title: Baseline assessment of circulating microRNAs near diagnosis of type 1 diabetes predicts future stimulated insulin secretion

city: Miami

first: Alberto

last: Pugliese

state: FL

address: 1450 NW 10th Ave.

department: Diabetes Research Institute

institute: University of Miami

summary: We investigated whether circulating microRNAs (miRNAs) are associated with residual insulin secretion at diagnosis and predict the severity of its future decline. We studied 53 newly diagnosed subjects enrolled in placebo groups of TrialNet clinical trials.  We measured serum levels of 2,083 miRNAs using RNAseq technology, in fasting samples from the baseline visit (<100 days from diagnosis), during which residual insulin secretion was measured with a mixed meal tolerance test (MMTT). Area under the curve (AUC) C-peptide and peak C-peptide were stratified by quartiles of expression of 31 miRNAs. After adjustment for baseline C-peptide, age, BMI and sex, baseline levels of miR-3187-3p, miR-4302, and the miRNA combination of miR-3187-3p/miR-103a-3p predicted differences in MMTT C-peptide AUC/peak levels at the 12-month visit; the combination miR-3187-3p/miR-4723-5p predicted proportions of subjects above/below the 200 pmol/L clinical trial eligibility threshold at the 12-month visit. Thus, miRNA assessment at baseline identifies associations with C-peptide and stratifies subjects for future severity of C-peptide loss after 1 year. We suggest that miRNAs may be useful in predicting future C-peptide decline for improved subject stratification in clinical trials.

overall_design: 53 newly diagnosed subjects enrolled in placebo groups of TrialNet clinical trial had measured serum levels of 2,083 miRNAs measured once using fasting samples from the baseline visit (<100 days from diagnosis), during which residual insulin secretion was measured with a mixed meal tolerance test (MMTT).

first: Isaac

last: Snowhite


title: SON inhibits megakaryocytic differentiation via repressing the megakaryocytic gene expression program in acute megakaryoblastic leukemia

status: Public on Sep 01 2020

city: Birmingham

first: Erin

last: Ahn

state: Alabama

address: 1824 6th Ave S

department: Pathology

country: USA

institute: University of Alabama in Birmingham

type: Expression profiling by high throughput sequencing

summary: A high incidence of acute megakaryoblastic leukemia (AMKL) in Down syndrome patients implies that chromosome 21 genes have a pivotal role in AMKL development, but the functional contribution of individual genes remains elusive.  Here, we report that SON, a chromosome 21-encoded DNA- and RNA-binding protein, inhibits megakaryocytic differentiation by suppressing RUNX1 and the megakaryocytic gene expression program. As megakaryocytic progenitors differentiate, SON expression is drastically reduced, with mature megakaryocytes having the lowest levels. In contrast, AMKL cells express an aberrantly high level of SON, and knockdown of SON induced the onset of megakaryocytic differentiation in AMKL cell lines. Genome-wide transcriptome analyses revealed that SON knockdown turns on the expression of pro-megakaryocytic genes while reducing erythroid gene expression. Mechanistically, SON represses RUNX1 expression by directly binding to the proximal promoter and two enhancer regions, the known +23 kb enhancer and the novel +139 kb enhancer, at the RUNX1 locus to suppress H3K4 methylation. In addition, SON represses the expression of the AP-1 complex subunits JUN, JUNB and FOSB which are required for late megakaryocytic gene expression. Our findings define SON as a negative regulator of RUNX1 and megakaryocytic differentiation, implicating SON overexpression in impaired differentiation during AMKL development.

overall_design: A 48-hour SON siRNA treatment was performed in AMKL cell line MEG-01.

first: Lana

last: Vukadin

last: Eun-Young Ahn


title: Single-Cell Transcriptomics of Engineered Cardiac Tissues from Patient-Specific Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveals Abnormal Developmental Trajectory and Intrinsic Contractile Defects in Hypoplastic Right Heart Syndrome

city: Hong Kong

first: Yin Yu

last: Lam

address: 102 Pokfulam Road

department: Department of Paediatrics and Adolescent Medicine

country: China

institute: The University of Hong Kong

summary: Pulmonary atresia with intact ventricular septum (PAIVS) is a subset of hypoplastic right heart syndrome, a form of congenital heart disease (CHD). Genomic studies on PAIVS patients revealed inconclusive genomic variations and polymorphisms and no animal model yet exists for this disease. Hence, we performed single cell RNA-sequencing (scRNA-seq) on PAIVS patient derived human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) and its bioengineered cardiac tissue constructs (Human cardiac anisotropic sheeet (hCAS) and cardiac tissue strip (hCTS)) to dissect the intrinsic cardiomyocyte defects. Using pseudotime analysis, we identified pro-maturational cues conferred to hiPSC-CMs by hCAS and hCTS and are attenduated in PAIVS. Moerover, we also identified diminished expression of cardiac contractile apparatus genes in PAIVS hiPSC-CMs and hCTS. Our findings reveal intrinsic abnormalities in cardiac contraction and development in PAIVS in the absence of secondary in vivo remodelling.

overall_design: Time-matched Day 30 hiPSC-CMs, D10 hCAS and D10 hCTS from two healthy subject and two PAIVS hiPSC lines.

first: Yin

first: Chun

last: Chan

first: Wendy

last: Keung

first: Ronald

middle: A

last: Li

first: Yiu

last: Cheung


title: Differential regulation of membrane potential during store-operated calcium entry in neutrophil subsets

city: SAINT LOUIS

first: Regina

last: Clemens

state: MO

address: 660 S. Euclid Ave.

department: Pediatrics

institute: Washington University School of Medicine in St. Louis

summary: Calcium signals are initiated in immune cells by the process of store-operated calcium entry (SOCE), where receptor activation triggers transient calcium release from the endoplasmic reticulum, followed by opening of plasma membrane calcium-release activated calcium (CRAC) channels. ORAI1, ORAI2 and ORAI3 are known to comprise the CRAC channel, however the contributions of individual isoforms to neutrophil function is not well understood. Here we show that loss of ORAI1 partially decreases calcium influx while loss of both ORAI1 and ORAI2 completely abolishes store-operated calcium entry. In other immune cell types, loss of ORAI2 enhances SOCE. In contrast, we find that ORAI2-deficient neutrophils display decreased calcium influx, which is correlated with measurable differences in regulation of neutrophil membrane potential via KCa3.1. Decreased SOCE in ORAI1-, ORAI2- and ORAI1/2-deficient neutrophils impairs multiple neutrophil functions including phagocytosis, degranulation, leukotriene and ROS production, rendering ORAI1/2-deficient mice highly susceptible to staphylococcal infection. This study demonstrates that ORAI1 and ORAI2 are the primary components of the neutrophil CRAC channel and identifies novel subpopulations of neutrophils where cell membrane potential functions as a rheostat to modulate the SOCE response. These findings have implications for new mechanisms that modulate neutrophil function during infection, acute and chronic inflammatory conditions, and cancer.

overall_design: Isolated mouse neutrophils loaded with a membrane potential sensitive dye were stimulated with ionomycin and sorted based on membrane potential response (depolarized or polarized). Three biological replicate pairs were submitted for analysis.

first: Derayvia

last: Grimes

first: Ryan

last: Johnson

first: Madeline

last: Pashos

first: Celeste

last: Cummings

first: Chen

last: Kang

last: Sampedro

first: Eric

last: Tycksen

first: Helen

middle: J

last: McBride

first: Rajan

last: Sah

first: Clifford

last: Lowell


title: Profiling primary osteoblast transcriptomes during differentiation

city: Philadelphia

first: Fanxin

last: Long

state: PENNSYLVANIA

address: 3615 Civic Center Boulevard, Abramson Research Center Room#904

department: Orthopedics

institute: Children's Hospital of Philadelphia

summary: The goal of this study is to compare next-generation sequencing-derived osteoblast transcriptome profilings to identify essential genes during isteoblast differnetiation.

overall_design: Total mRNA profiles of primary osteoblasts at different stages during differentiation were generated by deep sequencing.


title: Transcriptome analysis on wild type and mvp mutant zebrafish ventricles at 7dpa by Next Generation Sequencing

city: Nanjing

first: Yuxi

last: Yang

state: Jiangsu

address: Room 402, 12 Xuefu Road, Nanjing University

department: Medical School

institute: Nanjing University

summary: In contrast to mammals, the adult zebrafish hearts can regenerate within a short period. Upregulation of major vault protein (Mvp) expression after ventricle resection. To determine the impact of loss of mvp on transcriptome during heart regeneration, we pursued transcriptome analysis (RNA-Seq) on wild type and mvp mutant zebrafish hearts at 7 day-post-amputation.

overall_design: We perform ventricle resection or sham surgeries to adult wild type and mvp mutant zebrafish hearts. At 7 days post amputation, ventricle samples were collected in triplicate for RNA-seq.

first: Xue

last: Zhang

first: Xin

last: Lou


title: Multi-omic comparison of Alzheimer’s variants in human ESC-derived microglia reveals convergence at APOE [RNA-seq]

city: La Jolla

first: Timothy

last: Huang

address: 10901 N. Torrey Pines Rd

institute: SBP Medical Discovery Institute

summary: Variations in many genes linked to sporadic Alzheimer’s disease (AD), show abundant expression in microglia, however, relationships between these genes remain largely elusive. Here, we establish isogenic human ES-derived microglia-like cell lines (hMGLs) harboring AD variants in CD33, INPP5D, SORL1 and TREM2 loci, and curate a comprehensive atlas comprising ATACseq, ChIPseq, RNAseq and proteomics datasets. AD-like expression signatures are observed in AD mutant SORL1 and TREM2 hMGLs, while integrative multi-omic analysis of combined epigenetic and expression datasets indicates upregulation of APOE as a convergent pathogenic node. We also observe cross-regulatory relationships between SORL1 and TREM2, where SORL1R744X hMGLs induce TREM2 expression to enhance APOE expression. AD-associated SORL1 and TREM2 mutations also impaired hMGL Aβ uptake in an APOE-dependent manner in vitro, and attenuated Aβ uptake/clearance in mouse AD brain xenotransplants. Utilizing this modeling and analysis platform for human microglia, we provide new insight into epistatic interactions in AD genes and demonstrate convergence of microglial AD genes at the APOE locus.

overall_design: Examine gene expression profiles of isogenic human ES-derived microglia-like cell lines (hMGLs) harboring AD variants in CD33, INPP5D, SORL1 and TREM2 loci.

first: Tongfei

last: Liu

first: Bing

last: Zhu

first: Yan

first: Xiaoming

first: Jun

last: Yin

first: Xiaoguang

last: Li

first: LuLin

last: Jiang

first: Andrew

middle: P

last: Hodges

first: Sara

middle: B

last: Rosenthal

first: Lisa

last: Zhou

first: Joel

last: Yancey

first: Amanda

last: McQuade

first: Mathew

last: Blurton-Jones

first: Rudolph

middle: E

last: Tanzi

middle: Y

first: Huaxi

last: Xu


title: Sympathetic nervous tone limits the development of myeloid-derived suppressor cell

city: Farmington

first: Marmar

last: Moussa

state: CT

address: Farmington

department: School of Medicine

institute: University of Connecticut

summary: Sympathetic nerves that innervate lymphoid organs regulate immune development and function by releasing norepinephrine (NE) that is sensed by immune cells via their expression of adrenergic receptors (ARs). Here, we demonstrate that ablation of SNS signaling suppresses tumor immunity, and we dissect the mechanism of such immune suppression. We report that disruption of the SNS in mice removes a critical α-adrenergic signal required for maturation of myeloid cells in normal as well as tumor-bearing mice. In tumor-bearing mice, disruption of the α-adrenergic signal leads to the accumulation of immature myeloid-derived suppressor cells (MDSC) that suppress tumor immunity and promote tumor growth. Furthermore, we show that these SNS-responsive MDSCs drive expansion of regulatory T cells via secretion of the alarmin heterodimer S100A8/A9, thereby compounding their immunosuppressive activity. Our results describe a regulatory framework in which sympathetic tone controls the development of innate and adaptive immune cells and influences their activity in health and disease.

overall_design: scRNA seq of FACS-sorted CD3neg CD19neg single cells from SNS-ablated or control CT26 tumor-bearing BALB/c mouse

first: James

last: Nevin


title: Multi-omic comparison of Alzheimer’s variants in human ESC-derived microglia reveals convergence at APOE [ATAC-seq]

first: Timothy

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examine epigenomic profiles of isogenic human ES-derived microglia-like cell lines (hMGLs) harboring AD variants in CD33, INPP5D, SORL1 and TREM2 loci.

first: Tongfei

last: Zhang


title: The hepatic microenvironment uniquely protects leukemia cells through induction of growth and survival pathways mediated by LIPG

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

summary: Transcriptome comparison between leukemia stem cells residing in bone marrow and liver in a leukemia mouse model

overall_design: Leukemia stem cells were isolated from mouse bone marrow (BM) and liver. mRNAs were extracted for RNA-seq.

first: Craig

middle: T

last: Jordan

first: Haobin

last: Ye


title: Multi-omic comparison of Alzheimer’s variants in human ESC-derived microglia reveals convergence at APOE [ChIP-seq]

last: Huang

overall_design: Examine epigenomic profiles of isogenic human ES-derived microglia-like cell lines (hMGLs) harboring AD variants in CD33, INPP5D, SORL1 and TREM2 loci using ChIP-Seq

last: Liu

first: Bing

last: Zhu

first: Yan

first: Xiaoming

first: Jun

last: Yin

first: Xiaoguang


title: Chip array data for  human PDAC Suit2-007 in primary (pancreas) secondary organs (liver and lungs) of a PDAC rat model

city: Heidelberg

first: Martin

middle: R

last: Berger

address: INF 581

country: Germany

institute: DKFZ

summary: We report the gene expression profile of human PDAC Suit2-007 in primary (pancreas) secondary organs (liver and lungs) of a PDAC rat model

overall_design: Human PDAC Suit2-007 were orthotopicaly and intraportaly injected to respective primary (pancreas) and secondary (liver and lungs) for their growth. Tumor cells were re-isolated from these organs for a chip array. Suit2-007 cells growing in vitro were also evaluated.

first: Micah

middle: N

last: Sagini


title: Multi-omic comparison of Alzheimer’s variants in human ESC-derived microglia reveals convergence at APOE

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

overall_design: Refer to individual Series


title: A Treg cell Notch4-GDF15 Axis Licenses Tissue Inflammation in Asthma

city: Boston

first: KLaus

last: Schmitz-Abe

state: MA

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

summary: Elucidating the mechanisms that sustain asthmatic inflammation is critical for precision therapies. We found that IL-6 and STAT3-dependent upregulation of Notch4 on Iung tissue regulatory T (Treg) cells is necessary for allergens and particulate matter pollutants to promote airway inflammation. Notch4 subverted Treg cells into TH2 and TH17 effector T (Teff) cells by Wnt and Hippo pathway-dependent mechanisms. Wnt activation induced GDF15 expression in Treg cells, which activated group 2 innate lymphoid cells (ILC2) to provide a feed-forward mechanism for aggravated inflammation. Notch4, Wnt and Hippo were upregulated on circulating Treg cells of asthmatics as a function of disease severity, in association with reduced Treg cell-mediated suppression. Our studies thus identify Notch4-mediated immune tolerance subversion as a fundamental mechanism that licenses tissue inflammation in asthma.

overall_design: The mice were sensitized twice at days 0 and 14 with OVA i.p. The mice were then challenged with OVA+UFP on days 27, 28 and 29. There is two groups, the Foxp3YFPCre mice vs. Foxp3YFPCrexNotch4fl/fl group. The mice were sacked and the lungs were digested to sort the cells out for analysis.

first: Hani

last: Harb

first: Klaus

first: Talal

last: Chatila


title: Effect of ~ 25 days cortisol treatment on late gestation placenta

city: Gainesville

first: Maureen

last: Keller-Wood

state: Florida

address: 1225 Center Dr

department: Pharmacodynamics

institute: University of Florida

summary: Previous studies have suggested that increases in maternal cortisol or maternal stress in late pregnancy increase the risk of stillbirth at term.  In an ovine model with increased maternal cortisol over the last 0.20 of gestation, we have previously found evidence of disruption of fetal serum and cardiac metabolomics, and of expression of genes related to mitochondrial function and metabolism in biceps femoris, diaphragm and cardiac muscle. The present studies were designed to test for effects of chronically increased maternal cortisol on gene expression and metabolomics in placentomes near term. We hypothesized that changes in placenta may underlie or contribute to the alterations in fetal serum metabolomics, and thereby contribute to changes in striated muscle metabolism.  Multi-omic analysis indicates that amino acid metabolism, particularly of branched chain amino acids and glutamate occur in placenta; changes in amino acid metabolism, degradation or biosynthesis in placenta were consistent changes in valine, isoleucine, leucine and glycine in fetal serum. The analysis also indicates changes in glycerophospholipid metabolism, and suggests changes in ER stress and antioxidant status in the placenta. These findings suggest that changes in placental function occurring with excess maternal cortisol in late gestation may contribute to metabolic dysfunction in the fetus at birth.

overall_design: Placentomes were collected from pregnancies in early labor (143±1 d gestation) of control ewes (n=7) or ewe treated with cortisol (1 mg/kg/d Solu-Cortef iv; n=5) starting at day 115 of gestation. Transcriptomics and metabolomics were performed using an ovine gene expression microarray (Agilent 019921), HR-MAS NMR respectively.  Ewes carrying singleton sheep fetuses at 139-144d gestation (approximately term)  were used.

first: Serene

last: Joseph

first: Jacquelyn

middle: M

last: Walejko

first: Sicong

first: Arthur

middle: S

last: Edison


title: PDCD2 functions as an evolutionarily conserved chaperone dedicated for the 40S ribosomal protein uS5

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

summary: PDCD2 is an evolutionarily conserved protein that is essential for cell proliferation and embryonic development. To date, however, the function of PDCD2 underlying its fundamental cellular role has remained elusive. Here we used quantitative proteomics approaches to define the protein-protein interaction network of human PDCD2. Our data revealed that PDCD2 specifically interacts with the 40S ribosomal protein uS5 (RPS2) and that the PDCD2-uS5 complex is assembled co-translationally. Loss of PDCD2 expression leas  to defects in the synthesis of small ribosomal subunit  that phenocopies a uS5 deficiency. Notably, we showed that PDCD2 is important for the accumulation of soluble uS5 proteins as well as its incorporation into 40S ribosomal subunit. Our findings support that the essential molecular function of PDCD2 is to act as a dedicated chaperone that recognizes the ribosomal protein uS5 co-translationally in the cytoplasm and accompanies uS5 to ribosome assembly sites in the nucleolus. As most dedicated ribosomal protein chaperones have been identified in yeast, our study indicates that similar mechanisms exist in human cells to assist ribosomal proteins coordinate their folding, nuclear import, and assembly in pre-ribosomal particles.

overall_design: Libraries for control (siNT) and PDCD2-depleted HeLa cells were prepared using total RNA from two independent knockdown experiments and analyzed using the Illumina HiSeq technology.

first: François

last: Bachand

first: Danny

last: Bergeron

first: Anne-Marie

last: Landry-Voyer


title: Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified meduloblastoma

first: Venu

last: Thatikonda

address: Technologiepark III, Im Neuenheimer Feld

institute: German Cancer Research Center


title: Gene expression effects of PPAR-gamma serine 273 to alanine knock-in mutation in epididymal white adipose tissue

first: Alexander

last: Banks

address: 330 Brookline Ave, CLS 738

department: Endocrinology

institute: Beth Israel Deaconess Medical Center

summary: Mice maintained on high-fat diet (Research Diets #D12492) for 37 weeks.

overall_design: Overnutrition and obesity promote adipose tissue dysfunction, often leading to systemic insulin resistance. The thiazolidinediones (TZDs) are a potent class of insulin-sensitizing drugs and ligands of PPAR-gamma that improve insulin sensitivity, but their use is limited due to significant side effects. Recently, we demonstrated a mechanism by which TZDs improve insulin sensitivity distinct from receptor agonism and adipogenesis: reversal of obesity-linked phosphorylation of PPAR-gamma at Serine 273. However, the role of this modification has not been tested genetically. Here we demonstrate that mice encoding an allele of PPAR-gamma which cannot be phosphorylated at S273 are protected from insulin resistance, without exhibiting differences in body weight or TZD-associated side effects. Indeed, hyperinsulinemic-euglycemic clamp experiments confirm improved insulin sensitivity, as evidenced by increased whole-body glucose uptake. RNA-seq experiments reveal PPAR-gamma S273 phosphorylation specifically enhances transcription of Gdf3, a BMP family member. Ectopic expression of Gdf3 is sufficient to induce insulin resistance in lean, healthy mice. We find that Gdf3 can impact metabolism by inhibition of BMP signaling. Together, these results highlight the diabetogenic role of PPAR-gamma S273 phosphorylation and focuses attention on a putative target, Gdf3.

first: Jessica

last: Hall

first: Linus

last: Tsai

first: Christopher

last: Jacobs


title: Genome wide chromatin profile for Histone H1.4 (pan-H1.4) and Phosphorylated H1.4 (pS187-H1.4)

city: Bethesda

first: Ankita

last: Saha

state: Maryland

address: 41 Medlars Drive

institute: National Cancer Institute

summary: In this study, we use novel, highly specific custom antibodies against a linker histone variant and its modified form to conduct chromatin immunoprecipitation (ChIP)  followed by Next Generation Sequencing (NGS)  to investigate their binding profiles as a result of transcription inititation. Here we use an estrogen responsive breast cancer cell line, MCF7 to study the enrichment patterns of Histone H1.4 (pan-H1.4) and Phosphorylated H1.4 (pS187-H1.4) across the genome as a result of a short estrogen treatment (30 mins). We find that pS187-H1.4 is preferentially enriched at the promoters of active genes as opposed to the depletion of pan-H1.4 at the same site. Additionally, we use a short treatment of Flavopiridol- an inhibitory drug specific for Cyclin-dependent Kinase-9 (CDK9) which is responsible for the phosphorylation of H1.4 cells, to demonstrate the quenching of this signal at sites specificially activated as a result of the estrogen treatment. This demonstrates for the first time that pS187-H1.4 is associated with active genes and may even be involved in the regulation of gene activity.

overall_design: Examination of Histone H1.4 and pS187H1.4 marks across the genome to evaluate their response to transcription activation

last: Seward


title: Pioglitazone induces extensive PPARg-dependent hepatic expression of nuclear-mitochondrial genes [RNA-seq]

status: Public on Sep 02 2020

city: St. Louis

first: Paul

last: Cliften

address: 4320 Forest Park Parkway

department: Genetics

institute: Washington University

summary: We report the results of RNA-seq analysis on 5 month old wildtype and liver specific PPARg knockout male mice, fed control-diet or high fat-diet supplemented with Pio or vehicle from age 2-5 months

overall_design: Examination of the effect of Pioglitazone and high fat diet on liver RXR-DNA binding patterns

first: David

last: Rudnick

middle: F


title: Altered Enhancer and Promoter Usage Leads to Differential Gene Expression in the Normal and Failed Human Heart

city: Chicago

first: Anthony

middle: Martin

last: Gacita

state: IL

address: 303 E Superior St. Lurie 7-240

department: Center for Genetic Medicine

institute: Northwestern Univeristy Feinberg School of Medicine

summary: The failed heart is characterized by re-expression of a fetal gene program, which contributes to adaptation and maladaptation in heart failure. To define genomewide enhancer and promoter use in heart failure, Cap Analysis of Gene Expression (CAGE-seq) was applied to healthy and failed human left ventricles to define short RNAs associated with both promoters and enhancers. Integration of CAGE-seq data with RNA sequencing identified a combined ~17,000 promoters and ~1,500 enhancers active in healthy and failed human left ventricles. Comparing promoter usage between healthy and failed hearts highlighted promoter shifts which altered amino-terminal protein sequences. Comparing enhancer usage between healthy and failed hearts revealed a majority of differentially utilized heart failure enhancers were intronic and primarily localized within the first intron, identifying this position as a common feature associated with tissue-specific gene expression changes in the heart. This dataset defines the dynamic genomic regulatory landscape underlying heart failure and serves as an important resource for understanding genetic contributions to cardiac dysfunction.

overall_design: CAGE-seq and RNA-sequencing on 3 healthy and 4 failed left ventricle human samples.


title: Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified meduloblastoma [expression]

summary: MYC is a driver oncogene in many cancers. Inhibition of MYC promises high therapeutic potential, but specific MYC inhibitors remain unavailable for clinical use. Previous studies suggest that MYC amplified Medulloblastoma cells are vulnerable to HDAC inhibition. Using co-immunoprecipitation, mass spectrometry and ChIP-sequencing we show that HDAC2 is a cofactor of MYC in MYC amplified primary medulloblastoma and cell lines. The MYC-HDAC2 complex is bound to genes defining the MYC-dependent transcriptional profile. Class I HDAC inhibition leads to stabilization and reduced DNA binding of MYC protein inducing a down-regulation of MYC activated genes (MAGs) and up-regulation of MYC repressed genes (MRGs). MAGs and MRGs are characterized by opposing biological functions and distinct E-box distribution. We conclude that MYC and HDAC2 (class I) are localized in a complex in MYC amplified medulloblastoma and drive a MYC-specific transcriptional program, which is reversed by the class I HDAC inhibitor entinostat. Thus, the development of HDAC inhibitors for treatment of MYC amplified medulloblastoma should include HDAC2 in its profile in order to directly target MYC´s trans-activating and trans-repressing function.

overall_design: In this specific experiment with HDMB03 cells, three technical replicates before treatment (treated with DMSO) and three replicates after treatment with 5μM entinostat(MS275) for 6h were analyzed to understand the effect of treatment on global gene expression dynamics.

first: Jonas

last: Ecker

first: Gianluca

last: Sigismondo

first: Gintvile

last: Valinciute

first: Ina

last: Oehme

first: Carina

last: Müller

first: Juliane

middle: L

last: Buhl

first: Johannes

last: Ridinger

first: Diren

last: Usta

first: Florian

last: Selt

first: Cornelis

last: van Tilbur

first: Christel

last: Herold-Mende

first: Felix

last: Sahm

first: Frank

last: Westermann

first: Marcel

last: Kool

first: Robert

last: Wechsler-Reya

first: Lukas

last: Chavez

first: Jeroen

last: Krijgsveld

first: Natalie

last: Jäger

first: Stefan

last: Pfister

first: Olaf

last: Witt

first: Till

last: Milde


title: Phosphoproteomics identifies microglial Siglec-F inflammatory response during neurodegeneration

city: Cambridge

first: Forest

last: White

state: Massachusetts

address: 500 Main Street, MIT Room 76-353

department: Biological Engineering

institute: MIT

summary: We used mRNA-seq analysis to explore the transcriptional response induced in BV-2 cells by stable overexpression Siglec-F and related human Siglec receptors compared to loss-of-function 2xY->F mutant receptors.

overall_design: mRNA profiles of Siglec-expressing BV-2 cells were generated by deep sequencing.

first: Nader

last: Morshed


title: Chip array data for Suit2-007 cells treated by riproximin (Rpx)

first: Martin

last: Berger

summary: We report the effect of Rpx on human PDAC Suit2-007 cells after 48h time point

overall_design: Evaluation of the gene expression profile following Rpx treatment of Suit2-007 at 48h time point

first: Micah

last: Sagini


title: Next generation sequencing of MA-10 mouse Leydig tumor cells facilitates quantitative analysis of SINE B2-antisense transcripts with the RNAi system: wild type and Dicer1-knockdown transcriptomes

city: Los Angeles

first: Vassilios

last: Papadopoulos

state: CA

address: 1985 Zonal Avenue

department: Department of Pharmacology and Pharmaceutical Sciences, School of

institute: University of Southern California

summary: We report the comparison between SINE B2-AS transcriptome profiling and Dicer1-deficient-cell transcriptome profiling using RNA-seq analysis. We report that thousands of SINE B2 copies encode long B2-AS transcripts, which are constantly degraded by Dicer1. This new class of B2-AS transcripts regulates the expression of SINE B2 sense (B2-S) transcripts. Long B2-S is the main cause of cellular toxicity likely mediated by the multifunctional protein TSPO. Some B2-AS transcripts are putative miRNAs interconnected with the RNAi system. We propose that B2-AS transcripts have evolved as a self-defense mechanism to subvert the host RNAi system.

overall_design: Sequencing of SINE B2-AS specific transcripts and its comparison to the transcriptomes between Dicer1-deficienct cells vs. wild-type cells

first: Jinjiang

last: Fan


title: A Phase 2 Randomized, Double-blind Pilot Study of IL-17-Targeting with 2 Secukinumab in Moderate-to-Severe Atopic Dermatitis

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

summary: This randomized, double-blind, phase 2 study aimed to investigate the efficacy and safety of secukinumab as compared to placebo in 41 subjects with moderate-to-severe AD over a 16-week period, with evaluations of clinical outcomes and molecular and cellular profiles in skin.

overall_design: Trial Design: Randomized, double-blind, placebo-controlled pilot study  Participants: Chronic moderate-to-severe atopic dermatitis (AD patients)>18 years  Interventions: Secukinumab 300mg subcutaneous vs. placebo  Objective: To evaluate the efficacy of secukinumab in moderate-to-severe intrinsic or extrinsic A  Primary outcome: change in epidermal thickness of lesional skin at Week 16  Randomization: Patients were randomized to secukinumab or placebo 2:1  Blinding: Participants, care givers, and those assessing outcomes were blinded to treatment arm

first: Benjamin

last: Ungar

first: Randall

last: Li

first: Grace

last: Kimmel

first: John

last: Nia

first: Peter

last: Hashim

first: Hee

last: Kim

first: Anjali

last: Vekaria

first: Yeriel

last: Estrada

first: Hui

last: Xu

first: Xiangyu

last: Peng

first: Giselle

middle: K

last: Singer

first: Danielle

last: Baum

first: Yasaman

last: Mansouri

first: Mark

last: Taliercio

first: Emma

last: Guttman-Yassky


title: Disturbed mitochondrial dynamics in CD8+ TIL reinforce epigenetic programming linked with T cell exhaustion

city: Vienna

first: Hana

last: Imrichova

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM, Vienna

type: Methylation profiling by high throughput sequencing


title: Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified meduloblastoma [RNA-seq]

first: Venu

last: Thatikonda

overall_design:
In this specific experimental design, RNA-sequencing data from two MYC amplified Group 3 primary Medulloblastoma were generated fo the purpose of integrative analysis with MYC, HDAC2, H3K27ac ChIP-sequencing data.
**RAW data were deposited at EGA with id - EGAS00001003855**

first: Jonas

last: Ecker

first: Gianluca

last: Sigismondo

first: Gintvile

last: Valinciute

first: Ina

last: Oehme

first: Carina

last: Müller

first: Juliane

last: Buhl

first: Johannes

last: Ridinger

first: Diren

last: Usta

first: Florian

last: Selt

first: Cornelis

last: van Tilbur

first: Christel

last: Herold-Mende

first: Felix

last: Sahm

first: Frank

last: Westermann

first: Marcel

last: Kool

first: Robert

last: Wechsler-Reya

first: Lukas

last: Chavez

first: Jeroen

last: Krijgsveld

first: Natalie

last: Jäger

first: Stefan

last: Pfister

first: Olaf

last: Witt

first: Till

last: Milde


title: Reduced chromatin binding of MYC is a key effect of HDAC inhibition in MYC amplified meduloblastoma [ChIP-seq]

first: Venu

last: Thatikonda

overall_design:
In this specific experimental design, ChIP-sequencing data of MYC, HDAC2, H3K27ac and RNApolII was generated from three primary MYC amplified Group 3 medulloblastoma tumors. In addition to primary tumors, in order to assess the effect of HDAC inhibition, we generated MYC, HDAC2, H3K27ac and RNApolII ChIP-seq data from HDMB03 cells before and after subjecting to treatment with 5μM entinostat (MS275) for 6 hours.
**RAW data were deposited at EGA with id - EGAS00001003855**

first: Jonas

last: Ecker

first: Gianluca

last: Sigismondo

first: Gintvile

last: Valinciute

first: Ina

last: Oehme

first: Carina

last: Müller


title: RNA-sequencing analysis of differential expression in supt16h mutants

first: David

last: Traver

state: California

address: 9500 Gilman Drive, MC 0380

department: Division of Biological Sciences

institute: UCSD

summary: Haematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signalling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signalling components, genes essential for HSC development, due to abrogated transcription. Classically, Supt16h regulates transcription and nucleosome reorganization. Whereas global chromatin accessibility in supt16h mutants is unaffected, we observe a specific increase in accessibility at the p53 locus, causing an accumulation of p53 mRNA and protein. We further demonstrate that P53 levels directly influence expression of the Polycomb Group protein, phc1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues both loss of Notch and loss of HSC phenotypes in supt16h mutants. Taken together, our results highlight a previously uncharacterized relationship between supt16h, p53, and phc1 to specify HSCs via modulation of Notch signalling.

overall_design: RNA-sequencing was performed on 32hpf wildtype (WT) and supt16h-/- whole embryos to examine differential expression data. 40 embryos were collected for each replicate.

first: Sophia

last: Espanola


title: Muscle Specific Insulin Receptor Overexpression Protects Mice from Diet-Induced Glucose Intolerance but Leads to Post-Receptor Insulin Resistance

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Skeletal muscle insulin resistance is a prominent early feature in the pathogenesis of type 2 diabetes (T2D). In attempt to overcome this defect, we generated mice overexpressing insulin receptors (IR) specifically in skeletal muscle (IRMOE). On normal chow, IRMOE mice have similar body weight as controls, but an increase in lean mass and glycolytic muscle fibers and reduced fat mass. IRMOE mice also show higher basal phosphorylation of IR, IRS-1 and Akt in muscle and improved glucose tolerance compared to controls. When challenged with high fat diet (HFD), IRMOE mice are protected from diet-induced obesity. This is associated with reduced inflammation in fat and liver, improved glucose tolerance and improved systemic insulin sensitivity. Surprisingly, however, in both chow and HFD-fed mice, insulin stimulated Akt phosphorylation is significantly reduced in muscle of IRMOE mice, indicating post-receptor insulin resistance. RNA sequencing reveals downregulation of several post-receptor signaling proteins that contribute to this resistance. Thus, enhancing early insulin signaling in muscle by overexpression of the insulin receptor protects mice from diet-induced obesity and its effects on glucose metabolism. However, chronic overstimulation of this pathway leads to post-receptor desensitization, indicating the critical balance between normal signaling and hyperstimulation of the insulin signaling pathway.

overall_design: Male mice were used for studies unless indicated. Mice transgenic for loxP-stop-loxP insulin receptor (LSL-IR) were generated through pronuclear injection of a linearized cassette carrying mouse IR isoform A cDNA driven by CAG promoter and interrupted by a floxed beta-gal cDNA and a stop codon.  IRMOE mice were then generated by crossing the LSL-IR mice with mice carrying a Cre transgene driven by the human skeletal muscle actin (HSA) promoter. Muscle RNA of Control or IRMOE mice was extracted by homogenizing tissues in TRIzol, treating with chloroform, and precipitating in 70% ethanol. cDNA was made using High Capacity cDNA Reverse Transcription Kit (Applied Biosystems, catalog 4368813). RNA-seq libraries were made and sequencing was performed on an Illumina NextSeq 500.

first: Guoxiao

last: Wang

first: C

last: Kahn


title: Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin [ChIP-seq]

status: Public on Sep 06 2020

city: University Park

first: Shaun

last: Mahony

state: PA

address: 404 South Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

summary: While Hox genes encode for similar transcription factors (TFs), they induce different fates across body axes. We sought to understand how Hox TF genomic binding preferences relate to their patterning activities during neuronal differentiation. To generate the required neuronal diversity for locomotor activity, Hox TFs specify spinal motor neuron and interneuron subtypes along the rostro-caudal axis. Our data revelated that Hoxc6 and Hoxc8 of the central group induce limb-innervating fates by binding to the same sites. On the other hand, the posterior group Hox genes assign different positional identities: Hoxc9 (thoracic), Hoxc10 (limb-innervating) and Hox13 (axial elongation termination) by binding to distinct sites with the same primary motif. We find that their genomic binding distributions are explained by differential abilities to bind to previously inaccessible chromatin. Thus, the vertebrate posterior Hox expansion and its associated patterning diversification is the product of their differential abilities to associate with less accessible chromatin.

overall_design: ChIP-Seq was used to characterize Hox TF binding during ESC-to-MN differentiation

first: Milica

last: Bulajić

first: Divyanshi

last: Srivastava

first: Jeremy

last: Dasen

first: Hynek

last: Wichterle

first: Esteban

middle: O

last: Mazzoni


title: Comparative chromatin accessibility profiling of wildtype and supt16h-/- zebrafish using ATAC-sequencing

summary: Chromatin organization and accessibility are fundamental to how genes are transcriptionally controlled. We identify the first vertebrate mutant for supt16h, a component of the FACT (FAcilitates Chromatin Transcription) complex along with Ssrp1 known to reorganize nucleosomes and assist in transcriptional elongation. We demonstrate its importance in hematopoietic stem cell (HSC) specification by regulating the elongation of Notch genes. Unexpectedly, Assay for Transposase Accessible Chromatin (ATAC) sequencing revealed that loss of supt16h does not affect histone accessibility on a Notch-specific or global level. Although the majority of genes are unaffected, loss of supt16h alters chromatin accessibility significantly at the p53 locus, leading to its overexpression in mutants. Upon downregulation of p53, both loss of Notch and loss of HSC phenotypes are rescued. Notably, ssrp1 mutants possessed normal elongation of Notch genes, levels of P53, and specification of HSCs. Our results highlight the discrete effects of Supt16h and Ssrp1 during HSC specification. Additionally, we demonstrate the relationship between supt16h and p53 during transcriptional elongation to specify HSC fate via modulation of Notch signaling.

overall_design: Assay for Transposase Accessible Chromatin (ATAC) sequencing was performed 40 wildtype (WT) and supt16h-/- whole embryos at 32hpf to observe the effect of the histone chaperone, supt16h, on chromatin accessibility. Three biological replicates in two technical replicates were sequenced.


title: MiRNA regulation of auto-anticoagulation in hibernating black bears: A Novel Translational Approach

city: Worcester

first: Alper

last: Kucukural

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

type: Non-coding RNA profiling by high throughput sequencing

summary:
Hibernating American black bears have significantly different clotting parameters than their active summer counterparts, affording them innate protection against venous thromboembolism (VTE) despite prolonged periods of immobility. Physiologic changes that occur during hibernation are thought to result from differential gene expression, rather than novel genes, and there is increasing evidence miRNAs may play an important role this regulation. We propose that significant differences exist in miRNA expression in the plasma of hibernating black bears compared to their active counter parts (summer), which lead to critical gene regulation responsible for auto-anticoagulation during hibernation.
Methods: Blood was collected from 21 American black bears in the Northern Michigan Peninsula in summer 2017 and winter 2018 (11 active, 10 hibernating).  Plasma was extracted
Results: Fifteen miRNAs were differentially expressed in the plasma of hibernating black bears. Nine miRNAs were significantly downregulated (miR10b-3p, miR-136-3p, miR-181c-5p , miR-200a-3p, miR-200b-5p, miR-200c-3p, miR-320b, miR-320c and miR-320d) and six miRNAs were significantly upregulated (miR-15a-5p, miR-15b-3p, miR-15b-5p, miR-16-5p, miR-92a-3p, miR-150-5p) during hibernation.  Twelve miRNAs had no identifiable targets, but miR-200a-3p, miR-200b-5p and miR-200c-3p found to be targets of SERPINC1, the gene responsible for the production of antithrombin (AT).
Conclusions: Several miRNAs were differentially expressed in hibernating bears (12). Most importantly miR-200a-3p, miR-200b-5p and miR-200c-3p were all downregulated in hibernation and associated with increased expression of SERPINC1 and production of AT.  AT is a powerful anticoagulant and this finding may explain the hibernating black bears ability to achieve auto-anticoagulation and protection from VTE.

overall_design: We evaluated if significant differences exist between the expression of miRNAs in the plasma of hibernating black bears compared to their summer active counter parts.  Please note that  as some bears don't match due to unavailability of the same bears in summer time, differential expression analysis was carried out without pairing them.

first: Amanda

last: Fazzalari

first: Giacomo

last: Basadonna

first: Kahraman

last: Tanriverdi

first: Milka

last: Koupenova

first: Natalie

last: Pozzi

first: Jahnavi

last: Kakuturu

first: Ann

last: Friedrich

first: Ron

last: Korstanje

first: Nick

last: Fowler

first: Jerrold

last: Belant

first: Dean

last: Beyer Jr

first: Marjory

last: Brooks

first: Eric

middle: W

last: Dickson

first: Alexander

last: Palesty

first: Jane

last: Freedman

first: Mitchell

last: Cahan


title: Gene expression profiling in carmustine-resistant melanoma A2058 cells

status: Public on Aug 31 2020

city: New Taipei City

first: Shaochen

last: Lee

address: 510 Zhongzheng Rd., Xinzhuang Dist.

country: Taiwan

institute: FuJen Catholic University

summary: Analysis of gene expression and compare the significant changed genes with associated phenotypes.

overall_design: Total RNA extracted from parental or carmustine-resistant A2058 cells.

first: ShihSheng

last: Jiang

first: ShaoChen


title: The difference of microRNA profiles among control, normal high density lipoprotein-treated and proflammatory high density lipoprotein-treated endothelial cells

city: Guangzhou

first: Jingsong

last: Ou

state: Please Select

address: 58 Zhong Shan Er Road

department: Surgery/Cardiac Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: The potential mechanism were successfully illustrated through detecting different expression of microRNAs in between proinflammatory high density lipprotein (pHDL), nomal high density lipprotein (nHDL) and control group, to study whether microRNAs play important roles in the endothelial dysfunction caused by pHDL.

platform_organism:
Homo sapiens
Human alphaherpesvirus 2
Lymphocryptovirus
Rhadinovirus
JC polyomavirus
Human immunodeficiency virus 1
Merkel cell polyomavirus

overall_design:
1.To collect fasting blood of 6 coronary heart disease(CHD) patients with hypercholesterolemia and 6 normal subjects in 1st Affilated Hospital of SYSU.
2.Isolated HDL by density gradient centrifugation and measured its pro-inflammatory state.
3.Used PBS, HDL from normal subjects and CHD patients with hypercholesterolemia to treat HUVECs, and then extracted RNA.
4.Applied microarray method to observe the expression of microRNAs in HUVECs and qRT-PCR validation.
5.All experiments were repeated, with results expressed as mean ± standard deviation. Used one-way ANOVA or Kruskal-Wallis test to analyze variance between groups. Applied GraphPad Prism 5.0 and SPSS 13.0 to analyze experimental data. P<0.05, the difference was statistically significant.

We performed miRNA microarray analyses using endothelial-enriched RNAs obtained from the HUVECs after 24-hour nHDL, pHDL or control treatment.we found that 21 (14 upregulated and 7 downregulated) of 3100 miRNAs were significantly altered at 24 hours.

first: Mian

last: Wang


title: RNA-sequencing based linkage analysis identifies supt16h as a target gene from a forward genetic screen

city: La Jolla

first: David

last: Traver

overall_design: RNA-sequencing was performed on 32hpf wildtype (WT) and supt16h-/- whole embryos to perform single nucleotide polymorphism (SNP) based linkage mapping.

first: Sophia

last: Espanola


title: MR Imaging Distinguishes Tumor Hypoxia Levels of Different Prognostic and Biological Significance in Cervical Cancer

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

summary: Tumor hypoxia levels range from mild to severe and have different biological and therapeutical consequences, but are not easily assessable in patients. We present a method based on diagnostic dynamic contrast enhanced (DCE) magnetic resonance imaging (MRI) that visualizes a continuous range of hypoxia levels in tumors of cervical cancer patients. Hypoxia images were generated using an established approach based on pixel-wise combination of the DCE-MRI parameters e and Ktrans, reflecting oxygen consumption and supply, respectively. An algorithm to retrieve hypoxia levels from the images was developed and validated in 28 xenograft tumors, by comparing the MRI-defined levels with hypoxia levels derived from pimonidazole stained histological sections. We further established an indicator of hypoxia levels in patient tumors based on expression of nine hypoxia responsive genes. A strong correlation was found between these indicator values and the MRI-defined hypoxia levels in 63 patients. Chemoradiotherapy outcome of 74 patients was most strongly predicted by moderate hypoxia levels, whereas more severe or milder levels were less predictive. By combining gene expression profiles and MRI-defined hypoxia levels in cancer hallmark analysis, we identified a distribution of levels associated with each hallmark; oxidative phosphorylation and G2/M checkpoint were associated with moderate hypoxia, and epithelial-to-mesenchymal transition and inflammatory responses with significantly more severe levels. At the mildest levels, interferon response hallmarks, together with stabilization of HIF1A protein by immunohistochemistry, appearred significant. Thus, our method visualizes the distribution of hypoxia levels within patient tumors and has potential to distinguish levels of different prognostic and biological significance.

overall_design: Gene expression profiling of HeLa and SiHa cells exposed to hypoxia at 0.2%, 0.5%, 1%, 2% and 5% O2 and normoxia (95% air, control) was carried out, one replicate (hypoxia + control) for each O2 concentration.

first: Tiril

last: Hillestad

first: Tord

last: Hompland

first: Christina

last: Fjeldbo

first: Vilde

last: Skingen

first: Unn

last: Salberg

first: Eva-Katrine

last: Aarnes

first: Anja

last: Nilsen

first: Kjersti

middle: V

last: Lund

first: Tina

last: Evensen

first: Gunnar

last: Kristensen

first: Trond

last: Stokke


title: P53 based ChIP-sequencing of wildtype and mutant supt16h-/- zebrafish

summary: Hematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signaling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signaling components, genes essential for HSC development, due to abrogated transcription. Classically, Supt16h regulates transcription and nucleosome reorganization. Whereas global chromatin accessibility in supt16h mutants is unaffected, we observe a specific increase in accessibility at the p53 locus, causing an accumulation of p53 mRNA and protein. We further demonstrate that P53 levels directly influence expression of the Polycomb Group protein, phc1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues both loss of Notch and loss of HSC phenotypes in supt16h mutants. Taken together, our results highlight a previously uncharacterized relationship between supt16h, p53, and phc1 to specify HSCs via modulation of Notch signaling.

overall_design: ChIP-seq for the P53 protein was performed on roughly 1,000 of each wildtype (WT) and supt16h-/- whole embryos at 32hpf.


title: The Rac2 GTPase contributes to Cathepsin H-mediated protection against cytokine-induced β-cell apoptosis

city: Gentofte

first: Flemming

last: Pociot

address: Niels Steensens Vej 2

department: T1D Biology

country: Denmark

institute: Steno Diabetes Center Copenhagen

summary:
In type 1 diabetes (T1D), the pancreatic β-cells are specifically destroyed by the immune system. In this process, local release of pro-inflammatory cytokines, such as IL-1β and IFNγ, contribute to β-cell apoptosis. Genome-wide association studies have identified more than 60 risk loci for T1D, including chr15q25.1 with the candidate gene CTSH (cathepsin H). We previously showed that T1D-associated risk variants in CTSH affect the expression of CTSH and are associated with disease progression in children with newly diagnosed T1D.We further found that CTSH increases β-cell function and protects against cytokine-induced apoptosis. Using global gene expression analysis, the purpose of the present study was to identify the genes and mechanisms through which CTSH mediates its protective effects.
Microarray analysis identified a total of 63 annotated genes differentially expressed between stable CTSH-overexpressing insulin-secreting INS-1 cells and control cells transfected with an empty vector after treatment with IL-1β and IFNγ for 0, 6 and 16 hours. Permutation test taking all time-points into consideration identified 10 genes differentially expressed between the CTSH-overexpressing cells and the control cells: Elmod1, Fam49a, Gas7, Gna15, Msrb3, Nox1, Ptgs1, Rac2, Scn7a and Ttn. Pathway analysis identified one significant pathway “Inflammation mediated by chemokine and cytokine signaling pathway” with the genes Gna15, Ptgs1 and Rac2. Since Gna15 and Rac2 were upregulated by CTSH overexpression, their expression was knocked down using small interfering RNAs (siRNAs) to evaluate their potential as mediators of the protective effect of CTSH. Knockdown of Rac2 abolished the protective effect of CTSH overexpression on cytokine-induced apoptosis.

overall_design: We used one individual clone of INS-1 cells with stable overexpression of CTSH generated in our previous study (Floyel et al. PNAS 2014). Microarray analysis was performed on pCTSH#1 and pcDNA cells after treatment with IL-1β and IFNγ for 0, 6, and 16 hours. Untreated untransfected INS-1 cells were also included in the microarray analysis.


title: Genomic and Proteomic Biomarkers of Cardiac Allograft Vasculopathy

city: Vancouver

first: Bruce

middle: Maxwell

last: McManus

state: BC

address: 1081 Burrard Street

department: UBC James Hogg Research Centre

country: Canada

institute: PROOF Centre of Excellence

summary: Long-term survival of cardiac transplant recipients remains a significant hurdle largely due to cardiac allograft vasculopathy (CAV) as an expression of chronic rejection (CR).  Currently, coronary angiography and intravascular ultrasound, invasive and expensive modalities, are considered the standard for diagnosis of CAV.  In the current study, we combined assessment of blood mRNA and proteins to identify potential biomarkers for diagnosis of CAV.   Whole blood Affymetrix microarrays and plasma iTRAQ-MALDI-TOF/TOF proteomic analyses were carried out on 25 cardiac transplant patient samples. CAV diagnosis was made based on blinded quantitative analysis of angiograms, intravascular ultrasound images and clinical chart review. The genomics and proteomics data were assessed by moderated t-tests and discriminant analysis.    Two panels of 10 differentially expressed genes (FDR<5%), and 10 proteins with differential relative levels (p-values<0.025) between CAV and non-CAV samples were independently identified. Classification of new test samples revealed that the 10 genes together can discriminate between CAV and non-CAV samples with 83% sensitivity and specificity. Classification of the same samples using the 10 PGC’s dropped the sensitivity to 67%.   A combinatorial panel derived from the genomic and proteomic panels provided improvement in performance, at 100% sensitivity and 83% specificity.   Leave-one-out cross validation showed similar results.  Genomic, proteomic and combinatorial blood-based biomarkers are promising as potential minimally-invasive, sensitive and specific modalities for the diagnosis of CAV.    Classifier panels generated from current work are being evaluated in a prospective, multi-site observational trial.

overall_design: This study, approved by the Providence Health Care, the Vancouver Coastal Health and the UBC Research Ethics Boards, was carried out under the Biomarkers in Transplantation initiative on subjects who received a cardiac transplant and signed consent forms.   A total of 25 CAV and non-CAV blood samples, collected between year one and year five post-transplantation from 17 patients were selected for analyses. Thirteen subjects with ‘extreme phenotypes’ were selected for the biomarker discovery analysis, resulting in a training cohort of 7 CAV and 6 non-CAV samples, collected mostly at one year post-transplant. The remaining samples (6 CAV and 6 non-CAV) were subsequently utilized as the test cohort.  Diagnosis of CAV was made based on chart reviews (i.e., angiography and/or IVUS measurements) at timepoints corresponding to the blood sample collection dates.


title: Cell cycle-associated expression patterns predict gene function in mycobacteria

city: College Station

first: Thomas

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

summary: Gene expression is evaluated over roughly 1.5 cell cycles in a temperature-sensitive dnaA mutant of M. tuberculosis H37Rv to identify genes with periodic expression, or clusters of genes whose expression peaks at different timepoints correlating with distinct cell-cycle events like chromosome replication, septum formation, divisome assembly, and cytokinesis.

overall_design: RNAseq at 16 timepoints spanning 55 hours in 2 replicates each of dnaA cold-sensitive mutant and H37Rv wildtype strains

first: Aditya

middle: C

last: Bandekar

first: Christopher

last: Sassetti


title: Transcriptional affects of KLF2 deletion in bone marrow-derived macrophages

status: Public on Aug 26 2020

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary: We report bulk RNA-sequencing of bone marrow-derived macrophages (BMDMs) harvested from myeloid-specific KLF2 knockout (K2KO) and LysMCre control (LysM) mice

overall_design: BMDMs were isolated from 3 month old LysM or K2KO mice (n=4) according to standard protocols (see below) and transcriptional sequencing was performed.

first: David

last: Sweet

first: Mukesh

last: Jain

first: Vinesh

last: Vinayachandran

first: E


title: HIV-1 infection of CD4 T cells impairs antigen-specific B cell function

city: Heidelberg

first: Sheetal

last: Kaw

address: Im Neuenheimer Feld 344

department: CIID

institute: University of Heidelberg

summary:
Failures to produce neutralizing antibodies upon HIV-1 infection result in part from B cell dysfunction due to unspecific B cell activation. How HIV-1 affects antigen-specific B cell functions remains elusive. Using an adoptive transfer mouse model and ex vivo HIV infection of human tonsil tissue we found that expression of the HIV-1 pathogenesis factor NEF in CD4 T cells undermines their helper function and impairs cognate B cell functions including mounting of efficient specific IgG responses. NEF interfered with T cell help via a specific protein interaction motif that prevents polarized cytokine secretion at the T cell - B cell immune synapse. This interference reduced B cell activation and proliferation and thus disrupted germinal center formation and affinity maturation. These results identify NEF as a key component for HIV-mediated dysfunction of antigen-specific B cells. Therapeutic targeting of the identified molecular surface in NEF will facilitate host control of HIV infection.
We used microarray analysis  to understand

overall_design: 15 samples, naïve B cells, B cells cocultured with control T cells for 4hrs and 24hrs, B cells cocultured with (Nef-WT or Nef-mutant expressing) T cells for 4hrs and 24hrs

first: Oliver

last: Fackler


title: Modeling COVID-19 with Human Pluripotent Stem Cell-Derived Cells Reveals Synergistic Effects of Anti-inflammatory Macrophages with ACE2 Inhibition Against SARS-CoV-2

first: Joyce

middle: huanhuan

last: Chen

address: 5801 S Ellis Ave, Chicago

department: Pritzker School of Molecular Engineering

institute: Uchicago

summary: Study transcriptomes on the lung cells and macrophages derived from hESC

overall_design: scRNA profiles on hESC-derived lung cells and lung-macrophage co-cultured cells

first: Huanhuan

middle: J


title: RNA-Seq of CD8+ T cell subsets during LCMV infection III

status: Public on Aug 29 2020

first: Ananda

last: Goldrath

address: 9500 Gilman Dr

summary: Memory CD8 T lymphocytes are a long-lived population of immune cells that provide formidable protection against infections and malignancy, and are thus often central to vaccine and cancer immunotherapy efficacy. Here we refine the identity, developmental relationships, and functional roles of memory CD8 T cells through delineation of a descrete population that confers robust protection against reinfection and exhibits an unexpected molecular program bearing typically divergent characteristics of short-lived effector cells and long-lived memory T cells. Mass-cytometry and single-cell RNA sequencing analyses revealed an analogous population of cells in humans. These findings hold broad implications for both informing immunotherapy treatments and predicting their efficacy.

overall_design:
16 samples, 2 replicates, Day 55 LCMV infection CD8+ T cell subsets, Day 7 LCMV infection CD8+ effector T cells, Naive CD8+ T cells

This series includes samples re-analyzed from GSE107281 and GSE147080. These re-analyzed samples have been included here so that all raw data for this study is available from a single SRP.

first: J

last: Milner

first: H

last: Nguyen

first: K

middle: D

last: Omilusik

first: A


title: Survival Following Traumatic Brain Injury in Drosophila Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish

city: Madison

first: Laura

middle: Catherine

last: Swanson

state: WI

address: 2631 University Avenue Apt 6

department: Medical Genetics

institute: University of Wisconsin-Madison

summary: To identify genes regulated by Relish in both the absence and presence of TBI in Drosophila, we compared genome-wide mRNA expression of control flies, as well as flies that were heterozygous or homozygous for a null allele of relish with and without injury.

overall_design: Whole male fly mRNA profiles of 1-7 day old wild type (+/+), heterozygous (+/Reldel) and homozygous (Reldel/Reldel) Drosophila lines in a yw background were generated, 4 h following injury or without injury. Experiments were performed in quadruplicate, using Illumina NovaSeq 6000.

first: Barry

last: Ganetzky

middle: A

last: Wassarman


title: Transcriptome analysis of rice reveals the lncRNA-mRNA regulatory network in response to Rice black-streaked dwarf virus infection

status: Public on Aug 25 2020

city: Hangzhou

first: Tianze

last: Zhang

address: Yuhangtang Road 866

institute: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University

summary: To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant-pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant-pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV.

first: Qian

last: Liang

first: Jianxiang

last: Wu


title: Gene expression analysis in Tibialis anterior (TA) muscle upon titration of myonuclear numbers

city: Cincinnati

first: Douglas

last: Millay

address: 240 Albert Sabin Way  MLC 7020

institute: Cincinnati Children's Hospital Medical Center

summary:
Skeletal muscle myofibers accrue hundreds of nuclei during post-natal development via fusion with activated satellite cells (myoblasts), which is absolutely reliant on expression of the muscle fusogen myomaker (Mymk) in the myoblasts. Using an inducible genetic approach to render myoblasts non-fusogenic (by tamoxifen-inducible Pax7-CreER mediated recombination of the Mymk gene exclusively in satellite cells), we blocked myonuclear accrual at different time-points of post-natal development and thereby titrated the number of nuclei in resultant mutant myofibers. These Microarray assays were carried out on age day 28 (P28) using total RNA isolated from control and mutant muscle to determine changes in transcriptional profiles of these muscles to (a) assess effects of myonuclear titration, and (b) identify adaptive mechanisms elicited in mutant muscles in response to myonuclear deficiency.
We used microarrays to generate information about transcriptional profiles in muscles with varying levels of myonuclear deficiencies.

overall_design: TA muscle was isolated from day 28 (P28) old animals that had either full complement of myonuclei or had received tamoxifen on day 0 (D1w) or day 6 (D2w) to block myoblast fusion and therefore, accrue different myonuclei numbers.

first: Alyssa

last: Cramer

first: Vikram

last: Prasad

middle: P


title: Actvity-dependent profiling of lateral septum neurons following restraint stress

status: Public on Aug 30 2020

first: Jeffrey

middle: M

last: Friedman

address: 1230 York Avenue

institute: Rockefeller University

summary: We used the phospho-TRAP protocol (Knight et al., 2011) to profile lateral septum populations that are activated following 1 hour of restraint stress.

overall_design: Phosporylated ribosomes were immunoprecipitated from lateral sepum brain lysates that were dissected following 1 hour of restraint stress.

first: Sarah

last: Stern

first: Estefania

last: Azevedo


title: Genome-wide transcriptome of rice laser-microdissected crown root primordia reveals genes expressed specifically during the early differentiation stages of crown roots

city: Montpellier

first: Pascal

last: Gantet

address: Avenue Agropolis

department: IRD

country: France

institute: Université Montpellier 2

summary:
Crown roots constitute the main part of the rice root system. Several key genes involved in crown root initiation and development have been identified by genetics and functional genomics approaches. Nevertheless these approaches are impaired by gene function redundancy and mutant lethality. To overcome these limitations, genome-wide transcriptome analysis can help to identify genes involved in crown root formation and early development.  In this study we aimed to identify the genes speciffically expressed in developing crown root primordia in comparison with adjacent cortex tissue of stem at three different developmental stages before emergence from the stem. For this, we used Laser Capture Microdissection to collect crown root primordia in the stem base of 8-day-old rice seedlings.
Affymetrix microarrays were processed in the Microarray Core Facility “Transcriptome“ of the Institute in Regenerative Medicine and Biotherapy, CHU de Montpellier-INSERM-UM Montpellier, http://irmb.chu-montpellier.fr/ .

overall_design: Eight days after sowing, a total of six stem bases from WT cultivar Taichung 65 Oryza sativa, Japonica rice plantlets were fixed and cut into 15 µm sections.These sections were dissected on a LMD 7000 laser dissector (Leica Biosystems). CR primordia belonging to the three successive rings present in plantlets stem bases, corresponding to three primordia developmental stages, were collected and regrouped in three pools corresponding to the three developmental stages. Stem cortex tissues were sampled from the same sections where the CR primordia were collected from. Samples from two stem bases were pooled to perform  RNA extractions from the three primordia developmental stages and cortex, that correspond to one independent repetition of the experiment. In total 3 x 2 stem bases were processed that corespond to three intependant repetition of the experiment. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific).

last: Lavarenne

first: P


title: Molecular profiling of lateral septum neurotensin neurons using viralTRAP

city: New York

summary: The lateral septum contains a number of molecularly defined cell populations. We used the viral-TRAP protocol (Nectow et al.,2017) to profile lateral septum neurotensin neurons.

overall_design: Neurotensin-cre mice (JAX 017525) were injected with AAV-IV-NBL10 into the lateral septum. Sequencing enables identification of subpopulations within the neurotensin neurons of the lateral septum.


title: single-cell RNA-sequencing of murine intestine 24 hours following acute p53 activation due to Mdm2-loss (Mdm2FM/- Cag-CreERTg (FMTg)) compared to intestine that retain Mdm2 (Mdm2+/- Cag-CreERTg (Tg))

status: Public on Aug 24 2020

city: Houston

first: Yuan

last: Qi

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

summary: FMTg (Mdm2FM/- Cag-CreERTg) and Tg (Mdm2+/- Cag-CreERTg) mice were administered 6mg/40g of Tamoxifen dissolved in corn-oil and sacrificed 24 hours after injection. Single cells were isolated from fresh small intestine samples to compare single cell transcriptomes between intestine with high or control p53 activity

overall_design: One FMTg small intestine and one Tg small intestine were isolated from mice 24 hours following a single 6mg/40g tamoxifen injection. Single cells were isolated from fresh tissues and then processed through the 10X genomics platform

first: Sydney

last: Moyer


title: The CD4+ alike CD8+ memory T cell compartment diversification reveales CD8+ T cell subsets with cytotoxic and non-cytotoxic properties

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

summary: CD4+ memory T helper cells are organized in different subsets characterized by distinct functions and chemokine receptor expression patterns induced and maintained by divergent gene programs. We demonstrate here that identical chemokine receptor combinations are sufficient to separate analogous differentiated CD8+ memory T cell subsets with matching cytokine profiles. Tc2, Tc17 and Tc22 type CD8+ T cell subsets, in contrast to classical cytotoxic Tc1 and Tc17+1 cells, possess a CD4 helper type alike phenotype characterized by absent cytotoxicity and SLAMF7 expression as well their ability to express CD40L upon activation. Their highly disparate homing patterns and unique TCR repertoire associates them to distinct immune responses as compared to those cytotoxic CD8+ T cells exert their role in. The dermal T cell gene expression signature and enrichment in psoriasis patients indicates that peripheral helper type CD8+ T cells represent a circulatory variant of skin resident cells.

overall_design: mRNA profiles of 5 Tc and 5 Th lymphocyte subpopulations from three different donors

first: Lucie

last: Loyal

first: Andreas

last: Thiel

first: Ulrike

last: Krüger

first: Marten

last: Jäger


title: Multi-institutional prospective validation of prognostic mRNA signatures in early stage squamous lung cancer (Alliance) [cohort I]

status: Public on Aug 28 2020

first: Zhengming

last: Chen

address: 402 67th street

institute: Weill Cornell Medicine

summary:
Purpose: The primary objective of the current study was to validate biomarkers to identify the 10% to 27% of patients with stage I and 35% of patients with stage IIA squamous cell carcinoma of lung (SC) who are likely to recur following surgical resection, so that these patients may be offered enrollment in clinical trials evaluating directed ACT. A secondary objective was to identify patients with stage IIB SC who are unlikely to develop recurrences and might thereby be spared the potential significant toxicity and expense of ACT.
Methods: Two-stage validation used independent core laboratories, objective quality control standards, locked test parameters, and large multi-institutional specimen/data sets. First stage validation confirmed a signature’s ability to stratify patient survival. Second stage validation determined which signature(s) optimally improved risk discrimination when added to baseline clinical predictors. Participants were prospectively enrolled on institutional (Cohort I) or cooperative group (Cohort II) biospecimen/data collection protocols. All cases underwent central review of clinical, pathologic and biospecimen parameters using objective criteria to determine final inclusion (Cohort I: n=249; Cohort II: n=234). Primary selection required that a signature significantly predict 3-years survival after surgery in Cohort I. Signatures meeting this criterion were further tested in Cohort II, comparing risk prediction using baseline risk factors alone versus in combination with the signature.
Results: Male sex, advanced age, and higher stage were associated with shorter survival in Cohort I and established a baseline clinical model. Of three signatures validated in Cohort I, one signature was validated in Cohort II and statistically significantly enhanced prognosis relative to the baseline model (C-index difference 0.122; p<0.05).
Conclusions: These results represent the first rigorous validation of a test appropriate to direct adjuvant treatment or clinical trials for patients with lung squamous cell carcinoma.

overall_design: Total RNA from squamous cell carcinoma specimens were extracted for mRNA profiling with microarray analysis.

first: Raphael

last: Bueno

first: William

middle: G

last: Richards

first: David

middle: H

last: Harpole

first: Karla

last: Ballman

first: Ming-Sound

last: Tsao

first: Xiaofei

last: Wang

first: Guoan

first: Lucian

middle: R

last: Chirieac

first: M

last: Chui

first: Wilbur

last: Franklin

first: Thomas

last: Giordano

first: Ramaswamy

last: Govindan

first: Mary-Beth

last: Joshi

first: Daniel

middle: T

last: Merrick

first: Christopher

last: Rivard

last: Sporn

first: Adrie

last: van Bokhoven

first: Hui

last: Yu

first: Frances

last: Shepherd

first: Mark

last: Watson

last: Beer

first: Fred

last: Hirsch


title: Activation of proprotein convertase in the mouse habenula causes depressive-like behaviors through remodeling of extracellular matrix

city: Tokyo

first: Hikaru

last: Ito

address: 1-5-45 Yushima, Bunkyo-ku-ku

country: Japan

institute: Tokyo Medical and Dental University

summary: We performed RNA-seq in lateral habenula of mice with susceptibility to chronic social defeat stress.

overall_design: mRNA profiles in lateral habenula of nondefeated, stress-susceptible, and stress-resilient mice.

first: Hidenori

last: Aizawa


title: Multi-institutional prospective validation of prognostic mRNA signatures in early stage squamous lung cancer (Alliance)

first: Zhengming

last: Chen

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

overall_design: Refer to individual Series


title: TRAP-Seq uncovers post-transcriptional gene regulation after acute sleep deprivation

status: Public on Aug 27 2020

city: Iowa City

first: Yann

last: Vanrobaeys

state: IA

address: 2312 PBDB, 169 Newton Road

department: Neuroscience

institute: University of Iowa

summary: To identify the effects of sleep deprivation on the translatome, we took advantage of the RiboTag mouse line with an HA labeled ribosomal protein to express labeled Rpl22 in CaMKIIa neurons to selectively isolate and then sequence mRNA transcripts associated with ribosomes

overall_design: Ribosome associated mRNA from hippocampus of 2-3 months male mice.


title: PTK6 domain mutants modulates action in Triple-negative breast cancer

city: Minneapolis

first: Carol

last: Lange

state: Minnesota

address: 2231 6th St SE

department: Medicine

institute: University of Minnesota

summary: Protein tyrosine kinase 6 (PTK6; also called Brk) is overexpressed in 86% of breast cancer patients; high PTK6 expression predicts poor outcome. We reported PTK6 induction by HIF/GR complexes in response to either cellular or host stress. However, PTK6-driven signaling events in the context of TNBC remain undefined. In a mouse model of TNBC, manipulation of PTK6 levels (i.e. via knock-out or add-back) had little effect on primary tumor volume but altered lung metastasis. To delineate the mechanisms of PTK6 downstream signaling, we created kinase-dead (KM) and kinase-intact domain structure mutants of PTK6 via in frame deletions of the N-terminal SH3 or SH2 domains.  While the PTK6 kinase domain contributed to soft-agar colony formation, PTK6 kinase activity was entirely dispensable for cell migration. Specifically, TNBC models expressing a PTK6 variant lacking the SH2 domain (SH2-del PTK6) were unresponsive to growth factor-stimulated cell motility relative to SH3-del, KM or wild-type PTK6 controls. Reverse phase protein array (RPPA) revealed that while intact PTK6 mediates spheroid formation via p38 MAPK signaling, the SH2 domain of PTK6 limits this biology, and instead mediates TNBC cell motility via activation of the RhoA and/or AhR signaling pathways. Inhibition of RhoA and/or AhR blocked TNBC cell migration as well as the branching/invasive morphology of PTK6+/AhR+ primary breast tumor tissue organoids. Inhibition of RhoA also enhanced paclitaxel cytotoxicity in TNBC cells, including in a taxane-refractory TNBC model. Together, these studies reveal that the SH2-domain of PTK6 is a potent effector of advanced cancer phenotypes in TNBC and identify RhoA and AhR as novel therapeutic targets in PTK6+ breast tumors.

overall_design: Examination of the effect of HGF in TNBC cell line MDA-MB-231 with mutation in the ptk6 protein.

first: Amy

last: Dwyer

first: Carlos

last: Perez Kerkvliet


title: DNA methylation analysis in normal gastric epithelial cells and gastric cancer cell lines

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of normal gastric epuithelial cells and gastric cancer cell lines. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included 2 normal gastric epithelial cells and 14 gastric cancer cells.

overall_design: Bisulfite converted DNA from 2 normal gastric epithelial cells and 14 gastric cancer cells were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Atsushi

last: Okabe

first: Kie

middle: K

last: Huang

first: Patrick

last: Tan

last: Kaneda


title: Ribo-tag translatome analysis from Split-Cre transgenic mice

status: Public on Aug 18 2020

city: Rehovot

first: Jung-Seok

last: Kim

address: 234 Herzl street

department: Immunology

country: Israel

institute: Weizmann Institute of Science

summary: We generated Split-Cre transgenic mice strains to target microglia or Lyve1+ macrophages in the brain. To obtain translatome from the each population, Split-Cre mice were crossed with Ribo-tag reporter mice, and translatome were acquired with anti-HA antibody immuno-percipitation.

overall_design: HA-IP and IgG-IP control from each mouse brain. CX3XR1-CCre: Sall1-NCre: Ribo-tag and CX3CR1-CCre: Lyve1-NCre: Ribo-tag mice strain. Steady state and 12h LPS i.p injection.

first: Louise

last: Boura-Halfon

first: Zhana

last: Haimon

first: Sebastien

last: Trzebanski


title: Mitochondrial carrier homolog 2 (MTCH2) regulates the differentiation of AML cells by controlling pyruvate entry into the mitochondria, nuclear localization of pyruvate dehydrogenase complex and H3 and H4 histone acetylation

city: Toronto

first: Aaron

last: Schimmer

state: ON

address: 610 University avenue

institute: University Health Network

summary: Inhibiting MTCH2 or the Mitochondrial Pyruvate Carrier increased levels of pyruvate and pyruvate dehydrogenase in the nucleus leading to differentiation and loss of stemness in AML.

overall_design: Gene expression analysis upon knock-down of MTCH2 by two independent shRNAs

first: Dilshad

last: Khan


title: Transcriptomic profile of Calu-3 airway epithelial cells in response to flagellin

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: The purpose of the study is to compare the transcriptomic profile of the airway epithelial cell line Calu-3 in reponse to Pseudomonas aeruginosa virulence factor flagellin. CF is caused by mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR gene in Calu-3 cells was knockdown by CRISPR-Cas9 (TS) and a control cell line (CTL) was aslo generated using a non-targeting guide RNA. CTL and CFTR KD Calu3-cells were grown on Transwell filters, polarized at the air-liquid interface and exposed to flagellin for 6 hours.  We considered 2 non-stimulated (ND) conditions: CTL-NS and TS-NS, and 2 conditions stimulated with flagellin (Flag): CTL-Flag and TS-Flag.

overall_design: mRNA profiles between CFTR knockdown and control airway epithelial cells cultures exposed to flagellin were generated by deep sequencing using Illumina.

first: Aderonke

last: Sofoluwe

first: Alice

last: Zoso

first: Marc

last: Bacchetta

last: Lemeille

last: Chanson


title: Multi-institutional prospective validation of prognostic mRNA signatures in early stage squamous lung cancer (Alliance) [Cohort II]

first: Zhengming

last: Chen

first: Raphael

last: Bueno

first: William

last: Richards

first: David

last: Harpole

first: Karla

last: Ballman

first: Ming-Sound

last: Tsao

first: Xiaofei

last: Wang

first: Guoan

first: Lucian

last: Chirieac

first: M

last: Chui

first: Wilbur

last: Franklin

first: Thomas

last: Giordano

first: Ramaswamy

last: Govindan

first: Mary-Beth

last: Joshi

first: Daniel

last: Merrick

first: Christopher

last: Rivard

last: Sporn

first: Adrie

last: van Bokhoven

first: Hui

last: Yu

first: Frances

last: Shepherd

first: Mark

last: Watson

last: Beer

first: Fred

last: Hirsch


title: Inactivation of Par3/Hippo pathway promotes prostatic symmetric cell division and tumorigenesis

status: Public on Aug 10 2020

city: Hefei

first: Peijie

last: Zhou

state: Anhui

address: Lujiang road

department: Department of Radiation Oncology, The First Affiliated Hospital of USTC

institute: University of Science and Technology of China

summary:
Purpose: mRNA sequencing has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare mRNA level of WT and Par3KO derived prostate tissues
Methods: prostate mRNA profiles of 8-week-old wild-type (WT) and Par3 knockout (Par3−/−) mice were generated by sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA).
Results: Using an optimized data analysis method, we mapped about 20 million sequence reads per sample to the mouse genome and identified 12,014 transcripts in the prostate of WT and Par3−/− mice with BWA workflow and 24,115 transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 132 known housekeeping genes, and 120 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than three orders of magnitude and a goodness of fit (R2) of 0.9120. Approximately 10% of the transcripts showed differential expression between the WT and Par3−/− retina, with a fold change ≥2.0 and p value <0.05. Altered expression of 32 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method.
Conclusions: Our results reveal that Par3 KO promotes prostatic epithelium proliferation.

overall_design: prostate mRNA profiles of 8-week old wild type (WT) and Par3-/- mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Y

last: Fang

first: P


title: Expression data of human B lymphocytes from follicular lymphoma lymph nodes (FL)

city: RENNES

first: Celine

last: Pangault

address: 2, avenue du Léon Bernard

department: Medical School of Rennes

institute: Rennes University Hospital

summary: GEP on Affymetrix U133+2.0 microarrays was performed on ex vivo cell-sorted  B lymphocytes from FL patients, according to the CD20hiCD44loCD38posIgDnegCD138neg phenotype.

overall_design: GEP was performed on 10 FL lymph nodes

first: Karin

last: Tarte

first: Thierry

last: Fest


title: Coupling genome-wide transcriptomics and developmental toxicity profiles in zebrafish to characterize polycyclic aromatic hydrocarbon (PAH) hazard

status: Public on Aug 22 2020

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: Polycyclic Aromatic Hydrocarbons (PAHs) are diverse environmental pollutants associated with adverse human health effects. Many studies focus on the carcinogenic effects of a limited number of PAHs and there is an increasing need to understand mechanisms of developmental toxicity of more varied yet environmentally relevant PAHs. A previous study characterized the developmental toxicity of 123 PAHs in zebrafish. Based on phenotypic responses ranging from complete inactivity to acute mortality, we classified these PAHs into eight bins, selected 16 representative PAHs, and exposed developing zebrafish to the concentration of each PAH that induced 80% phenotypic effect. We conducted RNA sequencing at 48 h post fertilization to identify gene expression changes as a result of PAH exposure.

overall_design: Each biological sample consisted of 8 embryos with 4 biological replicates per condition, for a total of 72 samples. DMSO was used as the control on both sample collectiong days.

first: Prarthana

last: Shankar

first: Robyn

middle: L

last: Tanguay


title: Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF‐mediated intracellular functions

status: Public on Aug 20 2020

city: Athens

first: Zhihua

last: Hua

state: Ohio

address: 22 Richland Ave

department: Department of Environmental and Plant Biology

institute: Ohio University

summary:
Purpose: Ubiquitin-mediated proteolysis by the 26S proteasome is a critical regulatory mechanism controlling many biological processes.  The multi-subunit Skp1-Cullin1-F-box (SCF) complexes are designed to select substrates for ubiquitylation in all eukaryotes.  Within these complexes, the Skp1 protein is defined as the bridge between the F-box and the Cullin1 proteins.  In Arabidopsis thaliana, there are 19 Arabidopsis Skp1-Like (ASK) genes that encode Skp1 proteins.  Our previous genomics and evolutionary studies suggest that ASK1 plays a predominant role in the ASK family.  To demonstrate this hypothesis, we genetically introduced the same Ds insertion allele of ask1-1 in Ler into the Arabidopsis Col-0 reference genome.  The ask1-1 allele was initially obtained from an ask1-1(+/-)ask2-1(+/-)/LerWs double heterozygous mutant (Liu et al., 2004).  To identify the breadth and depth of SCF functions, we applied RNA-Seq sequencing to systematically analyze the perturbation of transcriptomes in both floral bud and open flower tissues in this novel ask1 mutant.
Method: Two replicates of total RNA were extracted from 10-50 mg of floral buds or open flowers from Col-0, ask1, and ASK1 (WT allele) primary inflorescences five hours after dawn grown under a long-day photoperiod condition. The NucleoSpin® RNA kit (Macherey-Nagel) was used for RNA extraction following the manufacturer’s instructions.  1 μg each from the 12 RNA samples was used for pair end 150-mer deep sequencing using a NovaSeq 6000 platform (Novogene).  Adapter and low-quality sequences in the raw FASTQ sequencing data were removed to produce valid sequences using Trimmomatic (phred=33, minimum length=36; (Bolger et al., 2014)), which were further aligned to the A. thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) via TOPHAT2 (Kim et al., 2013a) to identify accepted hits of each locus.  HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., 2015).  The resulting counts per locus were normalized to counts per million reads (CPM) among all 12 libraries and used to identify groups of SDEGs in bud and open flower tissues in ask1 and ASK1 through comparing to the WT bud and open flower tissues, respectively, by edgeR (Log2FC ≥ 1; FDR < 0.01%; (Robinson et al., 2010)).
Results: In total, 52 and 54 SDEGs were identified to be up-regulated and down-regulated, respectively, in ASK1 BC10F4 bud tissues; and 13 and 3 SDEGs were identified to be up-regulated and down-regulated, respectively, in ASK1 BC10F4 open flower tissues (2-fold change (FC) with a false discovery rate (FDR) < 0.01).  However, 306 and 941 SDEGs (in total 1,247) in ask1 bud tissues and 392 and 1,137 SDEGs (in total 1,529) in ask1 open flower tissues were identified to be up-regulated and down-regulated, respectively (2-FC and FDR < 0.01).
Conclusions: Compared to Col-0, 527 and 640 SDEGs were identified in Ler and Ws, respectively, which were greatly higher than the number of SDEGs identified in ASK1 floral bud (Fisher’s exact test, p = 6.0e-82 and 7.5e-112, respectively) and open flower tissues (Fisher’s exact test, p = 7.4e-150 and 1.2e-186, respectively).  Therefore, we concluded that the genetic background of ASK1 and ask1 are isogenic to Col-0.  The large array of SDEGs identified in both floral buds and open flower tissues in ask1 demonstrated a wide range of roles of ASK1-containing SCF complexes.

overall_design: Two replicates of total RNA were extracted from 10-50 mg of floral buds or open flowers from Col-0, ask1, and ASK1 (WT allele) primary inflorescences five hours after dawn grown under a long-day photoperiod condition. Transcriptome profiles were generated in duplicates by pair end 150-mer deep sequencing using a NovaSeq 6000 platform (Novogene).

first: Madhura

last: Yapa


title: Immune complex stimulation of human monocytes

status: Public on Aug 05 2020

city: South San Francisco

first: Jason

last: Hackney

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

summary: Systemic sclerosis (SSc) is an autoimmune disease and several distinct autoantibodies have been described in SSc patients, many correlating with specific clinical presentation. Numerous studies have documented the presence of immune complexes (IC) in sera, lungs and BAL of SSc patients, potentially implicating them in the pathogenesis. Monocyte/macrophage activation also have been observed in fibrotic SSc skin and lung tissue. While the upstream activators remain unknown, it is plausible that IC are amongst the key triggers in activating monocytes and sustaining the chronic inflammation and fibrosis in SSc tissue. To test this hypothesis and find the specific downstream genes regulated by IC, we compare the gene expressions of the monocytes stimulated by control medium, LPS and IC using RNA seq. OPN was one of these IC regulated genes. Our paper further suggested that circulating OPN levels serve as a systemic proxy for IC driven profibrotic macrophage activity, highlighting its potential as a promising biomarker in SSc-ILD.

overall_design:
CD14+ monocytes were purified from the PBMCs of 5 donors. Monocytes were then stimulated with either plate bound immune complex or LPS for 18 h, or left unstimulated.
Groups: 1) Unstimulated (5 samples), 1) LPS stimulated DMSO (5 samples), 3) IC stimulated DMSO (5 samples).

**Raw data not provided for patient privacy reasons**

first: Xia

last: Gao

first: Guiquan

last: Jia

first: Anna

last: Guttman

first: Daryle

last: DePianto

first: Katrina

last: Morshead

first: Kai-Hui

last: Sun

first: Nandhini

last: Ramamoorthi

last: Vander Heiden

first: Zora

last: Modrusan

first: Paul

last: Wolters

first: Angelika

last: Jahreis

first: Joseph

last: Arron

first: Dinesh

last: Khanna

first: Thirumalai

last: Ramalingam


title: RNA-seq Data of Newly-Formed Adipocytes from Adipose Stem Cells of Normal-Weight Polycystic Ovary Syndrome Women vs. Controls

status: Public on Aug 12 2020

city: Los Angeles

first: Greogorio

last: Chazenbalk

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: University of California, Los Angeles

summary: Normal-weight polycystic ovary syndrome (PCOS) women exhibit adipose tissue dysfunction in vivo accompanied by enhanced subcutaneous (SC) abdominal adipose stem cell (ASC) development to adipocytes with greater lipid accumulation per cell in vitro. The goal of this study was to determine whether this phenomenon is associated with abnormal adipogenic gene transcription using RNA-sequencing to examine differential transcription patterns in PCOS vs controls. We found enhanced activation of adipogenic and adipocyte function genes and decreased expression of genes within the Wnt signaling pathway. In this study we conclude that this altered expression of genes in PCOS cells may underlie their exaggerated lipid accumulation in vitro and could predispose to adipose dysfunction in vivo when caloric intake exceeds energy utilization.

overall_design: ASCs were isolated from SC adipose tissue following SC abdominal biopsy in 3 PCOS women and 3 age and BMI matched controls for RNA-sequencing. Second generation of stem cells were cultured until cells reached confluency and expanded for two additional generations until fourth generation. Fourth generation ASCs were then cultured in adipogenic differentiation medium for 3-12 days and isolated for RNA extraction at days 3, 7, and 12. Extracted RNA were processed using Roche KAPA HyperPrep mRNA kit according to manufacturer's instructions and subjected to sequencing on a HiSeq4000 single-end 50 nt.

first: Karen

last: Leung

first: Marco

last: Morselli

first: Xiangming

last: Ding

first: Feiyang

last: Ma

first: Matteo

last: Pellegrini

first: Xinmin

last: Li

first: Gregorio


title: Differential RNA abundance between S. cerevisiae yeast BY4741 strains with YAK1_WT and YAK1_Q578*

status: Public on Aug 11 2020

first: Frank

middle: Wolfgang

last: Albert

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

summary: Identification of the gene differentially expressed with and without a non-sense mutation in YAK1 gene. This analysis provided a better understanding of the mechanism underlying variants affecting differently mRNA and protein abundance of genes in TRANS. Data used in the preprint: https://www.biorxiv.org/content/10.1101/2020.07.02.185413v1

overall_design: Differential analysis performed using five biological replicates of BY4741 with YAK1_WT and five biological replicates of BY4741 with YAK1_Q578*. Strains were harvested at three fourth of exponential  growth phase in SC media.

first: Christian

last: Brion

first: Sheila

last: Lutz

middle: W


title: RNA-sequencing of mice 24 hours following acute p53 activation due to Mdm2-loss (Mdm2FM/- Cag-CreERTg (FMTg)) compared to mice that retain Mdm2 (Mdm2+/- Cag-CreERTg (Tg))

first: Yuan

last: Qi

address: 1400 Pressler St

summary: FMTg (Mdm2FM/- Cag-CreERTg) and Tg (Mdm2+/- Cag-CreERTg) mice were administered 6mg/40g of Tamoxifen dissolved in corn-oil and sacrificed 24 hours after injection. Tissues were flash frozen and RNA was isolated using TriZOL reagent as per manufacturers protocols. The goal of this study is to understand the differences and similarities between the p53 transcriptome in various murine tissues

overall_design: 5 Biological replicates of FMTg (Mdm2FM/- Cag-CreERTg) Pancreas, Kidney, Heart, Ovary, and Small Intestine and 3 biological replicates of Tg (Mdm2+/- Cag-CreERTg) Pancreas, Kidney, Heart, Ovary, and Small Intestine were submitted for RNA-sequencing

first: Sydney

last: Moyer