title: Neural crest cells bulldoze through the microenvironment using water channel proteins to stabilize filopodia

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: Neural crest migration requires cells to move through dense extracellular matrix and mesoderm to reach targets throughout the vertebrate embryo. Here, we use high-resolution microscopy, computational modeling, and in vitro and in vivo cell invasion assays to investigate the function of Aquaporin-1 (AQP-1) signaling. We find that migrating cranial neural crest cells express AQP-1 mRNA and protein within cell filopodia, implicating a biological role for water channel protein function during invasion. Differential AQP-1 levels affect neural crest cell speed, direction, and the length and stability of cell filopodia. Further, AQP-1 enhances matrix metalloprotease (MMP) activity and phosphorylated focal adhesion kinases (pFAK). Co-localization of AQP-1 expression with EphB guidance receptors in the same migrating neural crest cells raises novel implications for the concept of guided bulldozing by lead cells during migration.

overall_design: Cytometry, RNA-seq and Analysis: Premigratory neural crest were electroporated with either AQP-1 FL or pMES and eggs re-incubated for 24hrs. The neural crest stream adjacent in rhombomere 4 was isolated from healthy ~HH15 embryos. Five pMES transfected embryos were pooled for each of the 3 biological replicates (n=15 total). Four AQP-1 FL embryos were pooled for each of the 3 biological replicates (n=12 total). Tissue was dissociated as previously described (McLennan et al., 2015). Cells were isolated by FACS, which included forward scatter, side scatter, pulse width, live/dead stain (7AAD) and YFP gates as previously described (McLennan et al., 2015; Morrison et al., 2017). Cells were sorted directly into 7ul of Clontech lysis solution containing 0.05% RNase inhibitor. Following lysis for 5 minutes at room temperature, lysates were immediately frozen on dry ice and stored at -80C. Bulk RNA-seq lysates were thawed on ice. cDNA synthesis and library preparation were performed with SMART-seq v4 Ultra Low Input RNA-seq (634891, Takara, Kusatsu, Shiga, Japan) and Nextera XT DNA sample prep and indexing library preparation kits as recommended by the manufacturer (FC-131-2001, FC-131-2004, and FC-131-1096, Illumina, San Diego, CA). Resulting short fragment libraries were checked for quality and quantity using a Bioanalyzer (Agilent) and Qubit Fluorometer (Life Technologies). Libraries were pooled, re-quantified and sequenced as 50bp single reads on 2 lanes of the Illumina HiSeq 2500 in High Output mode using HiSeq Control Software v2.2.58 (Illumina). Following sequencing, Illumina Primary Analysis version RTA v1.18.64 and bcl2fastq2 v2.18 were run to demultiplex reads for all libraries and generate FASTQ files. More than 3 million total alignments were produced per sample. Single end 51-base reads were aligned to the chicken genome galGal4 from UCSC with annotations from Ensembl 84 using STAR (2.5.2b) with options –alignEndsType EndToEnd and sjdbScore 2. Downstream analysis was done in R (3.4.1). Differential expression analysis was performed using the edgeR package (3.18.1). Genes were denoted as differentially expressed if they had a p-value less than .05 and a fold change greater than 1.5-fold (absolute value). Gene ontology enrichment was done using a hypergeometric test on lists of differentially expressed genes.

first: Rebecca

last: McLennan

first: Mary

last: McKinney

first: Jessica

last: Teddy

first: Jason

middle: A

last: Morrison

first: Jennifer

last: Kasemeier-Kulesa

first: Dennis

last: Ridenour

first: Craig

last: Manthe

first: Rasa

last: Giniunaite

first: Martin

last: Robinson

first: Ruth

middle: E

last: Baker

first: Philip

last: Maini

first: Paul

last: Kulesa


title: Transcriptional Profiling of Maternal and Fetal Organs following Rat In Utero TCDD or TCDF Exposure

status: Public on Dec 15 2019

city: Indianapolis

first: Kamin

last: Johnson

state: IN

address: 9330 Zionsville Rd

country: USA

institute: Corteva Agriscience

type: Expression profiling by high throughput sequencing

summary: We report the RNAseq-based transcriptome profiles of rat gestation day 20 dam liver, fetal male and female liver, fetal male pituitary, and fetal testis following in utero exposure to either 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or 2,3,7,8-tetrachlorodibenzofuran (TCDF). Two exposure models were examined: 1) pregnant rats exposed to either a dose response series of TCDD or TCDF from gestation day 6 - 20 or 2) pregnant rats exposed to a single dose of TCDD or TCDF on gestation day 15. These data support a mode-of-action for dioxin-induced rat male reproductive toxicity involving key events in both the fetal pituitary (reduced gonadotropin production) and fetal testis (reduced Leydig cell cholesterologenesis and steroidogenesis) which are hypothesized to decrease perinatal Sertoli cell proliferation and culminate in reduced spermatogenesis. The lack of a TCDF effect on proposed key events may be due to a higher rate of metabolic clearance relative to TCDD.

overall_design: Rat dam liver, fetal liver, fetal pituitary, and fetal testis RNAseq profiles following in utero exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin or 2,3,7,8-tetrachlorodibenzofuran.

middle: J

first: Robert

last: Budinsky

first: Shreedharan

last: Sriram


title: A cytokine screen using CRISPR-Cas9 knock-in reporter pig iPS cells reveals that Activin A regulates NANOG

status: Public on Dec 13 2019

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

country: China

institute: China Agricultural University

summary: NANOG functions as the gateway for the generation of pluripotent stem cells (PSCs) in mice and humans. NANOG protein is highly expressed in pig pre-implantation embryos, indicating NANOG is a conserved pluripotency-associated factor. However, pig NANOG reporter PSCs have yet to be established, and the regulation of pluripotency by NANOG is not completely understood in this animal. In this study, pig NANOG tdTomato knock-in reporter PSCs were established using CRISPR/Cas9. The resulting cell line was treated with several cytokines and inhibitors to identify the key pathway that regulates NANOG expression and the development of pluripotency.

overall_design: In order to determine how NANOG expression affects RNA expression, we performed high-throughput RNA sequencing on knock-in and WT cells and then identified genes that were differentially expressed. Nanog knock-in reporter PC-iPS, WT PC-iPS and pig pre-implantation embryos were analysed together for determine the pluripotency of Nanog PC-iPS; We also analysed the Activin A treatment groups (Act) and SB 431542 treatment groups (SB), three replicates per group.

first: Junjun

last: Xu

first: Dengfeng

last: Gao


title: Enriched marine oils supplements increase peripheral blood SPM concentrations and reprogram host immune responses: A randomized double-blind placebo-controlled study

city: London

first: Esteban

middle: Alberto

last: Gomez Cifuentes

address: Charterhouse Square

department: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary University of London

summary: The aim of the present study was to establish the relationship(s) between supplement dose using a novel enriched marine oil preparation, peripheral blood SPM concentrations and cellular responses. We also aimed to assess the kinetics for these responses in order to provide 1) insights into the protective mechanisms activated by omega-3 supplements in humans and 2) novel potential biomarkers for determining the effectiveness of omega-3 supplements at regulating host immune responses.

overall_design: Double blinded, crossover, placebo-controlled study in 22 healthy volunteers: Using RNA sequencing we assessed the diferential gene expresion between patients from the placebo and marine oil supplementation groups.

first: Patricia

middle: R

last: Souza

first: Raquel

middle: M

last: Marques

last: Gomez

first: Romain

last: Colas

first: Roberta

last: De Matteis

first: Mital

last: Patel

first: David

last: Collier

first: Jesmond

last: Dalli


title: Convergent identification and interrogation of tumor-intrinsic factors for immune escape in vivo

city: West Haven

first: Sidi

last: Chen

state: CT

address: ISTC 320, 850 West Campus Dr

department: Genetics, Systems Biology

institute: Yale University

summary: Evading immune destruction is a hallmark of cancer and a key feature for the resistance to cancer immunotherapy. Genetic alterations can directly influence the nature of cancer cells in the native tumor microenvironment to mediate immune escape. Our genome-scale in vivo CRISPR screens robustly identified multiple regulators of tumor-intrinsic factors that alter the ability of cells to grow as tumors across different levels of immunocompetence. As a convergent hit from these screens, Prkar1a mutant cells are able to robustly outgrow as tumors in fully immunocompetent hosts. Functional interrogation showed that Prkar1a loss greatly altered the transcriptome and proteome involved in inflammatory and immune responses as well as extracellular protein production. Single cell transcriptomic profiling and flow cytometry analysis mapped the tumor microenvironment of Prkar1a mutant tumors, and revealed the transcriptomic alterations in host myeloid cells. Taken together, tumor-intrinsic mutations in Prkar1a led to drastic alterations in the genetic program of cancer cells, thereby remodeling the tumor microenvironment.

overall_design: Single-cell RNA-seq (scRNA-seq) was performed by DropSeq method for Prkar1a-deficient tumors in Rag1-/- and Nu/Nu mice, and for vector-control tumors in Rag1-/- mice. scRNA-seq was performed using the 10X Genomics method for Prkar1a-deficient tumors in C57Bl/6 mice.


title: Genome-wide transcriptomics leads to the identification of deregulated genes after deferasirox therapy in low-risk MDS patients

city: Salamanca

first: Jesus

middle: Maria

last: Hernandez Sanchez

state: España

address: Av Coimbra S/N

country: Spain

institute: Cancer Research of Salamanca

summary: The iron chelator deferasirox is widely used in patients with iron overload. Patients with low-grade myelodysplastic syndromes (MDS) get transfusion dependency and need to be treated with deferasirox to avoid iron overload. Moreover, in some patients an increase in both erythroid and platelets have been observed after deferasirox therapy. However, the mechanisms involved in these clinical findings are poorly understood. The aim of this work was to analyze, in patients treated with deferasirox, the changes in the gene expression profile after receiving the treatment. A total of fifteen patients with the diagnosis of low-grade MDS were studied. Microarrays were carried out in RNA from peripheral blood before and after 14 weeks of deferasirox therapy. Changes in 1,457 genes and 54 miRNAs were observed: deferasirox induced the downregulation of genes related to the Nf kB pathway leading of an overall inactivation of this pathway. In addition, the iron chelator also downregulated gamma interferon. Altogether these changes could be related to the improvement of erythroid response observed in these patients after therapy. Moreover, the inhibition of NFE2L2/ NRF2, which was predicted in silico, could be playing a critical role in the reduction of reactive oxygen species (ROS). Of note, miR-125b, overexpressed after deferasirox treatment, could be involved in the reduced inflammation and increased hematopoiesis observed in the patients after treatment. In summary this study shows, for the first time, the mechanisms that could be governing deferasirox impact in vivo.

overall_design: Paired analysis of low risk MDS treated with deferasirox.

first: Jesús

last: Hernández Sánchez

first: Ana

last: Rodríguez Vicente


title: Opn3 dependent changes in transcriptome of adipose and liver tissue in the postnatal mouse

status: Public on Dec 14 2019

city: Cincinnati

first: Gowri

last: Nayak Sarangdhar

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Opn3 knock out mice show transcriptional changes in these tissues that are indicative of deregulation of mitochondrial function, extracellular matrix and growth factor signaling, fatty acid oxidation and uptake defects.

overall_design: Intercapular adipose tissue, inguinal white adipose tissue and liver samples were collected from postnatal day 17, Opn3 wild-type and knock-out mice at ZT1.

middle: N

last: Sarangdhar


title: Loss of Glucocorticoid Receptor Expression Mediates in Vivo Dexamethasone Resistance in T-cell Acute Lymphoblastic Leukemia

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

summary: Despite decades of clinical use, mechanisms of glucocorticoid resistance are poorly understood. We treated primary murine T lineage acute lymphoblastic leukemias (T-ALLs) with the glucocorticoid dexamethasone (DEX) alone and in combination with the pan-PI3 kinase inhibitor GDC-0941 and observed a robust response to DEX that was modestly enhanced by GDC-0941. Continuous in vivo treatment invariably resulted in outgrowth of drug-resistant clones, ~30% of which showed markedly reduced glucocorticoid receptor (GR) protein expression. A similar proportion of relapsed human T-ALLs also exhibited low GR protein levels. De novo or pre-existing mutations in the gene encoding GR (Nr3c1) occurred in relapsed clones derived from multiple independent parental leukemias. CRISPR/Cas9 gene editing confirmed that loss of GR expression confers DEX resistance. Exposing drug-sensitive T-ALLs to DEX in vivo altered transcript levels of multiple genes, and this response was attenuated in relapsed T-ALLs. These data implicate reduced GR protein expression as a frequent cause of glucocorticoid resistance in T-ALL.

overall_design: Primary murine leukemias exposed to vehicle versus dexamethasone in vivo followed by collection for RNA sequencing

first: Anica

last: Wandler

first: James

last: Downing

first: Jinghui

last: Zhang

first: Kevin

last: Shannon


title: RNA sequencing data from androgenetic cells

status: Public on Dec 12 2019

city: Seoul

first: Kinarm

last: Ko

address: 120, Neungdong-ro, Gwangjin-gu

country: South Korea

institute: Konkuk University

summary:
Androgenetic induced pluripotent stem cells (AgHiPSCs) were generated from androgenetic fibroblasts derived from a complete hydatidiform mole. AgHiPSCs can be used in regenerative medicine, for analysis of genomic imprinting, to study imprinting-related development, and for disease modeling in humans.
To investigate the pluripotency state of AgHiPSCs, we analyzed their cellular and molecular characteristics (morphology, RT-PCR, qPCR, immunochemistry, and differentiation capacity in vitro and in vivo). We tested the DNA methylation status of imprinted genes using bisulfite sequencing and demonstrated the androgenetic identity of AgHiPSCs.

first: NaYoung

last: Choi


title: Expression data from CHO-K1 cells in putrescine-deprived conditions

city: Dublin

first: Berta

last: Capella Roca

address: The National Institute for Cellular Biotechnology, Dublin City University, Glasnevin

country: Ireland

summary:
CHO cells grown in serum-free medium have an absolute requirement for putrescine supplementation due to their deficiency in activity of the enzyme arginase. Consequently, principally in this system, polyamines play a central but poorly-understood role in cell proliferation
Cell growth arrest, mainly in the S- and G2/M phases was observed. We used differential gene expression data to investigate the impact of polyamine deprivation on the transcriptome of CHO cells

overall_design: CHO-K1 cells were grown in media deprived of putrescine (and any other polyamine and ornithine) for three days. A control culture, was grown in paralell in the same media but containing putrescine. Cell growth, viability and cell cycle were analysed during the three days. At day 3, samples for RNA extraction were collected from the biological triplicates of both conditions and hybridased in an Affymetrix microarray chip.

first: Padraig

last: Doolan

first: Niall

last: Barron

first: Fiona

last: O’Neill

first: Martin

last: Clynes


title: Effects of developmental N-Methyl D-aspartate (NMDA) receptor antagonism on adulthood hypothalamic gene expression in female C57Bl/6J mice.

city: Riyadh

first: Katharine

middle: Sara

last: Collison

state: Riyadh

address: Takhasussi Street

department: Department of Cell Biology

country: Saudi Arabia

institute: King Faisal Specialist Hospital and Research Centre

summary:
AIM: to examine changes in hypothalamic gene expression following developmental N-Methyl D-aspartate (NMDA) receptor antagonism in adult female C57Bl/6J mice.
AIM: to examine changes in hypothalamic gene expression following developmental N-Methyl D-aspartate (NMDA) receptor antagonism in adult female C57Bl/6J mice. This data will compliment on-going studies into the effect of developmental NMDA receptor antagonism on aspects of the Hypothalamic-Pituitary-Adrenal (HPA) axis.

overall_design: Hypothalamic gene expression in 18 pooled female offspring C57Bl/6J mice with developmental NMDA receptor antagonism was compared to 18  age-matched control mice.

first: Kate

middle: S

first: Angela

last: Inglis

first: Sherin

last: Shibin


title: Gene expression changes in adrenal and hypothalamus following developmental N-Methyl D-aspartate (NMDA) receptor antagonism in adult female C57Bl/6J mice

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

overall_design: Refer to individual Series


title: Altered Biogenesis and MicroRNA Content of Hippocampal Exosomes Following Experimental Status Epilepticus

city: Dublin 2

first: David

last: Henshall

address: 123 Saint Stephen Green

institute: FutureNeuro centre, Royal College of Surgeons in Ireland

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, we characterised the effects of experimental status epilepticus on the expression of exosome biosynthesis components and analysed microRNA content in exosome-enriched fractions prepared from the mouse hippocampus. Status epilepticus induced by unilateral intra-amygdala kainic acid resulted in acute subfield-specific, bi-directional changes in transcripts associated with exosome biosynthesis including up-regulation of ESCRT–dependent and –independent pathways. Increased expression of exosome components including Alix were detectable in samples obtained two weeks after status epilepticus and changes occurred in both the ipsilateral and contralateral hippocampus. Small RNAseq analysis of exosome-enriched fractions prepared using two different techniques detected a rich diversity of conserved microRNAs and determined status epilepticus selectively alters microRNA contents, including upregulation of the glia-enriched miR-21a-3p. We also characterized editing sites of the exosome-enriched miRNAs and found six exosome-enriched miRNAs that were Adenosine-to-Inosine (ADAR) edited with the majority of the editing events predicted to occur within miRNA seed regions. However, the prevalence of these editing events was not altered by status epilepticus. These studies demonstrate status epilepticus alters the exosome pathway and its microRNA content, but not editing patterns.

overall_design: Exosomes were extracted using two different methods (ultracentrifugation or using commercial extraction kit (ExoQuick) at two different time points (24 hrs and 2 weeks). Small RNA librarires were prepared from the exosomes and sequenced on Illumina Mi-Seq. Each group has 3 biological samples.

first: Aasia

last: Batool

first: Thomas

middle: D

last: Hill

first: Ngoc

middle: T

last: Nguyen

first: Elena

last: Langa

first: Mairead

last: Diviney

first: Catherine

last: Mooney

first: Gary

middle: P

last: Brennan

first: Niamh

middle: C

last: Connolly

first: Amaya

last: Sanz-Rodriguez

first: Brenton

last: Cavanagh


title: Effects of developmental N-Methyl D-aspartate (NMDA) receptor antagonism on adulthood adrenal gene expression in female C57Bl/6J mice.

summary: AIM: to examine changes in adrenal gene expression following developmental N-Methyl D-aspartate (NMDA) receptor antagonism in adult female C57Bl/6J mice. This data will compliment on-going studies into the effect of developmental NMDA receptor antagonism on aspects of the Hypothalamic-Pituitary-Adrenal (HPA) axis.

overall_design: Adrenal gene expression in 18 pooled female offspring C57Bl/6J mice with developmental NMDA receptor antagonism was compared to 18  age-matched control mice.


title: Distinct epigenetic features of tumor-reactive CD8+ T cells in colorectal cancer patients revealed by genome-wide DNA methylation analysis

first: Sijin

last: Cheng

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: Tumor-reactive CD8+ tumor infiltrating lymphocytes (TILs) represent a subtype of T cells that could recognize and destroy tumor specifically. Understanding the regulatory mechanism of tumor-reactive CD8+ T cells has important therapeutic implications. Yet the DNA methylation status of this T cell subtype has not been elucidated. In this study, we segregated tumor-reactive and bystander CD8+ TILs, as well as naïve and effector memory CD8+ T cell subtypes as controls from colorectal cancer (CRC) patients, to compare their transcriptome and methylome characteristics. Transcriptome profiling confirmed previous conclusion that tumor-reactive TILs have an exhausted tissue-resident memory signature. Whole-genome methylation profiling identified a distinct methylome pattern of tumor-reactive CD8+ T cells, with tumor-reactive markers (CD39 and CD103) being specifically demethylated. In addition, dynamic changes were observed during the transition of naïve T cells into tumor-reactive CD8+ T cells. Transcription factor (TF) binding motif enrichment analysis identified several immune-related TFs, including three exhaustion-related genes (NR4A1, BATF and EGR2) and VDR, that potentially play important regulatory role in tumor-reactive CD8+ T cells. Our study supports the involvement of DNA methylation in shaping tumor-reactive and bystander CD8+ TILs, and provides a valuable resource for the development of novel DNA methylation markers and future therapeutics.

overall_design:
We used whole-genome methylome profiling and RNA-seq to investigate the characteristics of tumor-reactive and bystander CD8+ TILs, as well as naive and effector memory CD8+ T cell subsets as controls from colorectal cancer patients. Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (https://bigd.big.ac.cn/gsa-human/browse/HRA000059) under accession HRA000059.

****Raw sequence data access provided at: China Genomic Sequence Archive (GSA) (https://bigd.big.ac.cn/gsa-human/browse/HRA000059) under accession HRA000059.

first: Rui

last: Yang

last: Luo

first: Ranran

last: Gao

first: Kezhuo

last: Yu

first: Boxi

last: Kang

first: Li

last: Wang

first: Qiming

last: Zhang

first: Qiao

last: Fang

first: Lei

first: Chen

last: Li

first: Aibin

last: He

first: Xueda

last: Hu

first: Jirun

last: Peng

first: Xianwen

last: Ren

first: Zemin


title: Repurposing the Streptococcus mutans CRISPR-Cas9 system to understand essential gene function

city: Jonesboro

first: Robert

middle: Colquhoun

last: Shields

state: Arkansas

address: Lab Science East

department: Biological Sciences

institute: Arkansas State University

summary: RNA-seq was utilized to compare the transcriptomes of S. mutans strains that had or hadn't experienced CRISPR interference of a green fluorescent protein gene

overall_design: Streptococcus mutans mRNA profiles were generated for a CRISPRi strain without induction, CRISPRi with induction, and a control strain lacking a sgRNA, by deep sequencing, in triplicate

first: Brinta

last: Chakraborty


title: Identification of an eight-protein biosignature for the diagnosis of tuberculosis II

city: Guangzhou

first: Huihua

address: 601, west Huangpu avenue, Tianhe district

department: Biomedicine Institute & Cell Biology Department

institute: Jinan University

summary: Mycobacterium tuberculosis (Mtb) antigen-specific cellular response is promising for detectionof Mtb infection, but not efficient for diagnosis of TB. We firstly identified 16 TB disease-specific protein markers measured in the culture  supernatant of Mtb-stimulated whole blood using a 640 human proteins array, the highest throughput antibody-based protein array available at the time when we did this study. Potential TB-related proteins were then analyzed across three different patient cohorts comprised of healthy controls, LTBI, non-TB pneumonia, and TB patients to evaluate how the biomarkers performed in diagnosing TB in the real clinical setting. The data finally reveal an eight-protein biosignature of TB.

overall_design: We identified 16 candidate biomarkers of tuberculosis in whole blood and developed into a custom multiplexed antibody array for biomarker validation. Tow cohorts of individuals were enrolled into for our study, including 419 individuals to establish and test the predictive model, and 102 individuals for biomarker validation.

first: Ruo-Pan

last: Huang

first: Xinchun

last: Chen


title: Elucidation of molecular and functional networks linked to sarcopenia prevention by caloric restriction in rhesus monkeys

status: Public on Dec 11 2019

city: Madison

first: Rozalyn

last: Anderson

state: WI

address: 2500 Overlook Terrace

department: Department of Medicine

institute: University of Wisconsin-Madison

summary: Caloric restriction (CR) improves survival in nonhuman primates and delays the onset of age-related morbidities including sarcopenia, the age-related loss of muscle mass and function. A shift in metabolism anticipates the onset of muscle aging phenotypes in nonhuman primates suggesting a potential role for metabolism in CR’s protective effects. Here we show that CR induced profound changes in muscle composition and the cellular metabolic environment. Bioinformatic analysis linked these adaptations to proteostasis, RNA processing, and lipid synthetic pathways. At the tissue level, CR maintained contractile content and attenuated age-related metabolic shifts among individual fiber types with higher mitochondrial activity, altered redox metabolism, and smaller lipid droplet size. Biometric and metabolic rate data confirm preserved metabolic efficiency in CR animals that correlated with attenuation of age-related muscle mass and physical activity. These data suggest that CR-induced reprogramming of metabolism plays a role in delayed aging of skeletal muscle in rhesus monkeys.

overall_design: Comparison of tissue from control-fed and caloric restricted-fed rhesus monkeys. N = 5 for control and 8 for CR

first: Timothy

middle: W

last: Rhoads

first: Josef

last: Clark

first: Grace

last: Gustafson

first: Karl

last: Miller

first: Matthew

last: Conklin

first: Tyler

last: DeMuth

first: Mark

last: Berres

first: Kevin

last: Eliceiri

first: Laura

middle: K

last: Vaughan

first: Christine

last: Lary

first: T

last: Beasley

first: Ricki

last: Colman


title: Transcriptomic responses to psychosocial stress in vervet monkey (Chlorocebus sabaeus)

city: Pittsburgh

first: Anna

last: Jasinska

state: PA

address: 3550 Terrace Street

department: School of Medicine

institute: University of Pittsburgh

summary: To identify genes involved in responses to psychosocial stressor, we analysed RNAseq  transcriptomic profiles in whole blood of 15 juvenile male vervet monkeys from the Caribbean island of St. Kitts at three experimental time points: day 0 (baseline), day 3 and day 5 of exposure to the stressor.

overall_design: We analysed one sample (total blood RNA) per animal at each of the three experimental time points: Tp1 (day 0), Tp2 (day 3), Tp4 (day15). Total blood RNA was extracted from PaxGene Blood RNA tubes (Preanalytix) using PAXgene Blood RNA Kit (Qiagen). For cDNA library creation, we used TruSeq Stranded RNA protocol using 100 ng of RNA with RiboZero and Globin treatment (Illumina). We generated 120 bp-long paired-end sequencing reads using high output flow cell lines on HiSeq 4000 sequencer (Illumina).

first: J

last: Jentsch


title: Cross-species analysis across 450 million years of evolution reveals conservation and divergence of the microglia program (bulk RNA-seq)

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: Here we characterize microglia transcriptional program across ten species spanning more than 450 million years of evolution. We find that microglia express a conserved core gene program of orthologous genes from rodents to human, including ligands and receptors associated with interactions between glia and neurons. In most species, microglia show a single dominant transcriptional state, while humans express significant microglia heterogeneity. In addition, we observed notable differences in complement, phagocytic and several critical signaling pathways that are enriched with susceptibility genes to brain disorders, including Alzheimer’s and Parkinson’s disease in microglia of common animal models as compared to human. Our study provides an essential resource of conserved and divergent microglia pathways across evolution with important implications for future development of microglia-based therapies in humans.

sample_organism:
Danio rerio
Gallus gallus
Callithrix jacchus
Macaca fascicularis
Homo sapiens
Ovis aries
Mesocricetus auratus
Mus musculus
Rattus norvegicus

overall_design:
Single cell and bulk RNA-seq of microglia from 10 different species and comparison of transcriptional landcape over species. Biological replicates of different species were n=3-6.
The raw data for human subjects will be submitted through EGA for controlled access.

first: Laufey

last: Geirsdottir

first: Eyal

last: David

first: Assaf

last: Weiner

first: Hadas

last: Keren-Shaul

first: Igor

last: Ulitsky


title: Murine cartilage tissues (tibia): Control vs ADAM10 flox/flox-Col2a1-Cre

city: Tokorozawa

first: Keisuke

last: Horiuchi

address: 3-2 Namiki, Tokorozawa

department: Department of Orthopedic Surgery

country: Japan

institute: National Defense Medical College

summary: Transcriptional profiling of mouse cartilage tissues comparing control and mutant mice (in which the Adam10 allele was excised under the control of a Col2a1 promoter) to negate ADAM10 activity in osteochondroprogenitors. Goal was to determine the effects of the loss of ADAM10 activity on cartilage gene expression.

overall_design: Two-condition experiment, Control vs. vs ADAM10 flox/flox-Col2a1-Cre mice. Biological replicates: 3 mice / each genotype.


title: Identification of region-specific astrocyte subtypes at single cell resolution

city: Leuven

first: Araks

last: Martirosyan

address: Herestraat 49

department: Center for Brain & Disease Research

country: Belgium

institute: VIB-KU Leuven

summary: Astrocytes, a major cell type found throughout the central nervous system, have general roles in the modulation of synapse formation and synaptic transmission, blood-brain-barrier formation and regulation of blood flow, as well as metabolic support of other brain resident cells. To investigate the true extent of astrocyte molecular diversity across forebrain regions, we used single cell RNA sequencing and generated a database containing ~2000 astrocytes. Our analysis identifies five transcriptomically distinct astrocyte subtypes in adult mouse cortex and hippocampus. Validation of our data in situ reveals distinct spatial positioning of defined subtypes, reflecting the distribution of morphologically and physiologically distinct astrocyte populations. Our findings are evidence for specialized astrocyte subtypes between and within brain regions.

overall_design: Single cell suspension for hippocampus and cortex from P56 C57/Bl6 mice was obtained using a papain-based protocol. A Percoll gradient was used to remove myelin. Astrocytes were then labeled with the ACSA-2 antibody (conjugated to the fluorophore phycoerythrin: PE which specifically recognizes the plasma membrane marker ATP1B2). Cells were isolated by FACS, with one cell deposited per single well of a PCR plate. Preparation of sequencing libraries was done using the optimized Smart-seq2 protocol. Libraries were sequenced using an Illumina NextSeq 500 system (75bp paired-end reads) to optimal coverage (~1 million reads per cell).  Sequencing reads were mapped against mouse reference genome M12 (GRCm38.p5), modified to take ERCC sequences into account using STAR 2.5.2b. Output alignment BAM files were then merged and sorted using Samtools version 1.4. Gene counts were generated using HTSeq version 0.6.1p1. Low quality libraries were removed based on FastQC and additional quality metrics.


title: The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [ChIP-Seq]

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The histone chaperone FACT and histone H2B ubiquitination (H2Bub) facilitate RNA Polymerase II passage through chromatin. It remains unknown to what extent they cooperate in vivo. Here, we used genome-wide, genetic, biochemical and microscopic approaches to dissect their interplay in the fission yeast Schizosaccharomyces pombe. We show that FACT and H2Bub repress antisense transcripts near the 5’ end and inside gene bodies, respectively. The accumulation of these transcripts accompanies with changes at genic nucleosomes in FACT and H2Bub mutants. Moreover, in the H2Bub mutant, FACT binding to histones is stabilized. Interestingly, analysis of FACT-H2Bub double mutants revealed that FACT depletion suppresses genic nucleosome loss in the H2Bub mutant. In addition, FACT, unlike H2Bub, maintains nucleosomes in intergenic regions. This is especially important for subtelomeric gene repression and in compacting chromatin into ‘knobs’. Collectively, our study demonstrates that FACT and H2Bub functionally interact with each other in a genome-context dependent manner. Further, our data indicate an involvement of FACT in higher order chromatin formation outside of euchromatin.

overall_design: ChIP-seq experiments in wild type, H2BK119R, pob3 and double mutant fission yeast.

first: Magdalena

last: Murawska

first: Andreas

middle: G

last: Ladurner


title: Polycomb group proteins regulate chromatin architecture in mouse oocytes and early embryos

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.

overall_design: Ring1-/-Rnf2fl/fl (Posfai et al., 2012) and Zp3-Cre (de Vries et al., 2000) mice were generated as previously described. Ring1-/-Rnf2fl/fl FGOs and Ring1/Rnf2 dKO FGOs were collected from Ring1-/-Rnf2fl/fl and Ring1-/-Rnf2fl/fl;Zp3-Cre mice separately. Total RNA-seq experiments were performed on these oocytes.

first: Nathalie

last: Véron

first: Evgeniy

middle: A

last: Ozonov

middle: H


title: RNASeq of LCMV Kb NP396+ CD45RBhi and CD45RBlo Memory CD8+ T Cells

city: Atlanta

first: Mandy

middle: L

last: Ford

state: GA

address: 101 Woodruff Circle, WMB 5105

department: Surgery

institute: Emory University

summary: We reported the differential expression of genes between CD45RBhi and CD45RBlo LCMV-specific CD8+ T cell memory.

overall_design: Gene expression analysis of naïve CD8+ T cells, CD45RBhi NP396+ CD8+ T cell memory, and CD45RBlo NP396+ CD8+ T cell memory.

first: Scott

last: Krummey


title: Genome-wide microRNA expression in WT and RBP-J KO BMDMs

city: Beijing

first: Xiang

last: Zhang

address: Tsinghuayuan Street

institute: Tsinghua University

summary: RBP-J is a master transcriptional factor of Notch signaling, which plays important roles in developmental processes as well as regulating macrophage-mediated inflammatory responses. However,  the regulation of RBP-J on miRNAs are less studied. So we sequenced microRNAs from BMDMs derived from the LyZ2 Cre control (WT) and RBP-J conditional knockout mice (RBP-J KO; Rbpjf/f LyZ2 Cre) to address the roles of RBP-J on regulating miRNAs in macrophages.

overall_design: Examination of differential microRNA expression levels in unstimulated BMDMs from WT and RBP-J KO mice

first: Sinead

last: Smith

first: Bin


title: Long non-coding RNA RP11-19E11.1 is an E2F1 target required for tumor cell proliferation and survival in basal breast cancer

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Long non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and progression. LncRNAs are differentially expressed in breast cancer subtypes. Basal-like breast cancers are generally poorly differentiated tumors, are enriched in embryonic stem cell signatures, lack expression of estrogen receptor, progesterone receptor, and HER2 (triple negative breast cancer, TNBC), and show activation of proliferation-associated factors. We hypothesized that lncRNAs are key regulators of basal breast cancers. Using The Cancer Genome Atlas we identified lncRNAs that are overexpressed in basal tumors compared to other breast cancer subtypes and expressed in at least 10% of patients. Remarkably, we identified lncRNAs whose expression correlated with patient prognosis. We then evaluated the function of a subset of lncRNA candidates in the oncogenic process in vitro. Here, we report the identification and characterization of the chromatin-associated lncRNA, RP11-19E11.1, which is up-regulated in 40% of basal primary breast cancers. Gene set enrichment analysis in primary tumors and in cell lines uncovered a correlation between RP11-19E11.1 expression level and the E2F oncogenic pathway. We show that this lncRNA is chromatin-associated and an E2F1 target, and its expression is necessary for cancer cell proliferation and survival. Finally, we used lncRNA expression levels as a tool for drug discovery in vitro, identifying Protein Kinase C (PKC) as a potential therapeutic target for a subset of basal-like breast cancers. Our findings suggest lncRNA overexpression is clinically relevant. Understanding deregulated lncRNA expression in basal-like breast cancer may lead to potential prognostic and therapeutic applications.

overall_design: RNA-seq data from HCC38, MDA-MB-468 and SUM149PT was obtained in duplicate after RP11-19E11.1 KD.

first: Ariadna

last: Giro-Perafita

first: Aristotelis

last: Tsirigos

first: Irma

last: Sanchez

first: Francisco

middle: J

last: Esteva


title: RNA-seq data for: A conserved mito-cytoplasmic translational balance links two longevity pathways

city: Amsterdam

first: Georges

last: Janssens

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

summary: Slowing down mRNA translation in either the cytoplasm or the mitochondria are both conserved longevity mechanisms. Here, we found a non-interventional natural correlation of mitochondrial and cytoplasmic ribosomal proteins when looking at mouse population genetics, suggesting a mito-cytoplasmic translational balance. Additionally, inhibiting mitochondrial translation in C. elegans in turn reduced cytoplasmic translation and repressed growth pathways while upregulating stress responses at both proteome and transcriptome levels. This coordinated repression of cytoplasmic translation is dependent on the atf-5/Atf4 transcription factor and is conserved in mammalian cells upon inhibiting mitochondrial translation pharmacologically with the antibiotic doxycycline. Lastly, extending this to a mammalian setting using doxycycline-treated germ-free mice, we found repressed cytoplasmic translation and ribosomal proteins in liver. These data demonstrate that inhibiting mitochondrial translation initiates a signaling cascade leading to coordinated repression of cytoplasmic translation, unlike previously described unidirectional cyto-to-mito translational communication in yeast, which can be targeted to promote healthy aging.

sample_organism:
Caenorhabditis elegans
Mus musculus

platform_organism:
Caenorhabditis elegans
Mus musculus

overall_design: In total 30 samples were sequenced: 18 were from C. elegans worms, 12 were from M. musculus mouse. Worm samples consisted of either (1) total RNA of whole worms, (2) polysomal RNA of whole worms, or (3) monosomal RNA of whole worms, performed in triplicate for both treatment (mrps-5 RNAi) and control (empty vector) worms. Mouse samples consisted of either (1) total RNA of liver or (2) polysomal RNA of liver, performed in triplicate for both treatment (doxycycline, 50mg/kg/d for two weeks) or control (amoxicillin, 50mg/kg/d for two weeks) in germ-free mice.

first: Marte

last: Molenaars

middle: E


title: The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions

first: Tamas

last: Schauer

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

overall_design: Refer to individual Series


title: The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [MNase-seq]

overall_design: MNase-seq experiment in wild type, H2BK119R, pob3 and double mutant fission yeast using various degree of Mnase digestion.

first: Magdalena

last: Murawska

first: Andreas


title: The chaperone FACT and H2B ubiquitination maintain S. pombe genome architecture through genic and subtelomeric functions [RNA-seq]

overall_design: RNA-seq experiment in wild type, H2BK119R, pob3 and double mutant fission yeast.

last: Ladurner


title: Intake of protein modulate immune function, POMC processing and IGF signaling gene expression pathways in peripheral mononuclear cells in home-dwelling old subjects - a transcriptomic approach

status: Public on Dec 10 2019

city: Oslo

first: Stine

middle: Marie

last: Ulven

address: Sognsvannsveien 9

department: Department of Nutrition

country: Norway

institute: University of oslo

summary: Adequate intake of protein among older adults is associated with better health outcomes, but conflicting results makes it difficult to define the optimal intake. To further understand the impact of protein intake on  metabolic processes we studied genome-wide gene expression changes in peripheral blood mononuclear cells (PBMCs) in home-dwelling old subjects after increased protein intake for 12 weeks.

overall_design: This study was a parallel design double blind randomized controlled intervention study. In total fifty home-dwelling men and women with reduced physical strength and/or performance  (≥ 70 yrs) were recrutied to the study. Subjects were stratified by gender and smoking into two groups, receiving either a protein-enriched milk (2 x 20 g protein/d) or an isocaloric carbohydrate drink for breakfast and evening meal for 12 weeks. The test drinks were provided by TINE SA and were identical in color, labeling and appearance, and was blinded to both the study participants and the study staff. Participants maintained their normal diet and physical activity levels during the study period. PBMCs were isolated before and after the intervention. mRNA was extracted using RNeasy Mini Kit (Qiagen) and the RNA quantity and quality was meassured using NanoDrop-1000 (NanoDrop Technologies, Inc., Delaware, USA), and Aglient 2100 Bioanalyzer (Agilent Technologies, Inc., California, USA), resepctilvely. Microarray analysis were performed using Illumina technology.  Thirty-six subjects finished the study, and five samples were excluded from the final analysis, leaving us with n=14 in the protein group and n=17 in the carbohydrate group.

first: Gyrd

middle: O

last: Gjevestad

first: Kirsten

middle: B

last: Holven

first: Amanda

last: Rundblad

first: Arna

last: Flatberg

first: Mari

last: Myhrstad

first: Karina

last: Karlsen

first: Shivaprakash

last: Mutt

first: Karl-Heinz

last: Herzig

first: Inger

last: Ottestad

middle: M


title: Capsular glycan recognition provides antibody-mediated protection against tuberculosis

city: Bronx

first: Jacqueline

last: Achkar

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

summary:
Increasing evidence suggests that antibodies (Abs) can have protective roles in M. tuberculosis (Mtb) infection but knowledge of the most relevant protective antigens and epitopes in humans is limited.
Using novel glycan arrays, we establish that human serum IgG induced against the M. tuberculosis (Mtb) capsular polysacharide arabinomannan (AM) in natural Mtb infection is highly heterogeneous in its binding specificity and differs in both its reactivity to oligosaccharide (OS) motifs within AM and its functions between BCG vaccination and/or controlled (latent) versus uncontrolled (TB) M. tuberculosis infection. We show that anti-AM IgG from asymptomatic but not diseased individuals is protective, and provide data suggesting a role of IgG2 and specific AM oligosaccharides. Filling a gap in the current knowledge of protective antigens in humans, our human data support the key role of the M. tuberculosis surface glycan AM and suggest the importance of targeting specific glycan epitopes within AM in antibody-mediated immunity against TB.

overall_design: Sera from 10 asymptomatic TST+/IGRA+ subjects and 13 symptomatic TB subjects were analyzed for anti-AM OS IgG reactivity. The anti-AM OS reactivities were then evaluated for correlations with Ab-mediated protective functions against M. tuberculosis.

first: Tingting

last: Chen

first: Caroline

last: Blanc

first: Maju

last: Joe

first: Todd

last: Lowary


title: RNA-seq of H1299 cells in which either PRKCI or SOX2 was silenced by validated lentiviral shRNA constructs

city: Jacksonville

first: E. Aubrey

last: Thompson

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

summary: RNA-seq data of H1299 from NT versus PRKCI KD and NT versus SOX2 KD cells. Analysis revealed activation of oncogenic signaling pathways by PRKCI and SOX2.

overall_design: Examination of active signaling in H1299 NT cells

first: Alan

last: Fields

first: Yi

last: Liu

first: Xue

last: Wang


title: Dissecting the role of PI3K activation in malignant mesothelioma development

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary:
Purpose: The PI3K/AKT/mTOR pathway  is activated in most MM. In MM the mechanism of this pathway activation has not been completely elucidated, although loss of expression of PI3K pathway regulator, PTEN, is a frequent event in MM. Pten;Trp53 combined genetic loss in mouse mesothelium leads to non-epithelioid MM development. We assessed more broadly the impact of PI3K activation in MM development by comparing the effects of Pik3ca activation versus Pten inactivation in combination with Trp53 deletion on MM development. RNAseq was performed from tumor samples derived from Ptenlox/lox ; Trp53lox/lox and  Pik3caH1047R/+; Trp53lox/lox mice derived sarcomatoid MM.
Results: Our data also reveal that Pten loss has stronger oncogenic properties than Pik3ca mutation in MM.

overall_design: Peritoneal MM developed in Ptenlox/lox;Trp53lox/lox and  Pik3caH1047R/+;Trp53lox/lox mice  following inoculation of adenoviruses coding for Cre-recombinase into the bladder wall. Mice were sacrificed  at humane endpoint and tumors collected for further analysis

first: Miriam

last: Marqués

last: Martínez de Villarreal


title: Transcriptome analysis of ankylosing spondylitis patients before and after TNF-α inhibitor therapy reveals the pathways affected

city: Brisbane

first: Jonathan

last: Ellis

state: Queensland

address: 37 Kent Street, Woolloongabba

country: Australia

institute: Queensland University of Technology

summary: mononuclear cells from AS patients pre and post treatment. We found 656 differentially expressed genes, including the

overall_design: 44 total RNA samples from ankylosing spondylitis patients before and after TNF alpha inhibitory therapy


title: Transcriptome analysis of total blood cells from sheep after vaccination with FMDV vaccines

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

summary: Transcriptome analysis of total blood cells from sheep collected at 0, 4 and 24 hours after vaccination with inactivated FMDV vaccine, and adenovirus (human Ad5)-based vaccines encoding FMDV antigens, with and without Montanide ISA206 VG adjuvant.

overall_design: RNA-seq of sheep total blood cells at 0, 4 and 24h after FMDV vaccination with 3 different vaccines (10 sheep per {time; vaccine} group).

first: Fleur

last: Costa

first: Bernard

last: Klonjkowski

first: Anthony

last: Relmy

first: Edouard

last: Guitton

first: Luc

last: Jouneau

first: Yan

last: Jaszczyszyn

first: Cloelia

last: Dard-Dascot

first: Isabelle

last: Schwartz


title: Shp-deletion induces dissociation of steatosis and inflammation in NASH

city: kansas city

first: Yuxia

last: Zhang

state: KS

address: 3901 Rainbow Blvd, Hemenway 4001

department: Pharmacology, Toxicology, and Therapeutics

institute: University of Kansas Medical Center

summary: Two months-old Shp flox/flox male mice were injected with either AAV8 expressing Cre recombinase driven by the thyroxine-binding globulin (Tbg) promoter (AAV8-Tbg-Cre) or control AAV8 (AAV8-Tbg-null) and fed chow or a diet enriched in high fat, cholesterol, and fructose (Research diet D09100301: 40 kcal% fat, 2% cholesterol, 20 kcal% fructose, hereafter referred to as HFCF diet) for 3 months. Liver RNA was isolated and submitted to RNA-seq.

overall_design: Analysis of hepatic gene expression from 3 WT mice on chow, 3 Shp Hep-/- mice on chow, 3 WT mice on HFCF diet, and 3 Shp Hep-/- mice on HFCF diet

first: Nancy

middle: S

last: Magee


title: Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development

city: LA JOLLA

first: Matteo

last: D'Antonio

address: 9500 Gilman Drive #0761

institute: UCSD

summary: Many current cellular models aimed to elucidate cancer biology do not recapitulate pathobiology including tumor heterogeneity, an inherent feature of cancer that underlies treatment resistance.  Here we introduce a new cancer modeling paradigm using genetically engineered human pluripotent stem cells (hiPSCs) that capture authentic cancer pathobiology.  Orthotopic engraftment of the neural progenitor cells derived from hiPSCs introduced with tumor-associated genetic driver mutations revealed by The Cancer Genome Atlas project for glioblastoma (GBM) results in formation of brain tumors.  As observed in GBM patient samples, these models harbor inter-tumor heterogeneity resembling different GBM molecular subtypes, and intra-tumor heterogeneity.  Further, re-engraftment of these tumor cells generate tumors with features characteristic of patient samples and present mutation-dependent patterns of tumor evolution.  Thus, these cancer avatar models provide a platform for a comprehensive longitudinal assessment of human tumor development as governed by molecular subtype mutations.

overall_design: iGBM models (all in duplicates): TP53-/-;PDGFRAΔ8-9; PTEN-/-;NF1-/-; and controls

first: Tomoyuki

last: Koga

first: Isaac

last: Chaim

first: Jorge

last: Benitez

first: Sebastian

last: Markmiller

first: Alison

middle: D

last: Parisian

first: Kristen

last: Turner

first: Florian

last: Hessenauer

last: D’Antonio

first: Nam-phuong

last: Nguyen

first: Shahram

last: Saberi

first: Jianhui

last: Ma

first: Shunichiro

last: Miki

first: Antonia

last: Boyer

first: John

last: Ravits

first: Kelly

last: Frazer

first: Vineet

last: Bafna

first: Clark

last: Chen

first: Paul

last: Mischel

first: Gene

last: Yeo

first: Frank

last: Furnari


title: Salmonella Typhimurium SL1344 RiboPools/RiboZero comparison

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: Comparison of RiboPools and RiboZero rRNA depletion strategies in total RNA from Salmonella Typhimurium, strain SL1344

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: One dataset for RiboPools-treated total RNA, two datasets for RiboZero-treated total RNA as replicates, one dataset for untreated total RNA

first: Iana

middle: V

last: Kim

first: Kristina

last: Döring

first: Sascha

last: Dietrich

first: Claus

last: Kuhn


title: CD94-CD56dim, CD94+CD56dim and CD94+CD56hi natural killer (NK) cell comparison

city: Worcester

first: Alan

last: Derr

state: Massachusetts

address: 55 Lake Ave North

department: Program in Bioinformatics and Integrative Biology

institute: University of Massachusetts Medical School

summary: We compared transcriptomes of 3 NK populations and found CD94+CD56hi NK cells exhibit unique transcriptome.

overall_design: CD94-CD56dim, CD94+CD56dim and CD94+CD56hi NK cells were sorted then subject to RNA-Seq.

first: Yetao

last: Wang

first: Lawrence

last: Lifshitz

first: Alper

last: Kucukural

first: Patrick

last: McDonel

first: Manuel

last: Garber

first: Jeremy

last: Luban


title: CD94-CD56dim, CD94+CD56dim and CD94+CD56hi natural killer (NK) cell chromatin accessibility assay

summary: ATAC-Seq was performed for 3 NK populations and found CD94+CD56hi NK cells exhibit unique chromatin accessible region

overall_design: CD94-CD56dim, CD94+CD56dim and CD94+CD56hi NK cells were sorted then subject to ATAC-Seq


title: Suppression of FOXM1 Activities and Breast Cancer Growth in Vitro and in Vivo by a New Class of Compounds

city: Urbana

first: Zeynep

last: Madak-Erdogan

state: Illinois

address: 1201 W. Gregory Dr, 359 ERML Hall

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Illinois

summary: The transcription factor FOXM1 is up-regulated and overexpressed in aggressive, therapy-resistant forms of hormone receptor-positive and triple negative breast cancers, and is associated with less good patient survival. FOXM1 pathway signaling is also a key driver in other aggressive cancers, including those in prostate, lung, ovary, and gastrointestinal tract. Therefore, our goal has been to identify compounds effective in suppressing FOXM1 activity and breast cancer proliferation, and displaying good potency and pharmacokinetic properties for in vivo antitumor efficacy. In this report, we describe our studies on the FOXM1 targeting activities of 1,1-diarylethylene mono- and diamine compounds and their methiodide salts in cell-free, cell-based, and in vivo assays. The compounds bind directly to FOXM1 and alter its proteolytic sensitivity, reduce the cellular level of FOXM1 protein, and suppress the proliferation of breast cancer cells. RNA-seq and gene set enrichment analyses indicate that the compounds NB-73 and NB-55 decrease the expression of FOXM1-regulated genes and suppress gene ontology processes known to be under FOXM1 regulation. Several compounds with favorable pharmacokinetic properties were studied in preclinical breast tumor models. One compound (NB-55) had good oral efficacy in suppressing the growth of FOXM1-containing breast tumors in NOD-SCID-gamma (NSG) mice, and several others (NB-73, NB-115, and NB-63) had good efficacy in tumor growth suppression by subcutaneous administration. Our findings identify and characterize a new class of compounds that effectively antagonize FOXM1 actions and tumor growth that may be suitable for further clinical evaluation in targeting aggressive breast cancers driven by FOXM1.

overall_design: Examine the effects of various FOXM1 inhibitors on gene expression in both  estrogen receptor positive and triple negative breast cancer cell lines.

first: Yvonne

last: Ziegler

first: Mary

last: Laws

first: Valeria

last: Sanabria Guillen

first: Sung

first: Brandi

middle: P

last: Smith

first: Ping

last: Gong

first: Noah

last: Bindman

first: Yuechao

last: Zhao

first: Kathryn

last: Carlson

first: Mayuri

last: Yasuda

first: Divya

last: Singh

first: Zhong

last: Li

first: Dorraya

last: El-Ashry

first: John

last: Katzenellenbogen

first: Benita


title: A transcriptomic continuum of differentiation arrest in acute leukemias

status: Public on Dec 09 2019

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge


title: Long non-coding RNA dysregulation is a frequent event in non-small cell lung carcinoma pathogenesis

city: Adelaide

first: Naiara

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

institute: The University of Adelaide

summary: Our aim was to contribute to a more comprehensive landscape for lncRNA deregulation in NSCLC by identifying lncRNA profiles that could significantly discriminate NSCLCs tissue from paired normal lung tissue. Therefore, we assessed the transcriptional profile of 44 paired tumour and adjacent normal lung tissue from NSCLC patients using an Agilent Custom 8x60K expression array (AMADID: 047718) designed by the GENCODE consortium. This microarray, based on the Gencode v15 catalog of human lncRNA, interrogates 17,535 randomly selected protein coding and 22,001 lncRNA transcripts, being each transcript targeted by two probes.

overall_design: Two-condition experiment, NSCLC vs. adjacent normal tissue. Biological replicates: 44 tumour and adjacent normal tissue pairs. Technical replicates: 3 tumour and adjacent normal tissue pairs.

first: Triantafillos

last: Liloglou

first: Amelia

last: Acha-Sagredo


title: Identification of a TAZ-dependent transcriptional program in non-small cell lung adenocarcinoma

city: Durham

first: Ann Marie

last: Pendergast

state: North Carolina

address: 308 Research Drive LSRC

department: Pharmacology and Cancer Biology

institute: Duke University

summary: The purpose of this study was to identify and generate a transcriptional target gene signature for the TAZ transcriptional co-activator in non-small cell lung adenocarcinoma (NSCLC).

overall_design: Samples were analyzed for differential gene expression in PC9 Parental (control) versus PC9 cells expressing active mutant TAZ4SA.

first: Jacob

last: Hoj

first: Ann


title: Analysis of transcriptomes of thymic populations isolated from neonatal thymi

summary: The transcriptional profiles of human acute leukemias frequently parallel those of normal hematopoietic precursors, and provide insight into mechanisms of oncogenesis in these leukemias. We extracted RNA from six phenotypically defined T-lymphoid progenitor groups that were isolated from a series of human thymi, and compared gene expression patterns with different subgroups of primary human acute leukemias.

overall_design: Total RNA was obtained from flow sorted populations of neonatal thymi and was used for Affymetrix microarray analysis.

first: Jonathan

last: Bond

first: Elizabeth

last: Macintyre


title: Modeling Progressive Fibrosis with Pluripotent Stem Cells Identifies an Anti-Fibrotic Small Molecule

city: Los Angeles

first: Brigitte

last: Gomperts

address: 650 Charles E. Young Drive; 9-240 Factor Building

institute: UCLA

summary: Progressive organ fibrosis accounts for one third of all deaths worldwide, yet preclinical models that mimic the complex, progressive nature of the disease are lacking and hence there are no curative therapies. Progressive fibrosis across organs shares common cellular and molecular pathways involving chronic injury, inflammation, and aberrant repair resulting in deposition of extracellular matrix, organ remodeling and ultimately organ failure. Here we describe the generation and characterization of an in vitro progressive fibrosis model that uses multiple different cell types derived from induced pluripotent stem cells.  Our model produces endogenous activated TGF-b and contains activated fibroblastic aggregates that progressively increase in size and stiffness with activation of known fibrotic molecular and cellular changes. We used this model as a phenotypic drug discovery platform for modulators of fibrosis. We validated this platform by identifying a compound that promotes resolution of fibrosis in in vivo and ex vivo models of ocular and lung fibrosis.

overall_design:
iFA Model (stepwise progression): Examination of aggregate cultures of mesenchymal-like cells from 3 patients at days 4 and 13.
iFA Model (AA5 treatment): Comparison of aggregate cultures of mesenchymal-like cells from 2 patients after DMSO-treated, prevention (AA5p) or reversal (AA5r) of iFA phenotype.
LSC (AA5 treatment): Comparison of DMSO- and AA5-treated Lung Slice Cultures (LSCs) from end-stage IPF lung tissue obtained at the time of lung transplantation from 6 patients.

first: Preethi

last: Vijayaraj

first: Aspram

last: Minasyan

first: Katherine

last: Chung

first: Weihong

last: Yan

first: David

last: Shia

first: Thomas

last: Graeber


title: Transcriptomic analysis of Acute Myeloid Leukemia and T Acute Lymphoblastic Leukemia

summary: Diagnostic classification of Acute Myeloid and Lymphoid Leukemias (AMLs and ALLs) is mostly based on immunophenotype. This approach can pose challenges for phenotypically heterogeneous immature leukemias, and doesn't take account of recent advances in understanding of the developmental multipotency of diverse hematopoietic progenitor populations. We performed transcriptional analyses of a large series of primary ALs, including a high proportion of immature cases, in order to understand the spectrum of differentation arrest in AL. These transcriptional profiles were compared with both normal hematopoietic progenitors and independent leukemia data-sets.

overall_design: Total RNA was obtained from bone marrow samples of Acute Myeloid Leukemia (AML) or T Acute Lymphoblastic Leukemia (T-ALL) patients, and was used for Affymetrix microarray analysis. The samples below were run over 2 batches (marked L or M below).


title: Gene expression from fibroblast-like synoviocytes (FLS) of three patients with rheumatoid arthritis (RA) that were cultured in four conditions: control medium (Basal), ATRA, TNF and ATRA+TNF.

city: Santiago de Compostela

first: Carmen

last: Conde

state: A Coruña

address: Choupana s/n

institute: Hospital Clinico Universitario

summary: The aim of this study was to investigate the response of FLS from RA patients to retinoic acid and retinoic acid combined with the central cytokine of RA, TNF.

overall_design: FLS from six RA patients were cultured for 12h in serum-deprived medium with 0.05% DMSO (Basal), 5mM ATRA, 10ng/ml TNF or 5mM ATRA+10ng/ml TNF. RNA was extracted and pooled (two pools of three patients each).

first: Nerea

last: Mosquera

first: Angela

last: Rodriguez-Trillo

first: Francisco

last: Blanco

first: Antonio

last: Mera-Varela

last: Gonzalez


title: Primary Mouse Hepatocytes treated with 500μM Metformin for 24 hours

status: Public on Dec 08 2019

city: Hamilton

first: Emily

middle: Anne

last: Day

state: Ontario

address: McMaster University, 1200 Main St W, Department of Medicine HSC 4N71

department: Medical Sciences

country: Canada

institute: McMaster University

summary: Anaylsis of gene expression in primary mouse hepatocytes treated with  500μM Metformin for 24 hours

overall_design: Total RNA was isolated from 4 replicates from both control and metformin treated wells were analyzed for a total of 8 samples.

first: Rebecca

last: Ford

first: Brennan

last: Smith

first: Pedrum

last: Mohammadi-Shemirani

first: Marisa

middle: R

last: Morrow

first: Robert

last: Gutgesell

first: Rachel

last: Lu

first: Amogelang

last: Raphenya

first: Mostafa

last: Kabiri

first: Andrew

last: McArthur

first: Natalia

last: McInnes

first: Sibylle

last: Hess

first: Guillaume

last: Paré

first: Hertzel

middle: C

last: Gerstein

first: Gregory

last: Steinberg


title: scRNA-Seq of negatively enriched NK cells 4 days post MCMV infection

city: Charlottesville

first: Awndre

last: Gamache

state: VA

address: 1122 Forest Hills Ave., B

department: Bierne B. Carter Center for Immunology Research

country: USA

institute: University of Virginia

summary: Ly49G2+ NK cells mediate essential control of murine cytomegalovirus (MCMV) infection in mice which express the H-2Dk class I molecule. As a cognate ligand for specific Ly49G2 inhibitory receptor allotypes, H-2Dk also licenses Ly49G2+ NK cells in naïve and MCMV-infected mice.  These findings suggest Ly49G2 may promote antiviral NK cell activities during MCMV infection. Indeed, in mice lacking the Ly49G2 receptor, MCMV resistance is fully abrogated.  Additionally, NK cells expressing Ly49R, an NK cell associated activation receptor that also recognizes H-2Dk, have their function augmented by Ly49G2 and are required for MCMV resistance.

overall_design: Since Ly49G2 promoted enhanced Ly49R+ NK cell effector responses during viral infection, we examined it’s influence on NK cell gene expression day 4 PI.  Single cell RNA sequencing (scRNA-Seq) was used to evaluate transcriptomic differences in single NK cells responding to MCMV across mouse strains expressing either, Ly49G2, H-2Dk or both. We also ascertained whether strain-specific differences in NK cell gene expression were simply due to different extrinsic signals based on host environment. scRNA-Seq analysis revealed that both extrinsic and intrinsic factors determined NK cell gene expression, such that expression of both receptor and ligand resulted in increased cell cycle regulation and proliferation during MCMV infection. In comparison, NK cells lacking self-MHC Dk recognition via Ly49G2 had significantly higher expression of inflammatory response pathways.

first: Michael

middle: G

last: Brown


title: Co-opted transposons help perpetuate conserved higher-order chromosomal structures

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St. Louis

summary: Co-option of transposable elements maintains conserved 3D genome structures via CTCF binding site turnover in human and mouse.

overall_design: in situ HiC and in situ Hybrid-capture HiC (HiC^2) were generated for L1M3f-del and LTR41-del GM12878 cell lines

first: Mayank

middle: N

last: Choudhary

first: Ting

last: Wang


title: Real-time quantitative PCR analysis of apple roots and leaves after ARD infection

city: Dresden

first: Stefanie

last: Reim

state: Saxony

address: Pillnitzer Platz 3a

department: Institut for Breeding Research on Fruits

institute: Julius Kühn Institut

summary:
Root and leave samples of 4 different apple genotypes were investigated in order to analyse the gene expression after infection with Apple Replant Disease (ARD). All genotypes were cultivated in ARD-infected soil and gamma-irradiated (disinfected) soil in the greenhouse for 7 days. The ARD soil originated from two different orchards representing two different soil compositions. After 7 days root tissue was collected from each plant and used for the subsequent gene expression analysis.

This work was part of the project BonaRes-ORDIAmur funded by the German Federal Ministry of Research and Education within the frame of the program BonaRes (grant no. 031B0025B). It was also funded by the German Research Foundation (DFG) via the research training group GRK1798 "Signaling at the Plant-Soil Interface" and a grant to BL and LB (BE 1174/19-1).

overall_design: qPCR gene expression profiling. Plant material of 5 repetitions of each genotype, each soil origin and each soil treatment were used as described in the summary. Equal amount total RNA from each plant was pooled prior to gene expression analysis.

first: Annmarie-Deetja

last: Rohr

first: Traud

last: Winkelmann

first: Stefan

last: Weiß

first: Benye

last: Liu

first: Ludger

last: Beerhues

first: Michaela

last: Schmitz

first: Magda-Viola

last: Hanke

first: Henryk

last: Flachowsky


title: Transcriptomic comparison of 3D retinal organoids derived from retinitis pigmentosa patient harboring PDE6B mutation and non-phenotype control

status: Public on Dec 06 2019

city: Wenzhou

first: Mei-Ling

last: Gao

state: Zhejiang

address: N0.207, West Xueyuan Road

department: Division of Ophthalmic Genetics

country: China

institute: Wenzhou Medical University

summary: Retinitis pigmentosa (RP) is a hereditary retinal degenerative disease.  Although an increasing number of disease genes have been identified, the exact cellular mechanisms of RP remain largely unclear.  Retinal organoids (ROs) derived from the induced pluripotent stem cells (iPSCs) of patients provide a potential but unvalidated platform for deciphering disease mechanisms.  Here, we developed patient ROs with a PDE6B mutation.To investigate the transcriptional effects of the PDE6B mutation, comparison of bulk RNA-seq profiles were performed in patient and control ROs, which were collected from the mid-stage (D90, 120, 150 and 180) to late-stage (D230). Transcriptome analysis revealed a remarkably distinct gene expression profile in the patient ROs at late-stage.Gene Ontology (GO) analysis of the transcripts significantly different at D230 between the patient and control ROs indicated an enrichment of genes implicated in G-protein-coupled receptor activity, G-protein-coupled receptor signaling pathway and calcium ion binding.

overall_design: Examination of 5 groups of retinal organoids derived from RP patient and control respectively

first: Zi-Bing

last: Jin

first: Fang

last: Han


title: The effect of acute sustained hypoxia on gene expression in liver, kidney and lung on different times-of-day

city: Rehovot

first: Gal

last: Manella

state: Israel

address: 234 Herzel St.

institute: Weizmann Institute of Science

summary: Many hypoxia related diseases present a time of day dependency. Here, we examine the difference in transcriptional response to hypoxia (4h, 6% O2), in different times of day, namely the middle of the light phase and the middle of the dark phase. Additionally, many rhythmic processes in mammals are controlled by the circadian clock. to examine the dependency of the hypoxic response on the molecular circadian clock, we repeated the experiment under constant darkness regimen with either wild type mice or Per1,2 double knock out mice (which lack a functional clock), and sequenced the liver transcriptome.

overall_design: The design contains 4 experimental conditions in light/dark regimen (LD): (1) 4h 21% O2 between ZT4-8, (2) 4h 6% O2 between ZT4-8, (3) 4h 21% O2 between ZT16-20, (4) 4h 6% O2 between ZT16-20. 4 biological replicates (mice) per condition. 3 tissues (liver, kidney, lung) were sequenced per mouse. For constant dark (DD) regimen, 8 conditions were used: (1) WT 21% O2 CT4-8, (2) WT 6% O2 CT4-8, (3), WT 21% O2 CT16-20, (4) WT 6% O2 CT16-20, (5) Per1,2 double knock-out (KO) 21% O2 CT4-8, (6) KO 6% O2 CT4-8, (7) KO 21% O2 CT16-20, (8) KO 6% O2 CT16-20. only liver RNA was sequenced in the constant dark design.

first: Gad

last: Asher


title: Bolitoglossa vallecula reference transcriptome

status: Public on Dec 07 2019

city: medellin

first: Jean

middle: Paul

last: Delgado

state: antioquia

department: Biology

country: Colombia

institute: University of Atioquia

summary:
The order Caudata of amphibians has been important in the study of tissue regeneration. The most complete genetic available data from salamanders are from Ambystoma mexicanum (Ambystomidae) and Notophthalmus viridescens (Salamandridae). Transcriptome data obtained with Next-generation sequencing technology has become a useful tool to discover new candidate genes in non-model organisms without a genome of reference. This study highlights the need of performing RNA-sequencing in other salamander species to compare and identify important clusters of genes that could be modulating important biological process in amphibians. Here we describe a de novo reference transcriptome and its annotation of a non-model terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). For this purpose, we utilized genome protein databases from vertebrates, nucleotide sequences obtained for salamander species, and a de novo reference transcriptomes of Bolitoglossa ramosi to conduct a homology analysis. While the majority of the transcripts recovered homologs with Bolitoglossa ramosi, only a minority of the data (22%; n= 94,739) recovered homologs with other vertebrates. We also compared the transcriptome profile of skin tissue between these Bolitoglossa species. We found a group of antimicrobial peptides, such as cathelicidins, which have been not previously described in salamanders and could be important modulators of different biological process.
All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015.

overall_design:
To assembly the reference transcriptome, we sequenced individual samples which had pools of different adult animals we did pools of different animals to get limb tissue (two biological replicates, n = 2 animals), heart (one biological replicate, n = 1 animal), skin (one biological replicate, n = 1 animal).

All animals used in this work were collected under the Contract on Genetic Access for scientific research for non commercial profit (Contrato de acceso a recursos genéticos para la investigación científica sin interés commercial) to Resources number 118–2015, which was delivered by the Ministerio del Medio Ambiente (Ministry of Environment) of Colombia to the Principal Investigator.

first: Claudia

last: Arenas

first: Ryan

last: Woodcock

first: Jeramiah

last: Smith

first: Randal

last: Voss


title: Maintaining iron homeostasis is the key role of lysosomal acidity for cell proliferation

city: NEW YORK

first: Kivanc

last: Birsoy

state: NY

address: 1230 YORK AVENUE,

institute: ROCKEFELLER UNIVERSITY

summary:
Purpose: In previous work, we found that iron supplementation to cells rescues impairment of cell viability and proliferation upon lysosomal dysfunction due to inhibition of the vATPase complex. The goal of this study is to characterize the transcriptomic changes (RNA-seq) upon Bafilomycin mediated lysosomal dysfunction with and without iron (Ferric Ammonium Citrate) supplementation.
Methods: mRNA profiles of wild type HEK293T cells treated +/- ferric ammonium citrate (0.1mg/ml) and +/- BafilomycinA1 (10nM) were generated by deep sequencing, in triplicate, using Illumina NextSeq500.
Results: We mapped about 30-40 million sequence reads per sample to the human genome (build GRCh38).
Conclusions: Our study characterizes the transcriptomic changes upon lysosomal dysfunction upon small molecule (Bafilomycin A1) inhibition of vATPase complex. We conclude that there are several notable trasncriptomic changes upon lysosomal dysfunction some of which are reversed by iron supplementation.

overall_design: Trasncriptional changes in HEK293T cells upon Bafilomyin A1 mediated lysosomal vATpase inhibition with and without ferric ammonium citate co-treatment.

first: Ross

middle: A

last: Weber


title: The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells

status: Public on Dec 05 2019

city: St. Louis

first: David

middle: Alexander

last: Anderson III

state: Missouri

address: 660. S Euclid Ave., Campus Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

summary:
The present study reveals LMYC and MXD1 as novel regulators of a transcriptional program that is modulated during the maturation of Batf3-dependent dendritic cells (also known as type I classical dendritic cells or cDC1s).
We used microarray analysis with ERCC spike in controls to determine the transcriptional effects of MYCL and MXD1 deficiency at steady state and after activation with poly IC. Mycl-deficient mice are available from Jackson laboratories as B6.129S6(C)-Mycltm1.1Kmm/J. Mxd1-/- mice were provided by R. Eisenman.

overall_design: Splenic cDC1s were isolated from wild type and Mycl-deficient mice treated with or without polyIC for 5 hours, or wild type or Mxd1-deficient mice treated with poly IC for 18 hours. Total RNA was isolated from FACS-purified cDC1s, ERCC spike in controls were added by normalizing to cell count, and RNA was amplified by GeneChip WT Pico Kit. Samples were in turn analyzed by expression microarray analysis on

first: Kenneth

last: Murphy


title: Microarray comparing CMV-specific CD8+ T cells from liver sinusoid and peripheral blood

city: Yuseong-gu

first: Ji Won

state: Daejeon

address: Daehak-ro 291

institute: KAIST

summary: The liver is an immunologically unique organ in terms of the regulation of immuno-tolerance and immune responses. Recently, non-recirculating tissue-resident memory T (TRM) cells expressing CD69 were found in various peripheral organs. In humans, a large population of CD69+CD8+ memory T cells residing in liver sinusoids shows reduced cytotoxicity. However, the trascriptional characteristics of human liver CD8+ T cells are still unknown. Therefore, we performed a microarray analysis to screen the gene expression profile in liver sinusoidal CD8+ T cells using CMV-specific CD8+ T cells from human peripheral blood and liver sinusoid.

overall_design: We performed microarray analysis after sorting HLA-A*0201-CMVpp65495 pentamer+CD8+ T cells from paired LSMCs and PBMCs.

first: Ji

middle: W

first: Jong

middle: H

last: Kim

first: Eui-Cheol

last: Shin


title: Schizophrenia-related microdeletion causes progressive brain ventricle enlargement through microRNA-dependent deceleration of motile cilia beating

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Progressive ventricular enlargement is one of the most reproducible and recognizable structural abnormalities in schizophrenia, and is associated with more severe symptoms and poorer clinical outcome. The mechanisms of ventricular enlargement in schizophrenia is unknown. We identified that progressive ventricular enlargement is associated with deceleration of motile cilia beating in ependymal cells lining ventricular walls in murine models of schizophrenia-associated 22q11 deletion syndrome (22q11DS). The cilia beating deficit is caused by an aberrant elevation of Drd1, which is highly enriched in the motile cilia. Haploinsufficiency of the microRNA-processing gene Dgcr8 is responsible for the Drd1 elevation in ependymal cells of 22q11DS mice, and is mediated by reduction of Drd1-targeting microRNAs miR-674-3p and miR-382-3p. Replenishing miR-674-3p or miR-382-3p in 22q11DS mice rescued the motile cilia beating abnormalities and normalized the ventricular size. Knockdown of these microRNA mimicked cilia beating and ventricular deficits. Ventricular enlargement was also caused by Crispr/cas9-mediated deletion of the Drd1 seed site for miR-674-3p/miR-382-3p. This suggests that Dgcr8-miR-674-3p/miR-382-3p-Drd1–dependent disruption of cilia motility in ependymal cells is a pathogenic event underlying schizophrenia-associated ventricular enlargement.

overall_design: Profilie the miRNA expression changes between wild type and mutant

first: Tae-Yeon

last: Eom

first: Seung

first: Jieun

first: Jay

last: Blundon

first: Jing

last: Yu

first: Matthew

last: Eicholtz

first: Derek

last: Rose

first: Kara

last: Anderson

first: Damian

last: Kaminski

first: Stanislav

last: Zakharenko


title: Prediagnostic breast milk DNA methylation alterations in women who develop breast cancer

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

summary: Prior candidate gene studies have shown tumor suppressor DNA methylation in breast milk related with history of breast biopsy, an established risk factor for breast cancer. To further establish the utility of breast milk as a tissue-specific biospecimen for investigations of breast carcinogenesis we measured genome-wide DNA methylation in breast milk from women with and without a diagnosis of breast cancer in two independent cohorts. In epigenome-wide analyses we identified 58 differentially methylated CpG sites associated with breast cancer diagnosis in the prospectively collected milk samples from the  breast that would develop cancer compared with women without a diagnosis of breast cancer (q-value < 0.05), using linear mixed effects models adjusted for history of breast biopsy, age, age of the baby, cell type proportion estimates, array chip, and subject as random effect. Nearly all sites associated with breast cancer diagnosis were hypomethylated in cases compared with controls, and CpG sites were enriched for CpG islands. In addition, inferred repeat element methylation was lower in breast milk DNA from cases compared to controls, and cases exhibited increased estimated epigenetic mitotic tick rate as well as DNA methylation age compared with controls. Breast milk has promise as a biospecimen for prospective assessment of disease risk, and for understanding the underlying molecular basis of breast cancer risk factors and improving primary and secondary prevention of breast cancer.

overall_design: Bisulphite converted DNA from breast milk from women with and without breast cancer diagnosis were hybridised to the Illumina Infinium HumanMethylation450k Beadchip

first: Sara

last: Lundgren

first: Eva

last: Browne

first: Elizabeth

last: Punska

first: Douglas

middle: L

last: Anderton

first: Margaret

last: Karagas

first: Kathleen

middle: F

last: Arcaro

first: Brock

last: Christensen


title: A single cell transcriptome atlas of the developing zebrafish hindbrain

city: London

first: David

last: Wilkinson

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

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

overall_design: Refer to individual Series


title: A single cell transcriptome atlas of the developing zebrafish hindbrain [fgfr1]

summary:
RNA-seq profile of transgenic hindbrains expressing heat-shock induced constitutively activated fgfR1 (Tg(hsp70:ca-fgfr1)) and compared to heat-shocked counterparts
Method: 22hpf embryos were heat-shocked for 30min at 38.5°C and then incubated for 2hr at 28.5°C . After hindbrains were microdissected and the RNA was extracted. fgfR1 overexpression was checked by qPCR and samples were selected for sequencing

overall_design: 4 control heat-shoked samples and 4 constitutively active fgfr1 were deep sequenced

first: Monica

last: Tambalo

first: Richard

last: Mitter


title: A single cell transcriptome atlas of the developing zebrafish hindbrain [scRNA-Seq]

summary:
Purpose: The goal of this study is to understand the progressive patterning of neurogenesis of the developing zebrafish hindbrain. 16hpf, 24hpf and 44hpf zebrafish hindbrains were used for single-cell RNA-sequencing with the aim to uncover hindbrain development.
Methods: 40 microdissected hindbrains per each stage were dissociated at loaded into the 10x Genomics Chromium Platform, and sequenced using Illumina HiSeq 4000.
Conclusions: Our study constitute a resource of hindbrain gene expression during development. We have identified transcriptional programs involved in: rhombomere segmental identity, dorso-ventral patterning, boundary and centre progenitor cells and temporal regulation of neurogenesis.

overall_design: 16hpf, 24hpf, 44hpf hindbrains were used for single-cell RNA-sequencing (10xGenomics Chromium Platform), and sequenced using Illumina HiSeq 4000.


title: Single-cell sequencing of sorted hepatocytes isolated from livers naïve and LCMV-infected (2 days) C57Bl/6J mice

city: Vienna

first: Andreas

last: Bergthaler

address: Lazarettgasse 14 AKH BT25.3

country: Austria

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

summary:
Purpose: Elucidate the hepatocyte-specific effects of innate antiviral response to a hepatotropic virus.
Methods: Hepatocytes were isolated using a standard 2 step perfusion protocol and viable CD45 negative single cells were sorted on a Sony SH800 instrument und subsequently processed using a 10x Genomics Controller according to standard protocols.
Results: Hepatocytes upregulate inflammatory genes and downregulate metabolic genes.
Conclusion: Hepatocytes are important innate immune signaling platforms in the liver during viral infection.

overall_design: sorted hepatocytes were processed with the 10X Genomics Chromium Single Cell and sequenced on the Illumina HiSeq 4000

first: Alexandra

last: Popa

first: Alexander

last: Lercher


title: A single cell transcriptome atlas of the developing zebrafish hindbrain [Fgf20a]

summary:
RNA-seq profile of Fgf20a homozygous mutant hindbrains compared with wilde-type hindbrains
Method: 24hpf hindbrains were microdissected and the RNA was extracted. Qulity of dissection was monitored by qPCR and samples were selected for sequencing

overall_design: 4 control wt (Cnt) and 3 Fgf20aHOM were deep sequenced


title: Microglia and infiltrating monocytes gene expression profiling during EAE progress

city: New York

first: Dan

last: Littman

address: 430 East 29th St Room 403

institute: New York University School of Medicine

summary: The project was designed to figure out the role of microglia in brain inflammation (EAE model). The first step was to find genes/pathways that are upregulated in the microglia during EAE progress but absent in the infiltrating monocytes. These genes/pathways may provide clues for studying the unique function of microglia in the brain inflammation that is disctinct from the infiltrating monocytes.

overall_design: Two biological replicates were included for every sample. Microglia cells from the spinal cord of MOCK immunized mice are used as healthy controls. Microglia and infiltrating monocytes were collected at three time points during EAE progression: preclinical (EAE onset), acute (peak), chronic.

first: Lin

last: Wu

first: Hernandez

middle: M

last: Silva


title: Temporal programming of T-helper 17 (TH17) cell differentiation by SAA1+IL6 measured by RNA-Seq

summary: We report that the Serum Amyloid A protein, SAA1, is a novel, soluble co-factor able to promote pathogenic TH17 differentiation.

overall_design: Examination of divergent in vitro TH17 differentiation strategies

first: June-Yong

last: Lee

first: Jason

last: Hall

first: Lina

last: Kroehling


title: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions

city: Yokohama

first: Kosuke

last: Hashimoto

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

institute: RIKEN


title: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (CAGE)

summary: Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodeling. To investigate the function of such RNAs,, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However they present still some limitations. Here, we introduce RNA and DNA interacting complexes ligated and sequenced (RADICL-seq), a novel technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation based methodology that reduces the bias for nascent transcription, increases genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.

overall_design: Identification of genome-wide RNA-chromatin interactions in 2 cell types

first: Alessandro

last: Bonetti

first: Piero

last: Carninci


title: a-synuclein accumulation in an iPSC derived model of early onset sporadic Parkinson’s Disease reveals novel drug targets

city: Los Angeles

first: Samuel

last: Sances

state: CA

address: 8500 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars Sinai

summary: iPSC derived dopaminergic neuron cultures sequenced from different patient lines.

overall_design: 3 control, 3 early onset PD

first: Alex

last: Laperle


title: Gene expression changes in liver upon LCMV Cl13 infection

summary: 2-3 month old female C57Bl/6J mice  were intravenously infected with 2x10^6 focus forming units of lymphocytic choriomeningitis virus strain Clone-13. Whole liver tissue was harvested in triplicates from uninfected control mice, uninfected control 123d old mice, and from infected mice at 2, 8, 30, 60, and 123 days post infection. Samples were subsequently analyzed on a HiSeq 2000 instrument using a 50 bp SE RNAseq protocol.

overall_design: We sequenced liver tissue from control and LCMV infected mice day 2, 8, 30 , 60, and 123 post-infection.

first: Anannya

last: Battaharya


title: Pair-feeding of LCMV Cl13 infected mice

summary: Mice were infected with LCMV Cl13 and food intake was measured up to 8dpi. Another group of uninfected mice received the amount of food the infected mice consumed. The third group of naïve mice received food ad libitum.

overall_design: We sequenced liver tissue from pair-fed, naïve and LCMV Cl13 infected at day 8 post-infection.


title: Naïve and LCMV Cl13 infected liver tissue of ERT2 AlbCre Ifnar1 fl/fl mice

summary: Age- and sex-matched (male, 2-3 months old) ERT2 AlbCre Ifnar fl/fl and ERT2 AlbCre Ifnar +/+ mice were injected intraperitoneally with 40 mg/kg tamoxifen for 5 consective days. Mice were then intravenously infected with 2x10^6 focus forming units of LCMV Cl13 and liver tissue of either genotype was harvested 1.5 days post infection and analyzed for transcriptomic changes (n = 3). Liver tissue of uninfected animals of both genotypes was harvested as control (n = 3).

overall_design: We sequenced liver tissue from naïve and LCMV Cl13 infected liver tissue from ERT2 AlbCre Ifnar1 fl/fl mice 1.5 days post infection.


title: Real-time quantitative PCR analysis for NF-kB related genes of mouse bone marrow with engrafted human leukemia cells after C-miR146a treatment

status: Public on Dec 04 2019

city: Duarte

first: Marcin

last: Kortylewski

state: California

address: 1500 E. Duarte Road

institute: City of Hope National Medical Center

summary: NF-κB is a key regulator of inflammation and cancer progression, with important role in leukemogenesis. Despite therapeutic potential, targeting NF-κB using pharmacologic inhibitors proved challenging. Here, we describe a myeloid cell-selective NF-κB inhibitor using miR146a mimic oligonucleotide conjugated to a scavenger receptor (SR)/Toll-like receptor 9 (TLR9) agonist (C-miR146a). Unlike an unconjugated miR-146a, C-miR146a was rapidly internalized and delivered to cytoplasm of target myeloid cells and leukemic cells. C-miR146a reduced expression of classic miR-146a targets, IRAK1 and TRAF6, thereby blocking NF-κB activation in target cells. Intravenous injections of C-miR146a mimic to miR-146-deficient mice prevented excessive NF-κB activation in myeloid cells, thereby alleviating myeloproliferation and mice hypersensitivity to bacterial challenge. Importantly, C-miR146a showed efficacy in dampening severe inflammation in clinically relevant models of chimeric antigen receptor (CAR) T-cell-induced cytokine release syndrome (CRS). Systemic administration of C-miR146a oligonucleotide alleviated human monocyte-dependent release of IL-1 and IL-6 in xenotransplanted B-cell lymphoma model without affecting CD19-specific CAR T-cell antitumor activity. Beyond anti-inflammatory functions, miR146a is a known tumor suppressor commonly deleted or expressed at reduced levels in human myeloid leukemia. Using TCGA AML dataset, we found inverse correlation of miR-146 levels with NF-κB-related genes and with patients’ survival.  Correspondingly, C-miR146a induced cytotoxic effects in human MDSL, HL-60 and MV4-11 leukemia cells in vitro. The repeated intravenous administration of C-miR146a inhibited expression of NF-κB target genes and thereby thwarted progression of disseminated HL-60 leukemia. Our results demonstrate potential of using myeloid cell-targeted miR146a mimics for treatment of inflammatory and myeloproliferative disorders.      NF-κB is a key regulator of inflammation and cancer progression, with important role in leukemogenesis. Despite therapeutic potential, targeting NF-κB using pharmacologic inhibitors proved challenging. Here, we describe a myeloid cell-selective NF-κB inhibitor using miR146a mimic oligonucleotide conjugated to a scavenger receptor (SR)/Toll-like receptor 9 (TLR9) agonist (C-miR146a). Unlike an unconjugated miR-146a, C-miR146a was rapidly internalized and delivered to cytoplasm of target myeloid cells and leukemic cells. C-miR146a reduced expression of classic miR-146a targets, IRAK1 and TRAF6, thereby blocking NF-κB activation in target cells. Intravenous injections of C-miR146a mimic to miR-146-deficient mice prevented excessive NF-κB activation in myeloid cells, thereby alleviating myeloproliferation and mice hypersensitivity to bacterial challenge. Importantly, C-miR146a showed efficacy in dampening severe inflammation in clinically relevant models of chimeric antigen receptor (CAR) T-cell-induced cytokine release syndrome (CRS). Systemic administration of C-miR146a oligonucleotide alleviated human monocyte-dependent release of IL-1 and IL-6 in xenotransplanted B-cell lymphoma model without affecting CD19-specific CAR T-cell antitumor activity. Beyond anti-inflammatory functions, miR146a is a known tumor suppressor commonly deleted or expressed at reduced levels in human myeloid leukemia. Using TCGA AML dataset, we found inverse correlation of miR-146 levels with NF-κB-related genes and with patients’ survival.  Correspondingly, C-miR146a induced cytotoxic effects in human MDSL, HL-60 and MV4-11 leukemia cells in vitro. The repeated intravenous administration of C-miR146a inhibited expression of NF-κB target genes and thereby thwarted progression of disseminated HL-60 leukemia. Our results demonstrate potential of using myeloid cell-targeted miR146a mimics for treatment of inflammatory and myeloproliferative disorders.

overall_design: For the systemic leukemia xenograft models, SGM3 mice were injected intravenously with 2×106 of HL-60LUC cells. Tumor progression was monitored using bioluminescent imaging on AmiX (Spectral Instruments). From day 9, mice were injected retro-orbitally with 10mg/kg of C-miR146a or C-scrRNA every other day for 10 days. Total RNA was isolated from bone marrow cells (n=3 from each group) and analyzed using the Human NF-κB Signaling Pathway RT2 Profiler PCR Arrays (Qiagen).

first: Yu-Lin

last: Su

first: Xiuli

last: Wang

first: Mati

last: Mann

first: Tomasz

last: Adamus

first: Dayson

last: Moreira

first: Dongfang

first: Zhuoran

last: Zhang

first: Ching

last: Ouyang

first: Xin

last: He

first: Bin

first: Piotr

last: Swiderski

first: Stephen

last: Forman

first: David

last: Baltimore

first: Ling

last: Li

first: Guido

last: Marcucci

first: Mark

last: Boldin


title: RNA sequencing data of Wild Type and Fmr1 KO hippocampal neuron

city: East Lansing

first: Zhuang

last: Miao

state: Michigan

address: 567 Wilson Road

department: Physiology

institute: Michigan State University

summary: Fragile X syndrome (FXS), caused by mutations in fragile X mental retardation 1 gene (FMR1), is a prevailing genetic disorder of intellectual disability and autism. Analysis of transcriptome outcome (differentially expressed genes between WT and Fmr1 KO hippocampal neuron) associated with FXS reveal promising value of gene signature-based computation in repurposing drugs for potential practical treatment.

overall_design: Primary DIV (Days in vitro) 14 Hippocampal neuron mRNA profiles of Wild Type (WT) and Fmr1 KO mice were generated in triplicate

first: Hongbing

first: Ferzin

last: Sethna

first: Qi

last: Ding

first: Xueting

last: Wu

first: Ping

last: Chen

first: Yueqi

first: Hua

last: Xiao

first: Wei

last: Feng

first: Yue

first: Xuan


title: RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions (RADICL-seq)

first: Kosuke

last: Hashimoto

first: Alessandro

last: Bonetti

first: Piero

last: Carninci