchymal progenitors is quickly emerging in various biological processes. Thus far an appropriate marker has been lacking. Here the fractionation of dissociated skeletal muscle and subsequent enrichment of MPs by an established method was employed. Endothelial and blood derived cells comprised the lineage positive fraction and the remaining cell suspension was fractionated using the surface marker Sca1(Ly6a) to enrich for MPs. RNA sequencing was performed on all fractions and subsequent transcriptomic data was interrogated for MP specific transcription factors. Hic1 was found to be highly enriched in the MP fraction.

overall_design: Transcripome wide profiling of multiple skeletal muscle cell populations in at least triplicate


title: AQP5-Expressing Cells Serve as Stem Cells and Cancer Origins in the Mouse and Human Pyloric Stomach

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

institute: VUB/ULB

summary: Isolating adult stem cells from human stomach epithelia has proven challenging due to a lack of surface markers that are amenable to antibody-based sorting approaches. Here, through comparative expression profiling of mouse Lgr5+ adult stem cells along the GI tract, we identify novel pylorus-specific stem cell markers, including the membrane protein Aqp5. FACS-based isolation of endogenous AQP5+ cells from healthy human pyloric stomach revealed their stem cell identity in organoid assays. Using new Aqp5-driven CreERT2 mouse models to selectively target conditional mutations to the pyloric stem cell compartment in vivo, we establish pyloric stem cells as a major source of Wnt-driven invasive gastric cancer. The new stem cell markers and mouse models described here will be an invaluable resource for deciphering early gastric cancer formation and for isolating and characterizing human stomach stem cells as a prerequisite to potentially exploiting their regenerative medicine potential in the clinic.

overall_design: Stem and differentiated popualtions from various mouse gastrointestinal tissues were isolated by FACS for RNA extraction and hybridization on Affymetrix microarrays. We sought to identify genes specifically enriched in pyloric stem cells relative to the other gastrointestinal populations.

first: Si

last: Tan

first: Yada

last: Swathi

first: Shawna

first: Jasmine

last: Goh

first: Ryo

last: Seishima

first: Liang

first: Esther

last: Wong

first: Seri

last: Mustafah

first: Khay

middle: G

last: Yeoh

first: Jimmy

last: So

first: Asim

last: Shabbir

first: Nick

last: Barker


title: RNA sequencing time-course of mesenchymal progenitors during regeneration after notexin induced muscle injury

first: Tully

last: Underhill

summary: After tissue injury mesenchymal progenitors undergo a transient proliferative expansion, morphological transition and migration from their perivascular niche. To gain transcriptomic insights into the transition of MPs out of the quiescent state and their role in muscle regeneration, a muscle-injury model was used to activate MPs and follow their contribution to tissue regeneration. tdTomato positive MPs were FACS purified from dissociated muscle at different time points after notexin-induced injury and transcriptomic analysis was performed using RNA sequencing of all samples.

overall_design: Transcriptome wide profiling of FACS purified mesenchymal progenitors at various timepoints during regeneration after notexin induced muscle injury.

first: R

last: Scott

first: T

middle: M


title: RNA-seq profiling of FACS purified MPs from adult skeletal muscle after conditional knockout of Hic1 [MP RNA-seq]

summary: To determine the effect of the deletion of the trancriptional repressor Hypermethylated in cancer 1 (Hic1) on quiescence, adult mesenchymal progenitors (MPs) were isolated from skeletal muscle of both wild type mice and those conditionally deleted for Hic1 and profiled by RNA sequencing. Comparison to MPs activated by using a muscle injury model of the tibialis anterior muscle revealed similar pathways affected under both conditions, highlighting the role for Hic1 in maintaining the quiescent state of MPs

overall_design: Transcriptome wide profiling of adult mesechymal progenitors from skeletal muscle of wild type and Hic1-/- mice in quadruplicate.


title: Expansion, in vivo-ex vivo cycling and genetic manipulation of primary human hepatocytes

status: Public on Dec 02 2019

city: New York

first: Inna

last: Ricardo-Lax

address: 1230 york avenue

institute: Rockefeller University

summary: Primary human hepatocytes (PHH) are an essential tool for modeling drug metabolism and liver disease. However, variable plating efficiencies, short lifespan in culture and resistance to genetic manipulation have limited their use. Here we show that retrorsine improves human hepatocyte repopulation of chimeric mice to levels where poor donor PHH can be isolated for ex vivo cultures. Mouse-passaged (mp)PHH cultures overcome the marked donor-to-donor variability of cryopreserved PHH and remain functional for months, as demonstrated by metabolic assays and infection with hepatitis B virus and Plasmodium falciparum. mpPHH can be efficiently genetically modified in culture, mobilized and then re-cultured as spheroids or re-transplanted to create highly humanized mice carrying a genetically altered hepatocyte graft. Together, these advances provide flexible tools for studying human liver disease and evaluating hepatocyte-targeted gene therapy approaches

overall_design: Stranded RNA-seq libraries were prepared from cryopreserved commercial primary human hepatocytes (PHH-two samples) and mouse passaged primary human hepatocytes (mpPHH) from the same donor. The mpPHH were generated from two independed transplant experiments, and each sample was generated from a separate mouse: 2 mice in the first experiment and 3 mice in the second experiment.

first: Eleftherios

last: Michailidis

first: Koen

last: Vercauteren

first: Liliana

last: Mancio-Silva

first: Linda

last: Andrus

first: Cyprien

last: Jahan

first: Chenhui

last: Zou

first: Mohammad

last: Kabbani

first: Paul

last: Park

first: Corrine

last: Quirk

first: Christina

last: Pyrgaki

first: Brandon

last: Razooky

first: Lieven

last: Verhoye

first: Irene

last: Zoluthkin

first: Wei-Yu

last: Lu

first: Stuart

last: Forbes

first: Luis

last: Chiriboga

first: Neil

middle: D

last: Theise

first: Roland

last: Herzog

first: Hiroshi

last: Suemizu

first: William

last: Schneider

first: Amir

last: Shlomai

first: Philip

last: Meuleman

first: Sangeeta

middle: N

last: Bhatia

first: Charles

last: Rice

first: Ype

last: de Jong


title: Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (RNAseq and ribosome profiling)

status: Public on Dec 01 2019

first: Geraldine

last: Seydoux

address: 725 N. wolfe St. PCTB 706

department: MBG

institute: Johns Hopkins University

summary: RNA granules are cellular condensates that contain RNAs and proteins. The mechanism that drive the recruitment of many mRNAs to RNA granules are not fully understood.  Here we characterize the assembly and transcriptome of the germ (P) granules of C. elegans. We find that mRNAs are recruited into P granules by condensation with the intrinsically-disordered protein MEG-3. MEG-3 binds ~500 mRNAs in C. elegans embryos in a sequence-independent manner that favors mRNAs with low ribosome coverage. Translational stress causes additional mRNAs to localize to P granules and translational activation correlates with P granule exit for two mRNAs coding for germ cell fate regulators. MEG-3/RNA condensates assembled in vitro are gel-like and trap mRNAs in a non-dynamic state. Our observations reveal similarities between P granules and stress granules and identify gelation with intrinsically-disordered proteins as a sequence-independent mechanism to enrich low-translation mRNAs in RNA granules

overall_design: 12 embryonic samples are included in this submission. It contains 6 RNAseq (3 wild type and 3 meg-3meg-4 mutant) and 6 corresponding ribosome profiling (3 wild type and 3 meg-3meg-4 mutant).

first: Chih-Yung

last: Lee


title: TRPS1 acts as a context-dependent regulator of mammary epithelial cell growth/differentiation and breast cancer development [RNA-Seq]

first: Lisette

last: Cornelissen

overall_design: RNAseq data of TRPS1 proficient and deficient HC11 cells, HC11 cells treated with and without the HDACi TrichostatinA, primary organoids derived from Cdh1F/F;Trps1+/+, Cdh1+/F;Trps1F/F and Cdh1F/F;Trps1F/F mice grown in matrigel for 14 or 28 days and mammary tumors derived from WAP-cre;Cdh1F/F;Trps1+/+ and WAP-cre;Cdh1F/F;Trps1F/F mice.

first: Anne

last: Drenth

first: Eline

last: van der Burg

first: Roebi

last: de Bruijn

first: Wilbert

last: Zwart

first: Jos

last: Jonkers


title: Circulating miR 802-5p and miR 194-5p and brain expression of MEF2C as novel biomarkers of breast cancer brain metastasis

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

institute: Public Health Agency of Canada

summary: We hypothesized that circulating miRNAs could work as biomarkers for early detection of breast cancer brain metastasis (BCBM), and their targets could constitute new targets for modulation. We used a mouse model of BCBM and Next-Generation Sequencing to establish the circulating miRNAs alterations along brain metastasis development and performed bioinformatics analysis to identify their targets with relevance in the metastatic process. We additionally analyzed human resected brain metastasis of breast cancer patients for target’s expression validation. In our mouse model, we observed a deregulation of circulating miRNAs profile during BCBM progression, with a downregulation of miR-802-5p and miR-194-5p in plasma prior to brain metastases detection. The transcription factor myocyte enhancer factor 2C (MEF2C), was identified as a target for both miRNAs, and its expression was increasingly observed in malignant cells along brain metastasis development. Its upregulation was also observed in peritumoral astrocytes and in human BCBM. Collectively, downregulation of circulating miR-802-5p and miR-194-5p appear as precocious biomarkers for BCBM and MEF2C emerges as a new player and a potential target for modulation.

overall_design: We used a mouse model of breast cancer brain metastasis (BCBM), relying on the innoculation of breast cancer cells (or vehicle; control) in the carotid artery of Balb/c mouse, as a reliable model of brain metastasization of breast cancer, and collected brain and plasma samples at different time points (3, 7 and 10 days). Brain metastasis development was profiled by histologic analysis of brain sections and alterations in the circulating miRNA signature were determined by Next-Generation Sequencing miRNA analysis of plasma samples. MiRNAs with an aberrant expression prior to brain metastasis detection were selected for further study. This included the validation of their altered expression by qPCR and the identification of their potential targets with relevance for the metastatic process by bioinformatics analayis. Finnally, the expression of the most promising target was determined by immunofluorescence analysis of brain sections along metastasis development and the data obtained in the mouse model was further validated by analysis of ressected brain metastasis from breast cancer patients.

first: Marta

last: Sereno

first: János

last: Hásko

first: Kinga

last: Molnár

first: Zita

last: Reisz

first: Rui

last: Malhó

first: Mafalda

last: Videira

first: László

last: Tiszlavicz

first: Stephanie

last: Booth

first: Imola

last: Wilhelm

first: István

last: Krizbai

first: Maria

last: Brito


title: Hic1 defines quiescent mesenchymal progenitor subpopulations with distinct functions and fates in skeletal muscle regeneration

first: Tully

last: Underhill


title: Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins

first: Geraldine

last: Seydoux


title: Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (RNAseq datasets)

overall_design: 6 biological embryonic samples are included in this submission. It contains 3 samples from wild-type and 3 samples from meg-3meg4 mutant embryos

first: Tu

last: Lu


title: Transcriptomic Reprogramming of Prostate Cancer Cells Driven by Stroma-Derived AREG

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Recent advances in next generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways and responses. We performed this study to investigate the transcriptome profiling (RNA-seq) of prostate cancer cells upon in vitro treatment with the conditioned media from prostate stromal cells exogenously expressing human AREG.

overall_design: Overall transcript profiles of prostate cancer cell lines including PC3 and DU145 were generated by deep sequencing, in triplicate, using Illumina HiSeq X10. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

first: Qixia

last: Xu


title: Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K14ac bivalent regions in young and aged liver.

city: Charlottesville

first: Irina

middle: M.

last: Bochkis

state: Virginia

address: 1340 Jefferson Park Ave

department: Department of Pharmacology

institute: University of Virginia School of Medicine

summary: Post-translational modifications of histone tails play a crucial role in gene regulation. Here, we performed chromatin profiling by quantitative targeted mass spectrometry to assess all possible modifications of the core histones. We discovered a novel bivalent combination, a dually-marked H3K9me3/H3K14ac modification in the liver, that is significantly decreased in old hepatocytes. Subsequent genome-wide location analysis (ChIP-Seq) identified 1032 and 668 bivalent regions in young and old livers, respectively, with 280 in common. Histone H3K9 deacetylase Hdac3, as well as H3K9 methyltransferase Setdb1, found in complex Kap1, occupied bivalent regions in both young and old livers, correlating to presence of H3K9me3. Expression of genes associated with bivalent regions in young liver, including those regulating cholesterol secretion and triglyceride synthesis, is upregulated in old liver once the bivalency is lost. Hence, H3K9me3/H3K14ac dually-marked regions define a poised inactive state that is resolved with loss of one or both of the chromatin marks, which subsequently leads to change in gene expression.

overall_design: Genome-wide location analysis (ChIP-Seq) of Setdb1,  Kap1, and H3K14ac  from young (3 months) and old (21 months) mouse livers

first: Andrew

last: Price


title: Transcriptomic analysis of naïve B cells and antigen-specific activated B cells and plasma cells from 4dpi NP-LPS immunized mice [NPLPS_PC]

first: Brian

last: Gaudette

summary: Little is known about the earliest transcriptomic events in plasma cell differentiation.  Indeed, activation of UPR-affiliated gene expression is seen in in-vitro plasma cell differentiation prior to Blimp1 upregulation and in the absence of Xbp1 as we show in linked companion series.  In this study, Blimp1 reporter mice were immunized with the T-independent antigen NP-LPS four days prior to spleen harvest and naïve B cells, NP-binding activated B cells and NP-binding plasma cells were analyzed by bulk RNA-seq.  Here we report the activation of ER remodeling gene expression in antigen-specific activated B cells in-vivo prior to upregulation of Blimp1 transcription.

overall_design: Samples are three celltypes from three biological replicates (mice) 4 days post NP-LPS immunization.  cDNA was prepared from RNA with 3' polyA capture method.  Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.

first: David

last: Allman

middle: T


title: Recruitment of mRNAs to P granules by gelation with intrinsically-disordered proteins (iCLIP results)

city: Baltimore

overall_design: This submission contain six iCLIP-seq results from C.elegans embryos. 2 sets of GFP::MEG-3, 2 sets of GFP::PGL-1 and 2 set of GFP control.

first: Chih-Yung

last: Lee


title: Investigation of RNA editing sites within bound regions of RNA-binding proteins

status: Public on Nov 30 2019

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

institute: Aalborg University

summary: Studies in epitranscriptomics indicates that RNA is modified by a variety of enzymes. Among these RNA modifications, A-to-I RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA-seq data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNAEditor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affects the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncover that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands are examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, HuR, was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme ADAR compared to the control—suggesting that the presence of RNA editing islands influences HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.

overall_design: The RNA editing enzyme, ADAR, was silenced in HEK-293 cells.


title: Transcriptional Correlates of Tolerance and Lethality from Mouse Models Predict Ebola Virus Disease Outcome

first: Adam

address: 722 West 168th St.

department: Center for Infection and Immunity

institute: Columbia University

summary: We report comparative outcome-dependent transcriptional profiles from spleen and liver from Collaborative Cross mice infected with mouse-adapted Ebola virus (MA-EBOV).

overall_design: Longitudinal transcriptional profiling (mRNA and miRNA) of 10 Collaborative Cross lines infected with mouse-adapted Ebola virus.

first: Angela

last: Rasmussen


title: STRIPAK directs PP2A activity to promote oncogenic transformation

city: Cambridge

first: Jong Wook

last: Kim

state: MA

address: 45 Main Street

department: Cancer Program

institute: Broad Institute

summary:
We evaluated the effects of suppressing MAP4K4 on transcriptome and YAP1 pathway based on the observation that partial suppression of MAP4K4 leads to transformation through activation of YAP1.
Mutations and deletions involving subunits of the serine-threonine phosphatase PP2A occur in a broad range of human cancers, and partial loss of PP2A function contributes to cell transformation. In particular, displacement of regulatory B subunits by the viral oncoprotein SV40 small-t antigen (ST) or mutation or deletion of PP2A subunits alters the abundance and types of PP2A complexes in cells and induces cell transformation in human cells. Here we show that ST not only displaces common PP2A B subunits but also promotes PP2A A-C subunit interactions with a set of alternative B subunits (B’’’, striatins) that are components of the Striatin-interacting phosphatase and kinase (STRIPAK) complex. We found that members of the STRIPAK complex are required for ST-PP2A induced cell transformation. PP2A interacts with and dephosphorylates the STRIPAK-associated kinase MAP4K4, which induces cell transformation in part through the regulation of the Hippo pathway effector YAP1. These observations identify an unanticipated role of MAP4K4 in transformation and show that the STRIPAK complex plays a key role in defining PP2A specificity and activity.

overall_design: Stable cell line expressing shRNA targeting MAP4K4 or Luciferase control HEK cells immortalized with hTERT, SV40 Large-T antigen, and H-RAS(G12V) was used to perform transcriptome analysis.

first: Jong

middle: W

first: Miju

first: James

last: DeCaprio

first: William

last: Hahn


title: Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells

city: Nijmegen

first: Tianran

last: Peng

address: Geert Grooteplein Zuid  28

department: Molecular Life Science

institute: Radboud University

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

overall_design: Refer to individual Series


title: Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells [RNA-seq]

summary: Mouse Embryonic Stem Cells (ESCs) grown in serum-supplemented conditions are characterized by an extremely short G1-phase due to the lack of G1-phase control. Concordantly, the G1-phase-specific P53-P21 pathway is compromised in serum ESCs. Here we provide evidence that P53 is activated upon transition of serum ESCs to their pluripotent ground state using serum-free 2i conditions and modulates G1-phase progression. Our data shows that the elongated G1-phase characteristic of ground state ESCs is dependent on P53. RNA-seq and ChIP-seq analyses reveal that P53 directly regulates the expression of the Retinoblastoma (RB) protein and that the hypo-phosphorylated, active RB protein plays a key role in G1-phase control. Our findings suggest that the P53-P21 pathway is active in ground state 2i ESCs and that its role in the G1-checkpoint is abolished in serum ESCs. Taken together, the data reveals a mechanism by which inactivation of P53 can lead to loss of RB and uncontrolled cell proliferation.

overall_design: FUCCI reporter constructed R1 mESCs were cultured in either serum or 2i conditions. G1-phase cells were sorted and collected using the BD FACS Aria. RNA were extracted from G1 cells and library prepared

first: Menno

last: ter Huurne

first: Hendrik

last: Stunnenberg


title: RNA-seq of A431 cells expressing control or ARID1A-targeting shRNAs

city: Beijing

first: Qingyu

last: Luo

address: Panjiayuannanli No.17#, Chaoyang District

department: State Key Laboratory of Molecular Oncology

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary: We examined gene expression level in A431 cells expressing control or ARID1A-targeting shRNAs to study the mechanism underlying the tumor suppressive effect of ARID1A.

overall_design: RNA-seq was performed using A431 cells expressing control or ARID1A-targeting shRNAs

first: Xiaowei

last: Wu


title: Sequencing analysis of sorted bone marrow endothelial cells

city: Cincinnati

first: Yi

last: Zheng

state: OH

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: The purpose of the study is to examine the pathway differences and the differential gene expression levels between WT endothelial cells and KRasG12D aberrant endothelial cells.

overall_design: Investigation of differential gene expression levels between WT endothelial cells and KRasG12D aberrant endothelial cells.

first: Cindy

last: Hochstetler


title: CPF is required for heterochromatin assembly and gene silencing [RNA-seq]

status: Public on Nov 29 2019

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: RNA sequencing in Schizosaccharomyces pombe

overall_design: RNA sequencing of WT and mutant strains grown at 18°C.

first: Tommy

middle: V

last: Vo

first: Martin

last: Zofall

first: Madeline

last: Larkin

first: Gobi

last: Thillainadesan

first: David

last: Wheeler

first: Sahana

last: Holla

first: Jothy

last: Dhakshnamoorthy

first: Vanivilasini

last: Balachandran

middle: I


title: Endogenous IGF Signaling Directs Heterogeneous Mesoderm Differentiation in Human Embryonic Stem Cells

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau

summary: We applied LY294002 in mesoderm downstream differentiation. LY294002-induced cells enriched in cardiomyocytes as well as WNT inhibitor IWP2.

overall_design: Total RNA obtained from H1 differentiation samples. After using CHIR99021 induce mesoderm, insulin, IWP2, LY294002, IWP2+LY294002 were applied from day 2 to day 5. Samples were collected on day 10 .

first: Guokai

last: Chen


title: CPF is required for heterochromatin assembly and gene silencing [ChIP-seq]

summary: Mapping of H3K9me2, 3' RNA processing and termination factors, and terminating RNA polymerase II in Schizosaccharomyces pombe

overall_design: Mapping of H3K9me2 in WT, swd22∆, and ssu72∆ strains cultured at 18°C for 3 days and maintained in mid-log phase. Iss1 mapping in WT and mmi1∆ strains at 32°C. Mapping of Dhp1 in WT at 32°C. Mapping of RNA polymerase II Ser2-P in WT, mmi1∆, swd22∆, and ssu72∆ strains at 32°C.


title: RNA-seq of KYSE410 cells expressing control, USP11 or ARID1A-targeting shRNAs

summary: We examined gene expression level in KYSE410 cells expressing control, USP11 or ARID1A-targeting shRNAs to study the mechanism underlying the tumor suppressive effect of ARID1A and USP11.

overall_design: RNA-seq was performed using KYSE410 cells expressing control, USP11 or ARID1A-targeting shRNAs


title: Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design

city: Boston

first: Pierce

last: Ogden

address: 3 Blackfan Circle, CLSB 528/4C

institute: Harvard

summary: An Adeno-Associated Virus capsid fitness landscape reveals a frameshifted viral gene and in vivo design principles, enabling machine-guided engineering.

overall_design: Multi-mutants were synthsized using agilent chips, and cloned and transfected to mice, tissue samples from the liver were collected after 2 weeks.

first: Eric

last: Kelsic

first: Sam

last: Sinai

first: George

last: Church


title: Critical role for P53 in regulating the cell cycle of ground state embryonic stem cells [ChIP-seq]

first: Tianran

last: Peng

overall_design: Mouse ESCs were cultured in either serum or 2i conditions. Fixed chromatin were pull down by anti-P53 antibody. Biological replicates included.

first: Menno

last: ter Huurne

first: Hendrik

last: Stunnenberg


title: Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast [RNA-seq]

status: Public on Nov 28 2019

city: Edinburgh

first: Elizabeth

middle: H

last: Bayne

address: Alexander Crum Brown Road

department: School of Biological Sciences

institute: University of Edinburgh

summary: RNA-seq was performed to identify transcripts differentially expressed in Schizosaccharomyces pombe cells lacking Mkt1.

overall_design: Three biological replicates of RNA profiles in WT and mkt1D.


title: Single-nucleus RNA sequencing reveals transcriptional changes of hippocampal neurons in APP23 mouse model of Alzheimer’s disease

status: Public on Nov 27 2019

city: Hefei

first: Yong

last: Shen

address: University of Science and Technology of China, No.96, JinZhai Road Baohe District

summary: Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that mostly strikes the elderly. However, the exact molecular and cellular pathogenesis of AD, especially the dynamic changes of neurons during disease progression, remains poorly understood. Here we used single-nucleus RNA sequencing (snRNA-seq) to access the transcriptional changes of hippocampal neurons in APP23 mouse model of AD. We performed snRNA-seq using a modified Smart-seq2 technique on 3,280 neuronal nuclei from the hippocampus of young and aged APP23 and control mice and identified four distinct subpopulations. Comparative transcriptional analysis showed multiple changes in different subtypes of hippocampal neurons of APP23 mice in comparison to control mice, as well as the transcriptional changes in these neurons during disease progression. Our findings revealed multiple neuronal subtype-specific transcriptional changes that may lead to targets for future studies of AD.

overall_design: revealed multiple neuronal subtype-specific transcriptional changes in 6-month old WT(wild type) mouse and 24-month old APP23 mouse

first: Shan

last: Zhong

first: Mengdi

last: Wang

first: Yaxi

last: Zhan


title: The transcriptional profile of Trichophyton rubrum co-cultured with human keratinocytes shows new insights about gene modulation by terbinafine.

city: Ribeirão Preto

first: Ana

middle: Lucia

last: Fachin

state: SP

address: Av. Costabile Romano, 2201

department: Biotechonology  Unit

country: Brazil

institute: Unaerp

summary:
Purpose: Evaluate the effect of terbinafine in T. rubrum gene expression using a co-culture model in conjunction with RNA-seq
Methods: T. rubrum and HaCat cells line were co-cultured in RPMI medium supplemented with 5% of fetal bovine serum and treated with 0.0162 µM of terbinafine.The co-culture was incubated for 24 h  at 37ºC in a humidified atmosphere containing 5% CO2  , followed RNA by extraction of both organisms, libraries construction and sequence.
Results: Our data demonstrated the modulation of several T. rubrum genes involved in the biosynthesis of ergosterol in addition to the target gene of terbinafine that is already known, genes encoding MFS- and ABC-type membrane transporters that are associated with the phenomenon of multidrug resistance, genes that have been discussed in the literature as possible novel targets for antifungal compounds and genes which do not have a known function in T. rubrum yet, but have been modulated in response to the drug.
Conclusions: RNA-seq sequencing of the T. rubrum co-culture in the presence of terbinafine showed that several genes of the ergosterol biosynthesis cascade were repressed.  We highlight the induction of transmembrane transporters, which may be associated with the efflux of this allylamine. In addition, other genes that could be involved in the pathogenicity of T. rubrum were also modulated in the presence of the drug. In addition, we observed the modulation of hypothetical genes with still unknown functions in T. rubrum but that possess orthologs in other dermatophytes.

sample_organism:
Trichophyton rubrum
Homo sapiens

platform_organism:
Trichophyton rubrum
Homo sapiens

overall_design: The present study is the first to evaluate the effect of terbinafine using a co-culture model of T. rubrum with human keratinocytes in conjunction with a large-scale sequencing technique. The results of large-scale analysis of the expression profile of T. rubrum co-cultured with human keratinocytes indicate that terbinafine can act on various targets related to the physiology of T. rubrum other than its main target of ergosterol biosynthetic pathway.These findings offer new perspectives for the discovery of novel antifungal targets or even for structural modifications in the terbinafine molecule that would allow to increase its spectrum of antifungal activity.

first: Monise

middle: F

last: Petrucelli

first: Josie

middle: B

last: Matsuda

first: Kamila

last: Peronni

first: Pablo

middle: R

last: Sanches

first: Wilson

middle: A

last: Silva Junior

first: Rene

middle: O

last: Beleboni

first: Nilce

last: Martinez-Rossi

first: Mozart

last: Marins


title: Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast [CRAC]

summary: CRAC analysis was performed to identify transcripts associated with the Mkt1 protein in Schizosaccharomyces pombe

overall_design: Two biological replicates of Mkt1 and control (parental strain) CRAC experiments


title: Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain

first: Devon

last: Svoboda

email: svobodadevon@gmail.com, barc@wi.mit.edu

address: 455 Main St

institute: Whitehead Institute


title: Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain [Single Cell RNAseq]

summary: iPSC derived microglial precursors were tranplanted into the brains of neonatal mice, FACS sorted out based on GFP+ following 2 months, and compared to in vitro differentiated iPSC derived microglia from the same precursors.

overall_design: Microglial Precursors were either transplanted into neonatal mice or plated for in vitro differentiation.  Transplanted GFP+ cells and in vitro differentiated cells were collected for FACS sorting and scRNA library prep following 60 days.  In vivo samples from four chimeric mice (n=4) and two in vitro samples (n=2) were collected.  For mice, n=one mouse.  For in vitro differentiated microglia, n=3 pooled well of a 6-well plate.

first: M

last: Barrasa

first: Jian

last: Shu

first: Peter

last: Berube

first: Rudolf

last: Jaenisch


title: Microarray data for Bhlhe40WT and Bhlhe40KO small intestine lamina propria CD4+ T cells

city: St. Louis

first: Brian

last: Edelson

state: MO

address: 425 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
The cytokines GM-CSF and IL-5 are thought to possess largely divergent functions despite a shared dependence on the common beta (βC) chain to initiate signaling. Although IL-5 is part of the core type 2 cytokine signature and is required for protection against some helminths, it is dispensable for immunity to others, such as Heligmosomoides polygyrus bakeri (H. polygyrus). Whether this is due to compensatory mechanisms is unclear. The transcription factor Bhlhe40 has been shown to control GM-CSF production and is proposed to be a novel regulator of T helper type 2 cells.
We have found that Bhlhe40 is required in T cells for a protective memory response to secondary H. polygyrus infection. H. polygyrus rechallenge elicited dramatic Bhlhe40-dependent changes in gene and cytokine expression by lamina propria CD4+ T cells and in vitro-polarized TH2 cells, including induction of GM-CSF and maximal production of type 2 cytokines including IL-5. βC chain-deficient, but not GM-CSF-deficient, mice rechallenged with H. polygyrus had severely impaired protective immunity. Our results demonstrate that Bhlhe40 is an essential regulator of TH2 cell immunity during helminth infection and reveal unexpected redundancy of βC chain-dependent cytokines.

overall_design: Bhlhe40+/+=Bhlhe40WT, Bhlhe40-/-=Bhlhe40KO. Naive CD4 T cells, 2 Bhlhe40+/+ and 2 Bhlhe40-/- samples sorted from naïve mice. H. polygyrus bakeri-rechallenge CD4 T cells, 3 Bhlhe40+/+ and 3 Bhlhe40-/- samples sorted from mice experiencing secondary infection with H. polygyrus bakeri.

first: Nicholas

last: Jarjour


title: Blue light regulates phosphate deficiency-dependent primary root growth inhibition in Arabidopsis

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: Plants have evolved mechanisms to improve utilization efficiency or acquisition of inorganic phosphate (Pi) in response to Pi deficiency, such as altering root architecture, secreting acid phosphatases, and activating the expression of genes related to Pi uptake and recycling. Although many genes responsive to Pi starvation have been identified, transcription factors that affect tolerance to Pi deficiency have not been well characterized. We show here that the ectopic expression of B-BOX32 (BBX32) and the mutation of ELONGATED HYPOCOTYL 5 (HY5), whose transcriptional activity is negatively regulated by BBX32, resulted in the tolerance to Pi deficiency in Arabidopsis. The primary root lengths of 35S:BBX32 and hy5 plants were only slightly inhibited under Pi deficient condition and the fresh weights were significantly higher than those of wild type. The Pi deficiency-tolerant root phenotype of hy5 was similarly observed when grown on the medium without Pi. In addition, a double mutant, hy5 slr1, without lateral roots also showed a long primary root phenotype under phosphate deficiency, indicating that the root phenotype of hy5 does not result from increase of external Pi uptake. Moreover, we found that blue light may regulate Pi deficiency-dependent primary root growth inhibition through activating peroxidase gene expression, suggesting the Pi-deficiency tolerant root phenotype of hy5 may be due to blockage of blue-light responses. Altogether, this study points out light quality may play an important role in the regulation of Pi deficiency responses. It may contribute to regulate plant growth under Pi deficiency through a proper illumination.

overall_design: Transcriptomes of 24 different samples (wild type, mutant and transgenic plant, grown under different light conditions and phosphate deficient / sufficient condition) were measured to see their difference.

first: Yeh

last: Chuan-Ming

first: Mitsuda

last: Nobutaka


title: Transcriptomic analysis of pretreated rectal cancer biopsies and association to the tumor regression score.

status: Public on Nov 26 2019

city: CLEVELAND

first: Matthew

last: Kalady

state: OHIO

address: 9500 EUCLID AVE

department: Cancer Biology Department

institute: CLEVELAND CLINIC

summary: To determine a preditcive marker of treatment resistance for rectal cancer, we have employed a microarray gene profiling analysis on pretreated rectal biopsies and compared with their response to therapy as defined by the American Joint Commission on Cancer (AJCC) and the American College of Pathologists.

overall_design: Frozen rectal cancer biopsies utilized for the transcriptomic analysis were from 33 patients seen between 2006 and 2009 at Cleveland Clinic Main Campus in Cleveland, Ohio. After collection of biopsie and diagnosis, patients generally underwent surgery with curative intent approximately 8–12 weeks after completion of neoadjuvant chemoradiotherapy with 5-fluorouracil as radiation sensitizer and 50.4Gy in 25 fractions. The resected tumor is assessed by pathologists to determine AJCC score.

first: Sylvain

last: Ferrandon

first: Jennifer

last: DeVecchio

first: Leonardo

last: Duraes

first: Hanumant

last: Chouhan

first: Georgios

last: Karagkounis

first: Jacqueline

last: Davenport

last: Orloff

first: David

last: Liska


title: Pharmacological activation of pyruvate kinase M2 (PKM2) inhibits CD4+ T cell pathogenicity and suppresses autoimmunity

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

summary: Pyruvate kinase (PK) catalyzes the conversion of phosphoenolpyruvate to pyruvate during glycolysis. The PK isoform PKM2 has additional roles in regulation of gene transcription and protein phosphorylation. PKM2 controls macrophage metabolic remodeling in inflammation, but its role in T cell biology is poorly understood. These results show that TEPP-46, an activator of PKM2, reduces CD4+ T cell activation, proliferation, and cytokine production by inhibiting essential signaling pathways and preventing glycolysis.

overall_design: RNA-Seq was performed on resting or activated CD4+ T cells treated with or without the PKM2 activator TEPP-46.

first: Stefano

last: Angiari

first: Marah

middle: C

last: Runtsch

first: Caroline

middle: E

last: Sutton

first: Eva

last: Palsson-McDermott

first: Beth

last: Kelly

first: Nisha

last: Rana

first: Harry

last: Kane

first: Gina

last: Papadopoulou

first: Erika

middle: L

last: Pearce

first: Kingston

last: Mills

first: Luke

last: O'Neill


title: MicroRNA expression profiles in plexiform neurofibromas and malignant peripheral nerve sheath tumors derived from the same neurofibromatosis type 1 patient

city: Rotterdam

first: Erik

last: Wiemer

address: Wytemaweg 80

department: Medical Oncology

institute: Erasmus University Medical Center

summary: Malignant peripheral nerve sheath tumors (MPNST) are aggressive cancers that occur spontaneously (sporadic MPNST) or from pre-existing, benign plexiform neurofibromas in neurofibromatosis type 1 (NF1) patients. MPNSTs metastasize easily, are resistant to therapeutic intervention and are frequently fatal. The molecular changes underlying the transition to malignancy in the NF1 setting are incompletely understood. Here we investigate the involvement of microRNAs in this process. Using an RT-PCR platform microRNA expression profiles were determined from a unique series of archival paired samples of plexiform neurofibroma and MPNST. At least 90 differentially expressed microRNAs (p<0.025; FDR<10%) were identified between the paired samples. Most microRNAs (91%) were found downregulated and 9% of the microRNAs were upregulated in MPNST. Based on the fold changes and statistical significance three downregulated microRNAs (let-7b-5p, miR-143-3p, miR-145-5p) and two upregulated microRNAs (miR135b-5p and miR-889-3p) were selected for further functional characterization. Their expression levels were validated in a relevant cell line panel and a series of unpaired fresh frozen tumor samples containing plexiform neurofibromas, atypical neurofibromas and MPNSTs. As part of the validation process we also determined and analyzed microRNA expression profiles of sporadic MPNSTs observing that microRNA expression discriminates NF1-associated and sporadic MPNSTs emphasizing their different etiologies. The involvement of microRNAs in tumorigenesis and cancer progression was examined in NF1-derived MPNST cell lines through modulating microRNA levels by transient transfection of microRNA mimics or inhibitors. The effects of microRNAs on cellular proliferation, migration, invasion and Wnt/ẞ-catenin signaling were determined. Our findings indicate that, some of the selected microRNAs affect migratory and invasive capabilities and Wnt signaling activity. It was observed that the functional effects upon microRNA modulation are distinct in different cell lines. From our study we conclude that miRNAs play essential regulatory roles in MPNST facilitating tumor progression.

overall_design: To study the involvement of microRNAs in the malignant transition of benign plexiform neurofibromas into MPNST, we determined the microRNA expression profiles of a unique series of nine paired plexiform neurofibromas and MPNST samples. Each plexiform neurofibroma / MPNST pair was derived from the same neurofibromatosis type 1 (NF1) patient. MicroRNA expression profiles were determined from 18 archival formalin-fixed paraffin-embedded (FFPE) tumor samples (9 plexiform neurofibromas and 9 NF1-derived MPNSTs). TaqMan® Low Density Array (TLDA) Human MicroRNA Cards (A card v2.0, B card v3.0; Applied Biosystems/Thermo Fisher Scientific) were used. The microRNA expression profiling data was used for a comparison between the benign plexiform neurofibromas and the MPNST in order to determine differentially expressed microRNAs.

first: Azadeh

last: Amirnasr

first: Robert

middle: M

last: Verdijk

first: Patricia

last: van Kuijk

first: Pinar

last: Kartal

first: Anne

last: Vriends

first: Pim

middle: J

last: French

first: Martin

last: van Royen

first: Walter

last: Taal

first: Stefan

last: Sleijfer


title: The effects of tRNA editing deficiency on hematopoietic stem cells

city: La Jolla

last: Signer

state: California

address: 3855 Health Sciences Drive

department: Division of Regenerative Medicine

institute: UCSD

summary: To test how translational control of proteome quality affects stem cell function, we examined Aarssti/sti mice that harbor a mutation in the alanyl-tRNA synthetase, which causes a tRNA editing defect that increases amino acid misincorporation errors during translation. Aarssti/sti mice exhibited reduced HSC numbers, increased HSC proliferation and significantly diminished HSC serial reconstituting activity in vivo, but did not exhibit defects within restricted progenitors. Modest accumulation of misfolded proteins partially overwhelmed the capacity of the proteasome within HSCs, which was associated with stabilization and increased abundance of c-Myc. Conditional deletion of a single copy of Myc partially rescued serial reconstitution defects in Aarssti/sti HSCs. HSCs are thus dependent on the maintenance of proteome quality and homeostasis to preserve their self-renewal activity in vivo.

overall_design:
RNA-seq experiment to examine the effects of a tRNA editing defect on the hematopoietic stem cell transcriptome
2 samples with 3 replicates each (6 total)


title: Single-cell RNA sequencing of visceral adipose tissue leukocytes reveals that caloric restriction following obesity promotes the accumulation of a distinct macrophage population with features of phagocytic cells

city: New York

first: Emily

last: Brown

state: NY

address: 435 E 30th St

department: Medicine

institute: NYU Langone

summary: Obesity can lead to type 2 diabetes and is an epidemic. A major contributor to its adverse effects is inflammation of the visceral adipose tisse (VAT). Life-long caloric restriction (CR), in contrast, results in extended lifespan, enhanced glucose tolerance/ insulin sensitivity, and other favorable phenotypes. The effects of CR following obesity are incompletely established, but studies show multiple benefits. Many leukocyte types, macrophages predominantly, reside in VAT in homeostatic and pathological states. CR following obesity transiently increases VAT macrophage content prior to resolution of inflammation and obesity, suggesting that macrophage content and phenotype play critical roles. Here, we examined the heterogeneity of VAT leukocytes and the effects of obesity and CR. In general, our single-cell RNA-sequencing data demonstrate that macrophages are the most abundant and diverse subpopulation of leukocytes in VAT. Obesity induced significant transcriptional changes in all 15 leukocyte subpopulations, with many genes showing coordinated changes in expression across leukocyte subpopulations. Additionally, obese VAT displayed expansion of one major macrophage subpopulation, which, in silico was enriched in lipid binding and metabolic processes. This subpopulation returned from dominance in obesity to lean proportions after only 2 weeks of CR, although the pattern of gene expression overall remained similar. Surprisingly, CR VAT is dominated by a different macrophage subpopulation, which is absent in lean conditions. This subpopulation is enriched in genes related to phagocytosis and we postulate that its function includes clearance of dead cells as well as excess lipids, contributing to limiting VAT inflammation and restoration of the homeostatic state.

overall_design: Single-cell RNA sequencing of CD45+ VAT cells.

first: Ada

last: Weinstock

first: Michela

last: Garabedian

first: Stephanie

last: Pena

first: Monika

last: Sharma

first: Juan

last: Lafaille

first: Kathryn

last: Moore

first: Edward

last: Fisher


title: Transcriptomic analysis of ETV6/RUNX1 KO lymphoid cell line generated by CRISPR/Cas9 showed a distinct expression signature and a deregulation of its downstream signaling genes

city: Salamanca

first: Adrian

last: Montano

address: Campus Miguel de Unamuno SN

country: Spain

institute: Cancer research center

summary: The gene expression profile of E/R KO clones versus REH cells and controls clones, analysed by total RNA-sequencing, showed a total of 342 genes differentially expressed (q<0.05), 182 upregulated and 160 downregulated. The heatmap of the top50 of the most deregulated genes according to fold change (FC) values showed a distinct expression signature of E/R KO clones as compared with REH cells and control clones

overall_design: Purpose: Analyse the gene expression profile of ETV6/RUNX1 KO clones versus REH cells and controls clones by total RNA-sequencing to elucidate the functional effects of fusion gene abrogation in ALL cells.

first: Jesús

last: Hernández Rivas


title: Time series transcritpome in wild-type mice and XBP1 liver-specific knockout mice

city: Pittsburgh

first: Shuchang

last: Liu

address: 203 Lothrop Street

institute: University of Pittsburgh

summary: We reported the liver transcritpome (taken at 2h interval for a total of 48 hrs) in the liver of wild-type mice and XBP1 liver-specific knockout mice

overall_design: Liver samples were taken at 2h interval for a total of 48 hours from the liver of wild-type mice and XBP1 liver-specific knockout mice that are kept under constant darkness

first: Bokai

last: Zhu

first: Silvia


title: Time series XBP1s ChIP-Seq in wild-type mice and XBP1 liver-specific knockout mice

address: 100 Technology Dr, Bridgeside point

summary: We reported the liver XBP1s cistrome (taken at 4h interval for a total of 48 hrs) in the liver of wild-type mice and XBP1 liver-specific knockout mice

overall_design: Liver samples were taken at 4h intervals for a total of 48 hours from the liver of wild-type mice and XBP1 liver-specific knockout mice that are kept under constant darkness


title: Association of aneuploidy with centromeric features

city: Paris

first: Riccardo

last: Gamba

address: 12 rue Lhomond

institute: Insitut Curie

summary: In human cells chromosome specific aneuploidy was measured. Then, using NGS methods, centromeric features were measured for each chromosome (including centromere length and amount of centromeric proteins). The study aims at testing an association between centromeric features and missegregation rate.

overall_design: On RPE-1 cells:4 replicates of WGS, 3 replicates of CENPB Cut&Run-seq, 3 replicates of CENPC Cut&Run-seq, 1 single CENP-A Cut&Run-seq, 2 CENP-T Cut&Run-seq experiments. On DLD-1 cells: one WGS and one CENP-C Cut&Run-seq.

first: Marie

last: Dumont

first: Daniele

last: Fachinetti

first: Pierre

last: Gestraud

first: S

last: Klaasen

first: J

last: Worrall

middle: G

last: De Vries

first: V

last: Boudreau

first: P

middle: S

last: Maddox

last: Lens

first: G

last: Kops

first: Sara

last: McClelland

first: Karen

last: Miga


title: Comparative transcriptome analysis of artificially induced rough-type Brucella strain RM57 and its parent strain

city: Beijing

first: Hao

last: Dong

address: Huatuo road NO.31

institute: National Institutes for Food and Drug Control

summary: Purpose: To uncover the related mechanisms underlie virulence attenuation of RM57 vaccine candidate. Methods: Three Brucella melitensis M1981 strains and three Brucella melitensis RM57 strains were grown in TSB at 37℃ until the log phase was reached, total RNA was isolated using the TRIzol according to the manufacturer’s instructions.The sequencing library of each RNA sample was prepared by using NEB Next Ultra Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer.The HiSeq 4000 platform was used to perform the transcriptome sequencing. Results: The results revealed that expressions of 1205 genes were significantly different between RM57 and M1981. Data analysis showed that in the gene ontology term, the different expressed genes involved in energy production and conversion, and translation, ribosomal structure and biogenesis were significantly enriched. Pathway enrichment analysis indicated that the genes involved in oxidative phosphorylation, ribosome, nitrogen metabolism, tyrosine metabolism and two-component system were significantly affected.

overall_design: mRNA profiles of Three Brucella melitensis M1981 strains and three Brucella melitensis RM57 strains were generated by deep sequencing


title: Dual blockade of IL-4 and IL-13 with dupilumab, an IL-4Ra antibody, is required to broadly inhibit type 2 inflammation

status: Public on Nov 25 2019

city: Tarrytown

first: Wei Keat

last: Lim

address: 777 Old Saw Mill River Rd

institute: Regeneron Pharmaceuticals

summary:
Background: Dupilumab, a fully human monoclonal antibody that binds IL-4Ra and inhibits signaling of both IL-4 and IL-13, has shown efficacy across multiple diseases with underlying type 2 signatures and is approved for treatment of asthma, atopic dermatitis and chronic sinusitis with nasal polyposis. We sought to provide a comprehensive analysis of the redundant and distinct roles of IL-4 and IL-13 in type 2 inflammation and report dupilumab mechanisms of action.
Methods: Using primary cell assays and a mouse model of house dust mite induced asthma, we compared IL-4 versus IL-13 versus IL-4Ra blockers.
Results: Intranasal administration of either IL-4 or IL-13 confers an asthma-like phenotype in mice by inducing immune cell lung infiltration, including eosinophils, increasing cytokine/chemokine expression and mucus production, thus demonstrating redundant functions of these cytokines. We further teased out their respective contributions using human in vitro culture systems. Then, in a mouse asthma model by comparing in head to head studies, either IL-4 or IL-13 inhibition to dual IL-4/IL-13 inhibition, we demonstrate that blockade of both IL-4 and IL-13 is required to broadly block type 2 inflammation, which translates to protection from allergen-induced lung function impairment. Notably, only dual IL-4/IL-13 blockade prevented eosinophil infiltration into lung tissue without affecting circulating eosinophils, demonstrating that tissue, but not circulating eosinophils contribute to disease pathology.
Conclusions: Overall, these data support IL-4 and IL-13 as key drivers of type 2 inflammation, and help provide insight into the therapeutic mechanism of dupilumab, a dual IL-4/IL-13 blocker, in multiple type 2 diseases.

overall_design: [1] Bone marrow-derived human mast cells were treated with IL4 or IL13 at 100nM for 24 hours, primed with Fel d 1-specific IgE for 18 hours, and activated with Fel d 1 antigen for 4h. Samples were analyzed for RNA expression profiling of chemokine/cytokine-related genes (NGS). [2] Il4rahu/hu Il4hu/hu mice were exposed intranasally to 50 μg house dust mite (HDM) 3 times per week for 4 consecutive weeks. HDM-exposed mice either received no antibody treatment, or twice-weekly subcutaneous injections of IL4Ra Ab (dupilumab), IL4 Ab, mouse IL13Ra2-Fc or a corresponding isotype control antibody (human IgG4 and mouse IgG2a) starting 3 days before the first HDM exposure. At the end of the studies, mice were sacrificed, and lungs were harvested for RNA expression profiling of chemokine/cytokine-related genes (NGS).

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