title: Circulating miR-4763-3p is a novel potential biomarker candidate for human adult fulminant myocarditis

city: Wuhan

first: xiang

last: nie

address: 1095# Jiefang Ave.

institute: Tongji Hospital, Tongji Medical College

summary:
Circulating miRNA expression profiles were detected by microarray analysis.qPCR arrays were performed to validate the potential miRNAs.KEGG pathway analysis was used to determine the critical roles of these circulating miRNAs in FM. Correlation analysis was employed between miRNAs and the parameters of cardiac functions in FM. The sensitivity and specificity of circulating lncRNA expression in FM diagnosis were evaluated using receiver operating characteristic curve analysis.
Microarray and qPCR analysis showed that the expression of miR-4763-3p and miR-4281 were up-regulated in the plasma of FM at the onset, and their levels were restored as the clinical symptom recovered. The predicted target genes of miR-4763-3p and miR-4281 are involved in several pathways, mainly inflammatory and cardiac injury response. Moreover, the miRNAs enrichment was negatively correlated with the severity of FM. In addition, the expression levels of circulating miR-4763-3p was unchanged in MI and patients and miR-4281 showed high sensitivity and specificity for FM diagnosis.This study provides global profile of circulating miRNAs in patients with FM, among which miR-4763-3p and miR-4281 could serve as potential biomarkers.

overall_design: Firstly, miRNA expression profile was analyzed using blood serum from five FM patients at the onset (FM1-2, FM16-1, FM9-1, FM2-1, FM5-1) (rep2) and four healthy controls (Con4, Con5, Con7, Con8) (rep2). Then, another group of patients including three FM patients at the onset (FM3-1, FM10-1, FM19-1) (rep1) and three healthy controls (Con1, Con2, Con3) (rep1) was also recruited in this study to explore miRNAs expression profile. Furthermore, after a systematic and comprehensive treatment (such as mechanical life support, immunological modulation, antiviral reagents, etc.) based on the Chinese society of cardiology expert consensus statement on the diagnosis and treatment of adult fulminant myocarditis (PMID:30519877), blood serum from the above FM patients (FM1-14, FM5-6m, FM10-12, FM16-9, FM19-1m, FM2-13, FM9-15, FM3-13) were collecting and analyzing by miRNAs array. Annotation: FM1-14 mean the blood serum of patient FM1 was collecting at the 14th day after treatment, etc. Besides, the blood serum of myocardial infarction patients at the onset diagnosed by the coronary arteriography (coronary artery stenosis greater than 50%) (M2, M3, M4, M5, M6) (rep1) were also collecting for miRNAs array.

first: Xiang

last: Nie

first: Mengying

last: He


title: Bisulfite-seq: Analysis of CpG methylation at two CTCF binding sites flanking the CTG repeats of DMPK.

status: Public on Apr 07 2020

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: University of Lausanne

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

type: Methylation profiling by high throughput sequencing

summary: Bisulfite sequencing was performed on GM04604 (UN-B), GM06077 (DM1-A), and GM04648 (DM1-B) patient cells to determine the levels of CpG methylation present at two CTCF sites closely flanking the CTG repeats of DMPK.

overall_design: Analysis of the CpG methylation levels of two CTCF binding sites flanking the CTG repeats of DMPK in GM04604 (UN-B), GM06077 (DM1-A), and GM04648 (DM1-B) patient cells. Two amplicons were generated (upstream and downstream, relative to transcription of DMPK).

middle: A

first: Tuncay

last: Baubec

first: Vincent

last: Dion


title: Organoid-transplant model systems to study the effects of obesity on the pancreatic carcinogenesis in vivo

city: Milano

first: Pietro

last: Delfino

address: Via Olgettina 58

country: Italy

institute: San Raffaele Scientific Institute

type: Expression profiling by high throughput sequencing

summary:
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer-related mortality among adults in developed countries. The discovery of the most common genetic alterations as well as the development of organoids models’ of pancreatic cancer has provided insight into the fundamental pathways driving tumour progression from a normal cell, to non-invasive precursor lesion, to widely metastatic disease, offering new opportunities for identifying the key driver of cancer evolution. Obesity is one of the most serious public health challenges of the 21st century. Several epidemiological studies have shown the positive association between obesity and cancer-related morbidity/mortality, as well as poor prognosis and poorer treatment outcome. Despite strong evidence indicates a link between obesity and cancer incidence, the molecular basis of the initiating events remains largely elusive. This is mainly due to the lack of an accurate and reliable model of pancreatic carcinogenesis that mimics human obesity-associated PDAC, making data interpretation difficult and often confusing.
Here we propose a suitable and manageable preclinical tool, organoids-based, to study the effects of obesity on pancreatic carcinogenesis. Therefore, we tracked the effects of obesity on the natural evolution of PDAC in a genetically defined transplantable model of the syngeneic murine pancreatic preneoplastic lesion (mP) and tumour (mT) derived-organoids that recapitulates the progression of human disease from early preinvasive lesions to metastatic disease.
Our results suggest that organoid-derived transplants in obese mice represent a suitable system to study early steps of pancreatic carcinogenesis and support the hypothesis that inflammation induced by obesity stimulates tumour progression and metastatization during pancreatic carcinogenesis.

overall_design: Male C57BL/6 WT and leptin-deficient mice (C57BL/6J; ob/ob) were obtained from Charles River. Mice were at the age of 4 weeks divided in three groups fed with different chow (Brogaarden, Lynge, Denmark). A group receiving standard rodent chow, a group receiving a High-Fat Diet (HFD) with 60% of calories from fat, and a group receiving Low-Fat Diet (LFD) for 10 weeks (n = 20). All mice were housed and treated in accordance with the guidelines of the University of Verona Animal Ethic Committee.

first: Francesca

last: Lupo

first: Geny

last: Piro

first: Lorena

last: Torroni

first: Rosalinda

last: Trovato

first: Boris

last: Rusev

first: Alessandra

last: Fiore

first: Dea

last: Filippini

first: Francesco

last: De Sanctis

first: Marcello

last: Manfredi

first: Emilio

last: Marengo

first: Rita

last: Lawlor

first: Maurizio

last: Martini

first: Giampaolo

last: Tortora

first: Stefano

last: Ugel

first: Vincenzo

last: Corbo

first: Davide

last: Melisi

first: Carmine

last: Carbone


title: 4C-seq: Three-dimensional chromatin interactions of FMR1, HTT, DMPK, and GFP viewpoints.

first: Gustavo

last: Ruiz Buendía

summary: Expanded CAG/CTG repeats underlie thirteen neurological disorders, including myotonic dystrophy type 1 (DM1) and Huntington’s disease (HD). Upon expansion, CAG/CTG repeat loci acquire heterochromatic characteristics. This observation raises the hypothesis that repeat expansion provokes changes to higher-order chromatin conformation and thereby affects both gene expression in cis and the genetic instability of the repeat tract. Here we tested this hypothesis directly by performing 4C sequencing at the DMPK and HTT loci from DM1 and HD patient-derived cells. Surprisingly, chromatin contacts remain unchanged upon repeat expansion at both loci. This was true for expanded alleles with different DNA methylation levels and CTCF binding. Repeat tract sizes ranging from 15 to 1,700 repeats displayed strikingly similar chromatin interaction profiles. Moreover, the ectopic insertion of an expanded CAG repeat tract did not change the three-dimensional chromatin conformation of the surrounding genomic region. Our findings argue that extensive changes in heterochromatic properties are not enough to alter chromatin conformation at expanded CAG/CTG repeat loci. We conclude that 3D chromatin conformation is unlikely to drive repeat expansions or changes in gene expression in expanded CAG/CTG repeat disorders.

overall_design: 4C-seq analysis of 3D chromatin interactions of FMR1, HTT, DMPK, and GFP 4C viewpoints. The cell lines used are unaffected: GM09236 (UN-A), GM04604 (UN-B), and GM02180 (UN-C); FXS: GM09237 (FXS); HD: GM02164 (HD-A), GM03620 (HD-B), GM14044 (HD-C); DM1: GM06077 (DM1-A) and GM04648 (DM1-B). Two additional HEK293-derived clonal cell populations were used for the GFP viewpoint: GFP(CAG)15 and GFP(CAG)270. Each 4C library was done in triplicate (except for the DMPK_u65 and DMPK_d73 viewpoints).

first: Marion

last: Leleu

first: Vincent

last: Dion


title: Molecular mechanisms for Krüppel-like factor 13 actions in hippocampal neurons [RNA-seq]

status: Public on Apr 09 2020

city: Ann Arbor

first: Robert

middle: J

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

country: USA

institute: University of Michigan

summary: Changes in gene expression in HT22 cells after forced expression of KLF13 for 8 hr were analyzed by RNA sequencing

overall_design: The mouse hippocampus-derived neuronal cell line HT22 was engineered to control Klf13 expression by addition of doxycycline. Cells were treated with or without doxycycline for 8 hr before harvesting RNA for RNA sequencing.

first: José

last: Ávila-Mendoza

first: Arasakumar

last: Subramani

first: Christopher

last: Sifuentes


title: Identification of gene expression changes in MEF cell lines with a targeted MDMX mutation that disrupts binding to CK1-alpha kinase

city: Tampa

first: Jiandong

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Molecular Oncology Department

institute: Moffitt Cancer Center

summary: The goal of this experiment is to identify genes differentially expressed in MEF cell lines with a targeted MDMX mutation that prevents binding and inhibition of CK1-alpha kinase.

overall_design: MDMX-SG (MDMX with W201S/W202G substitutions) knock-in mutant mouse was crossed into p53-null background to generate p53-/-;MDMXSG/SG homozygous MEFs (SG) and p53-/-;MDMXWT/WT control MEFs (WT). Three cell lines of each genotype (SG1/SG2/SG3 versus WT3/WT9/WT11), each cell line generated from one embryo, were compared to identify genes affected by the MDMX-SG mutation.

first: Qingling

last: Huang


title: ChIP-seq: Analysis of CTCF occupancy in unaffected and DM1 patient lymphoblastoid cell lines.

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed CTCF ChIP-seq to determine the extent of CTCF occupancy alterations in two DM1 patient lymphoblastoid cell lines (LCLs) compared to an unaffected control LCL. Our results show that there were no large-scale changes in CTCF occupancy in the DM1 patient cells either genome-wide or in a 2 Mb region centered around the expanded repeats of DMPK.

overall_design: We performed CTCF ChIP-seq using a CTCF antibody (Diagenode) in the unaffected LCL GM04604 (UN-B) and two DM1 patient-derived LCLs GM06077 (DM1-A) and GM04648 (DM1-B). Each CTCF ChIP-seq library was prepared in triplicate.

first: Ludovica

last: Vanzan

first: Victor

last: Ythier

first: Rabih

last: Murr


title: Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei [ddSeq]

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300E Biological Sciences 3

institute: UC Irvine

summary: FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is thought to be the pathogenic cause of FSHD, DUX4 is lowly expressed in patient samples, and analysis of the consequences of DUX4 expression has largely relied on artificial overexpression. To better understand the native expression profile of DUX4 and its targets, we first performed pooled RNA-seq on a 6-day differentiation time-course in FSHD2 patient-derived primary myoblasts. We identify a set of 54 FSHD-induced genes upregulated in FSHD2 cells starting at day 2 of differentiation through the end of the time-course. Using single-cell and single-nucleus RNA-seq on FSHD2 myoblasts and day 3 and day 5 differentiated myotubes respectively, we captured, for the first time, DUX4 expressed at the single-nucleus level in a native state. We identified two populations of FSHD myotube nuclei based on low or high enrichment of DUX4 and FSHD-induced genes (FSHD-Lo and “FSHD Hi”, respectively). FSHD-Hi nuclei upregulate many cell cycle related genes with significant enrichment of E2F target genes and p53 signaling activation. In FSHD-Hi myotube nuclei, multiple DUX4 target genes are co-expressed including a set of transcription factors, such as DUXA, ZSCAN4 and LEUTX.  DUXA (the DUX4 paralog) is more widely expressed than DUX4, and depletion of DUXA suppressed the expression of LEUTX and ZSCAN4 in late, but not early, differentiation. The results indicate that the DUXA can take over the role of DUX4 and maintain target gene expression.  These results may provide explanation as to why it is easier to detect and monitor DUX4 target genes than DUX4 itself in patient cells and suggest a self-sustaining network of gene dysregulation that perpetuates this disease after DUX4 is no longer expressed.

overall_design: 3' end single-nucleus RNA-seq on 3 and 5 day differentiated primary myoblasts from FSHD2 patient and control biopsies

first: Katherine

middle: E

last: Williams

first: S


title: Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [ATAC-seq]

city: Kyoto

first: Yotaro

last: Ochi

address: Yoshida-Konoe-cho

department: Department of Pathology and Tumor Biology

country: Japan

institute: Kyoto Univiersity

summary: STAG2 encodes a cohesin component and is frequently mutated in myeloid neoplasms, showing highly significant co-mutation patterns with other drivers, including RUNX1.  However, the molecular basis of cohesin-mutated leukemogenesis remains poorly understood.  Here we show a critical role of an interplay between Stag2 and Runx1 in the regulation of enhancer-promoter looping and transcription in hematopoiesis.  Combined loss of Stag2 and Runx1, which co-localize at enhancer-rich, Ctcf-deficient sites, synergistically attenuates enhancer-promoter loops, particularly at sites enriched for RNA polymerase II and Mediator, and deregulates gene expression, leading to myeloid-skewed expansion of hematopoietic stem/progenitor cells (HSPCs) and myelodysplastic syndromes (MDS). Attenuated enhancer-promoter loops in Stag2/Runx1-deficient cells are associated with downregulation of genes with high basal transcriptional pausing, which are important for the regulation of HSPCs.　Down-regulation of high-pausing genes is also confirmed in STAG2/cohesin-mutated primary AML/MDS samples.  Our results highlight a unique STAG2/RUNX1 interplay in gene regulation and provide insights into cohesin-mutated leukemogenesis.

overall_design: Comprehensive epigenome sequencing (RNA-seq, ATAC-seq, ChIP-seq and Hi-C) in WT, Stag2 knockout, Runx1 knockout, and double knockout cells.

first: Seishi

last: Ogawa


title: Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei

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

overall_design: Refer to individual Series


title: Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [RNA-seq]

summary: STAG2 encodes a cohesin component and is frequently mutated in myeloid neoplasms, showing highly significant co-mutation patterns with other drivers, including RUNX1. However, the molecular basis of cohesin-mutated leukemogenesis remains poorly understood. Here we show a critical role of an interplay between Stag2 and Runx1 in the regulation of enhancer-promoter looping and transcription in hematopoiesis. Combined loss of Stag2 and Runx1, which co-localize at enhancer-rich, Ctcf-deficient sites, synergistically attenuates enhancer-promoter loops, particularly at sites enriched for RNA polymerase II and Mediator, and deregulates gene expression, leading to myeloid-skewed expansion of hematopoietic stem/progenitor cells (HSPCs) and myelodysplastic syndromes (MDS). Attenuated enhancer-promoter loops in Stag2/Runx1-deficient cells are associated with downregulation of genes with high basal transcriptional pausing, which are important for the regulation of HSPCs.　Down-regulation of high-pausing genes is also confirmed in STAG2/cohesin-mutated primary AML/MDS samples. Our results highlight a unique STAG2/RUNX1 interplay in gene regulation and provide insights into cohesin-mutated leukemogenesis.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: SMAD1 promoter hypermethylation and lack of SMAD1 expression in Hodgkin Lymphoma

status: Public on Apr 06 2020

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary: Global gene expression analysis was performed of several cell lines, mostly classical Hodgkin lymphoma, one DLBCL cell line and one NLPHL cell line.

overall_design: Cells were cultured according to standard conditions, harvested, underwent RNA extraction and gene expression profiling was performed using the Affymetrix Gene Array

first: Alexandar

last: Tzankov

first: Sylvia

last: Hartmann


title: RNA-seq: Analysis of differential gene expression between HD and DM1 patient lymphoblastoid cell lines (LCLs) compared to unaffected LCLs.

first: Gustavo

last: Ruiz Buendía

summary: Transcriptome from HD, DM1, and unaffected LCLs.

overall_design: Data from two unaffected LCLs: GM04604 (UN-B) and GM02180 (UN-C). From three HD patient LCLs: GM02164 (HD-A), GM03620 (HD-B), and GM14044 (HD-C). And from two DM1 patient LCLs: GM06077 (DM1-A) and GM04648 (DM1-B). Two replicates per sample were sequenced and the unaffected LCLs were used as the control condition.

first: Jennifer

middle: Y

last: Tan

first: Vincent

last: Dion


title: Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [Hi-C]


title: Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei [Time course]

overall_design: Time-course of primary FSHD2 myoblasts from tibialis anterior, control myoblasts from tibialis anterior, and control myoblasts from quadricep


title: Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei [Fluidigm]

overall_design: Full length single-cell and single-nucleus RNA-seq using SmartSeq on the Fluidigm C1 platform for control and FSHD2 myoblast cells and myotube nuclei.


title: Inhibition of Apoptosis Reduces Diploidization of Haploid Mouse Embryonic Stem Cells during the Differentiation

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

country: China

institute: Nankai University

summary: Phenotypes of haploid embryonic stem cells (haESCs) are dominant for recessive traits in mice. However, one major obstacle to their use is self-diploidization in daily culture. Although haESCs maintain haploidy well by deleting p53, whether they can sustain haploidy in differentiated status and the mechanism behind remain unknown. To address that, we induced p53-deficient haESCs into multiple differentiated lineages keeping a haploid status in vitro. Besides, haploid cells also remained in chimeric embryos and teratomas arising from p53-null haESCs. Transcriptome analysis revealed that apoptosis genes were down-regulated in p53-null haESCs, comparing to that in wild-type haESCs. Finally, we knocked-out p73, another apoptosis gene, and observed stabilization of haploidy in haESCs, either. These results indicated that the main mechanism of diploidization was apoptosis-related genes triggered cell death in haploid cell cultures. Thus, we can derive haploid somatic cells by manipulating apoptosis gene, facilitating genetic screens of lineage-specific development.

overall_design: Comparation of the transcriptomes between p53-KO haESCs and WT-haESCs by RNA-seq analysis, in triplicate

first: Yanni

last: Li

first: Wenhao

last: Zhang


title: VEGF-B Signaling Impairs Endothelial Glucose Transcytosis via an LDLR-dependent Decrease in Membrane Cholesterol Loading [HBMEC]

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

summary: Regulation of endothelial nutrient transport is poorly understood. Vascular endothelial growth factor (VEGF)-B signaling in endothelial cells promotes uptake and transcytosis of fatty acids (FA) from the bloodstream to the underlying tissue, advancing pathological lipid accumulation and lipotoxicity in diabetic complications. Here we demonstrate a VEGF-B dependent obstruction of endothelial glucose transport attributed to plasma membrane lipid alterations affecting glucose transporter 1 function, which was independent of FA uptake. Specifically, VEGF-B signaling impaired recycling of low-density lipoprotein receptor to the plasma membrane, leading to reduced cholesterol uptake and membrane cholesterol loading, decreasing endothelial glucose uptake capacity. Inhibiting VEGF-B in vivo was accordingly linked to reconstitution of membrane cholesterol and induction of glucose uptake, of particular relevance for conditions inferring insulin resistance and diabetic complications. In summary, our study reveals a novel mechanism of action for VEGF-B in endothelial nutrient uptake and highlights the impact of membrane cholesterol for the regulation of endothelial glucose transport.

overall_design: 15 samples; n = 3 per treatment group, 5 treatments

first: Christine

last: Moessinger

first: Ingrid

last: Nilsson

first: Manuel

last: Zeitelhofer

first: Benjamin

last: Heller Sahlgren

first: Josefin

last: Skogsberg

first: Ulf

last: Eriksson


title: Transcriptome profiles of P. aeruginosa treated with manuka honey and its key components

city: Ultimo

first: Liz

last: Harry

state: NSW

address: 15 Broadway

country: Australia

institute: ithree institute

summary: The aim of this study was to characterise the transcriptomic changes in P. aeruginosa PA14 following treatment with antimicrobial manuka honey and its key components (sugar, methyglyoxal, sugar + methylglyoxal) for 30 minutes at a subinhibitory concentration (0.5x MIC). mRNA profiling was conducted to gain mechanistic insights into the mode of action of antimicrobial manuka honey.

overall_design: mRNA profiles of mid-exponentially growing P. aeruginosa treated with manuka honey and its key components (sugar, methyglyoxal, sugar + methylglyoxal) at subinhibitory concentrations for 30 minutes were measured by RNA-sequencing, in triplicate, on an Illumina HiSeq4000 sequencer

first: Daniel

last: Bouzo

first: Nural

last: Cokcetin

first: Liping

first: Giulia

last: Ballerin

first: Amy

last: Bottomley

first: James

last: Lazenby

first: Cynthia

last: Whitchurch

first: Ian

last: Paulsen

first: Karl

last: Hassan


title: Mouse models of neutropenia reveal progenitor-stage-specific defects [scATAC-Seq]

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

summary: Advances in genetics and sequencing have lead to a deluge of disease-associated and disease-causing genetic alterations. Resolving causality between genetics and disease requires generating accurate models for molecular dissection; however, the rapid expansion of single-cell landscapes presents a major challenge to accurate comparisons between mutants and their wild type equivalents. Here, we generated mouse models of human severe congenital neutropenia (SCN) using patient-derived mutations in the Growth factor independent-1 (GFI1) transcription factor. To delineate the impact of SCN mutations, we first generated single-cell references for granulopoietic genomic states with linked epitopes, then developed a new computational approach to align mutant cells to their wild-type equivalent and derive differentially expressed genes. Surprisingly, the majority of differentially expressed GFI1-target genes are sequentially altered as cells traverse successive states. These cell-state-specific insights facilitated genetic rescue of granulocytic specification but not post-commitment defects in the expression of innate-immune effectors, providing regulatory insights into granulocyte dysfunction.

overall_design: Single cell ATAC-seq of Gfi1 wild-type and SCN R412X mutant model from combined modified GMP and Ly6g gates

first: David

last: Muench

first: Andre

last: Olsson

first: Kashish

last: Chetal

first: Nathan

last: Salomonis

first: H

middle: L


title: Combined Cohesin-Runx1 Deficiency Synergistically Perturbs Chromatin Looping and Causes Myelodysplastic Syndromes [ChIP-seq]

first: Yotaro

last: Ochi

first: Seishi

last: Ogawa


title: VEGF-B Signaling Impairs Endothelial Glucose Transcytosis via an LDLR-dependent Decrease in Membrane Cholesterol Loading

first: Lars

last: Muhl


title: VEGF-B Signaling Impairs Endothelial Glucose Transcytosis via an LDLR-dependent Decrease in Membrane Cholesterol Loading [mouse heart]

overall_design: 8 samples were analyzed, n = 4 per genotype

first: Christine

last: Moessinger

first: Ingrid

last: Nilsson

first: Manuel

last: Zeitelhofer

first: Benjamin

last: Heller Sahlgren

first: Josefin

last: Skogsberg

first: Ulf

last: Eriksson


title: TGF-beta couples pluripotency and epithelial character via ZNF398

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: Human pluripotent stem cells (hPSCs) have the capacity to give rise to all differentiated cells of the adult. TGF-beta is used routinely for expansion of conventional hPSCs as flat epithelial colonies expressing the transcription factors POU5F1/OCT4, NANOG, SOX2. Here we report a global analysis of the transcriptional program controlled by TGF-beta followed by an unbiased gain-of-function screening in multiple hPSC lines to identify factors mediating TGF-beta activity. We identify a quartet of transcriptional regulators promoting hPSC self-renewal including ZNF398, a human-specific mediator of pluripotency and epithelial character in hPSCs. Mechanistically, ZNF398 binds active promoters and enhancers together with SMAD3 and the histone acetyltransferase EP300, enabling transcription of TGF-beta targets. In the context of somatic cell reprogramming, inhibition of ZNF398 abolishes activation of pluripotency and epithelial genes and iPSC colony formation. Our findings have clear implications for the generation of bona fide hPSCs for regenerative medicine.

overall_design: Stable transgenic hPSCs expressing candidates and SB43 treatment

first: Irene

last: Zorzan

first: Marco

last: Pellegrini

first: Mattia

last: Arboit

first: Mara

last: Maldotti

last: Forcato

first: Guidantonio

middle: M

last: Tagliazucchi

first: Elena

last: Carbognin

last: Montagner

first: Salvatore

last: Oliviero

first: Graziano

last: Martello


title: Mouse models of neutropenia reveal progenitor-stage-specific defects [Fluidigm]

first: H. Leighton

last: Grimes

overall_design: Single cell RNA seq (Fluidigm) of Neutrophils from healthy donors and SCN patients

first: David

last: Muench

first: Andre

last: Olsson

first: Kashish

last: Chetal

first: Nathan

last: Salomonis

first: H


title: Mouse models of neutropenia reveal progenitor-stage-specific defects [ChIP-Seq]

overall_design: ChIP-Seq of Gfi1 protein in Gfi1 R412X-R412X GMP cells


title: Discovery of a selective inhibitor of Doublecortin Like Kinase 1

city: Boston

first: Behnam

last: Nabet

state: MA

address: 360 Longwood Ave, LC-2100

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Doublecortin like kinase 1 (DCLK1) is an understudied kinase that is upregulated in a wide range of cancers, including pancreatic ductal adenocarcinoma (PDAC). However, little is known about its potential as a therapeutic target. We leveraged chemoproteomic profiling and structure-based design to develop the first selective, in vivo-compatible chemical probe of the DCLK1 kinase domain, DCLK1-IN-1. We demonstrate activity of DCLK1-IN-1 against clinically relevant patient-derived PDAC organoid models and use a combination of RNA sequencing, proteomics and phosphoproteomics analysis to reveal that DCLK1 inhibition modulates proteins and pathways associated with cell motility in this context. DCLK1-IN-1 will serve as a versatile tool to investigate DCLK1 biology and establish its role in cancer.

overall_design: We performed an ERCC spike-in normalized RNA-sequencing experiment to quantify transcriptional changes upon DMSO or DCLK1-IN-1 treatment of PDAC cell lines. We profiled PATU-8988T and PATU-8902 cells treated with DMSO or DCLK1-IN-1 for 6 or 24 h. All samples were prepared in biological triplicate.


title: Mouse models of neutropenia reveal progenitor-stage-specific defects [CITE-Seq]

overall_design: Single cell RNA seq of Gfi1 wild-type, SCN mutant and genetic rescue models from modified GMP and Ly6g gates


title: small RNA sequences from grafted Arabidopsis thaliana expressing SucSUL inverted repeat

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

institute: ETH

type: Non-coding RNA profiling by high throughput sequencing

summary: We aimed at characterizing the identity of the silencing signal i.e. siRNA or longer dsRNA precursor thereof. We used transgenic dsRNA, endogenous dsRNA or virus infection as sources of siRNAs combined to sophisticated immunoprecipitation-based procedures coupled to deep-sequencing. We found that siRNAs populations are highly similar between incipient and recipient cells in the three systems. Additionally, a significant depletion of 5’U and 5’A content in the recipient cells suggested Argonaute-loading dependent depletion of these siRNAs during their movement over multiple cell layers. Using the PAZ-domain mutants ago1-18 and ago1-42 confirmed that the observed depletion of mobile siRNAs is the result of RISC loading. The results advocate movement of individual siRNA duplexes as opposed to their precursors and that loading into Argonaut proteins renders those small RNAs cell-autonomous.

overall_design: 4 samples examined: shoot and root from Arabidopsis thaliana where plant expressing SucSUL transgene were grafted to Col0 WT plants (in both directions)

first: Emanuel

last: Devers

first: Christopher

last: Brosnan

first: Daniele

last: Albertini

first: Andrea

middle: C

last: Amsler

first: Florian

last: Brioudes

first: Pauline

last: Jullien

first: Peiqi

last: Lim

first: Gregory

last: Schott

first: Olivier

last: Voinnet


title: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [Gfi1-R412X-HMZ]

first: H. Leighton

overall_design: Single cell RNA seq of Gfi1-R412X mutant GMP subpopulations


title: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [WT-GMP-P]

overall_design: Single cell RNA seq of wild-type GMP-P subpopulations

first: David


title: Detection of siRNA movement in Arabidopsis thaliana using P19 under root cell layer specific expression

summary: We aimed at characterizing the identity of the silencing signal i.e. siRNA or longer dsRNA precursor thereof. We used transgenic dsRNA, endogenous dsRNA or virus infection as sources of siRNAs combined to sophisticated immunoprecipitation-based procedures coupled to deep-sequencing. We found that although they are diluted as they move away from their sites of production, siRNAs population are highly similar between incipient and recipient cells in the three systems. Additionally, a significant depletion of 5’U and 5’A content in the recipient cells suggested Argonaute-loading dependent depletion of these siRNAs during their movement over multiple cell layers. Using the PAZ-domain mutants ago1-18 and ago1-42 confirmed that the observed depletion of mobile siRNAs is the result of RISC loading. The results advocate movement of individual siRNA duplexes as opposed to their precursors and that loading into Argonaut proteins renders those small RNAs cell-autonomous.

overall_design: 8 sample examined: small RNA from input and Immunoprecipitation of Flag-HA-P19 protein expressed under stele (pSHR) or epidermis (pWER) promoter in Arabidopsis thaliana Col0 plants expressing SucSUL inverted repeat under SUC2 promoter (samples 1-4) or infected by TuYV (samples 5-8)


title: RNA-seq of CD4+T cells derived from spleens of SIVcpz and HIV-1 infected humanized BLT-mice

city: Lincoln

first: Qingsheng

last: Li

state: NE

address: 4240 Fair Street

institute: University of Nebraska Lincoln

summary: There are many DEGs between SIVcpz and HIV-1 infected humanized BLT-mice.

overall_design: To compare the transcriptome profile of human CD4+T cells between SIVcpz and HIV-1 infected humanized BLT-mice.

first: Zhe

last: Yuan

first: Lance

last: Daharsh


title: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment

last: Grimes

overall_design: Refer to individual Series


title: Mu opioid receptor (Oprm1) knockdown in the medial preoptic area (MPOA) on patterns of gene expression in the MPOA of adolescent male rats

status: Public on Apr 03 2020

city: MADISON

first: Changjiu

last: Zhao

state: WI

address: 430 Lincoln Drive

department: Integrative Biology

institute: University of Wisconsin-Madison

summary: We investigate effects of Oprm1 downregulation in the MPOA on gene expression profiles in adolescent male rats using RNA-Seq. We conducted differential gene expression analysis of RNA-Seq data using the EdgeR Bioconductor Package. We evaluated differential gene expression between Oprm1 knockdown and control groups and found 349 genes were differentially expressed, with some genes being involved in neuronal signaling exhibited altered expression due to Oprm1 knockdown.

overall_design: Examination of patterns of gene expression after Oprm1 knockdown in adolescent male rats

first: Liza

last: Chang

first: Anthony

middle: P

last: Auger

first: Stephen

last: Gammie

first: Lauren

middle: V

last: Riters


title: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [CITE-seq-GMP-WT]

overall_design: Single cell RNA seq of wild-type Modified GMP

last: Muench

first: Kashish

last: Chetal

first: Nathan

last: Salomonis

first: H


title: Evaluation of global gene expression in regenerate tissues during Masquelet treatment

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

summary: We present RNAseq data obtained from tissues harvested directly from rat segmental osteotomies managed using the Masquelet induced membrane technique or left empty.

overall_design: Rats received bilateral osteotomies that were stabilized with a plate. One osteotomy was left empty (control). A PMMA cement spacer was inserted into the defect of the contralateral limb as per the Masquelet induced membrane protocol. After 4 weeks of healing, two different comparable tissue types were harvested from each of the two osteotomy environments.

first: Andrea

last: Alford

first: Mark

last: Hake

first: Rebecca

last: Tagett


title: Vascular contribution to 16p11.2 deletion autism syndrome modeled in mice

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

summary: While the neuronal underpinnings of autism spectrum disorders (ASD) are being unraveled, vascular contributions to ASD remain elusive.  Here, we investigated postnatal cerebrovascular development in the 16p11.2df/+ mouse model of 16p11.2 deletion ASD syndrome.  We discovered that 16p11.2 hemizygosity leads to male-specific, endothelium-dependent structural and functional neurovascular abnormalities.  In 16p11.2df/+ mice, endothelial dysfunction resulted in impaired cerebral angiogenesis at postnatal day (P) 14, and in altered neurovascular coupling and cerebrovascular reactivity at P50.   Moreover, we showed defective angiogenesis in primary 16p11.2df/+ mouse brain endothelial cells and in iPSC-derived endothelial cells from human 16p11.2 deletion carriers.  Finally, we found that mice with endothelium-specific 16p11.2 deletion (16p11.2DEC) partially recapitulated some behavioral changes seen in 16p11.2 syndrome, specifically hyperactivity and impaired motor learning.  By showing that developmental 16p11.2 haploinsufficiency from endothelial cells results in neurovascular and behavioral changes in adults, our results point to a potential role for endothelial impairment in ASD.

overall_design: 16 RNA samples (i.e. 16 biological replicates) from 32 mice were produced in total for RNA deep sequencing.

first: Julie

last: Ouellette

first: Qing

first: Sonia

last: Leclerc

first: Youlian

last: Pan

first: Baptiste

last: Lacoste


title: Knockdown of transcription factor Creb3l1 in anterior pituitary mouse corticotroph cell line AtT20

city: Bristol

first: Michael

middle: Paul

last: Greenwood

address: Whitson Street

department: Bristol Medical School / Translational Health Sciences

country: United Kingdom

institute: University of Bristol

summary: Transcription factor Creb3l1 is a non-classical ER stress molecule that is emerging as an important component for cellular homeostasis, particularly within cell-types with high peptide secretory capabilities. We have previously shown that Creb3l1 serves an important role in body fluid homeostasis through its transcriptional control of the gene coding for antidiuretic hormone arginine vasopressin in the neuropeptide rich magnocellular neurons of the supraoptic nucleus. To identify other genes regulated by transcription factor Creb3l1 in secretory cells, we performed RNA-sequencing of Creb3l1 knockdown anterior pituitary mouse corticotroph cell line AtT20.

overall_design: Total RNA was extracted from AtT20/D16v-F2 cells stably transduced with lentivirus expressing Creb3l1 shRNA (GAGTCGGATTTCCTCAACAAT) or non-targeting control shRNA (ATCATGTTAGGCGTACGGACT).  RNA samples (n=5 each group) were sent for RNA sequencing.

first: Mingkwan

first: Alex

last: Paterson

first: Parveen

last: Rahman

first: Benjamin

middle: T

last: Gillard

first: Sydney

last: Langley

first: Yasumasa

last: Iwasaki

first: David

last: Murphy


title: PROM1(CD133)-dependent expressed genes from mouse embryonic DRG neurons

status: Public on Apr 02 2020

city: Dalseonggun, Daegu

first: Yongcheol

last: Cho

state: Daegu

address: 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun

department: Department of Brain Sciences

country: South Korea

institute: DGIST

summary: Prom1, also knwon as CD133 is a stem cell marker that are down-regulated during developmental process. Here we first reports that PROM1 is a regulator of expression of specific sets of genes from DRG neurons.

overall_design: E13.5 Embryonic DRG neurons culture, Control vs human PROM1 overexpression, Total RNA. All conditions are from biologically duplicated samples. (Control 2 vs hPROM1 Overexpression 2)

first: Jinyoung

last: Lee

first: Jung Eun

last: Shin

first: Bohm

first: Hyemin

last: Kim

first: Yewon

last: Jeon

first: Seung Hyun

last: Ahn

first: Sung Wook

last: Chi


title: Tissue-resident memory T cell reactivation by diverse antigen-presenting cells imparts distinct functional responses [I]

city: La Jolla

first: Susan

last: Kaech

address: 10010 N Torrey Pines Rd

institute: Salk Institute

summary: Global profiling to investigate the consequence of the lack of TAP-1 on hematopoetic cell or non-hematopoetic cell on the qualitative response of reactivated antigen-specific Trm cells

overall_design: Three groups of bone marrow chimeras were generated by reconstituting irradiated WT recipients with WT or TAP1KO bone marrow, or irradiated TAP1KO recipients with WT bone marrow. 8 weeks after reconstitution, TCR-transgenic P14 and OT-I T cells were adoptively transferred to generate immune bone marrow chimeras. At 48hours post infection, TCR-transgenic P14 Trm cells were sorted based on their Nur77-GFP reporter expression, in triplicate.

first: Jun

middle: S

last: Low


title: Maintenance of neural stem cell positional identity by Mixed-lineage leukemia 1

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

summary: Neural stem cells (NSCs) in the developing and postnatal brain have distinct positional identities that dictate the types of neurons they generate. While morphogens initially establish NSC positional identity in the neural tube, it is unclear how such regional differences are maintained as the forebrain grows much larger and anatomically more complex.  We found that the maintenance of NSC positional identity requires a Mixed-lineage leukemia 1 (Mll1)-dependent epigenetic memory system.  After establishment by sonic hedgehog (SHH), ventral NSC identity became independent of this morphogen.  Even transient MLL1 inhibition caused a durable loss of ventral identity, resulting in the generation of neurons with the characteristics of dorsal NSCs in vivo.  Thus, spatial information provided by morphogens can be transitioned to epigenetic mechanisms that maintain regionally distinct developmental programs in the forebrain.

overall_design: Differential expression of cultured V-SVZ NSCs, including Dorsal vs. Ventral NSCs, UBC-CreER;SmoF/F vs control, UBC-CreER;Mll1F/F vs control, MM-401-treated vs control, and MM-401-washed out vs control, in duplicate. Genome-wide chromatin analysis by CnR for H3K27ac, H3K4me1, HeK4me3, and H3K27me3 marks on MM-401-treated, control-treated, MM-401-washout, and control-washout ventral NSCs, in duplicate

first: Ryan

middle: N

last: Delgado


title: Transcriptomic analysis of blastocyst according to peripubertal age of bull (12 vs 16 months)

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: The transcriptome pattern in blastocyst produced by bulls at different age was investigated. Embryos were in vitro fertilized from 4 different bulls at 12 and 16 month each with matched adult cows. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 bulls, all collected at 12 and 16 months old

first: Chongyang

last: Wu

first: Patrick

last: Blondin

first: Christian

last: Vigneault

first: Rémi

last: Labrecque


title: Sex-specific role for the long non-coding RNA linc00473 in depression

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Depression is a common disorder that affects women at twice the rate of men. Here we report that long non-coding RNAs (lncRNAs), a recently discovered class of regulatory transcripts, represent about one-third of the differentially expressed genes in the brains of depressed humans, and display complex region- and sex-specific patterns of regulation. We identified the primate-specific, neuronal-enriched gene, linc00473, as downregulated in prefrontal cortex of depressed females but not males. Using viral-mediated gene transfer to express linc00473 in mouse prefrontal cortex neurons, we mirrored the human sex-specific phenotype by inducing stress resilience solely in female mice. This sex-specific phenotype was accompanied by changes in synaptic function and gene expression selectively in female mice and, along with studies of human neuron-like cells in culture, implicates linc00473 as a CREB effector. Together, our studies identify linc00473 as a female-specific driver of stress resilience that is aberrant in female depression.

overall_design:
RNA profiled in mPFC of female mice expressing linc00473 or GFP only in mPFC, either at baseline or after CVS (chronic variable stress).
RNA-seq of NPCs derived from male or female healthy human subjects after knockdown of linc00473;
Chromatin isolation by RNA purification (ChIRP) followed by DNA-sequencing (DNA-seq) to identify direct partners for linc00473 in human cells;

first: Orna

last: Issler

first: Li

last: Shen

first: Eric

last: Nestler


title: The age of the bull influences the transcriptome and epigenome of the blastocysts

type:
Expression profiling by array
Methylation profiling by array

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


title: DNA methylation analysis of blastocyst according to peripubertal age of bull (10 vs 16 months)

summary: The DNA methylation pattern in blastocyst produced by bulls at different age was investigated. Embryos were in vitro fertilized from 4 different bulls at 10 and 16 month each with matched adult cows. Genome-wide DNA methylation analysis was performed by micro array using EDMA platform.

overall_design: Two condition experiment,  4 bulls, all collected at 10 and 16 months old


title: Single cell sequencing data of CD34+ AML stem/progenitor cells derived from AML patients before and after cusatuzumab treatment

city: Bern

first: Carsten

last: Riether

address: Murtenstrasse 35

department: Department for BioMedical Research

institute: University of Bern

summary: Purpose: The goal of this study was compare the transcriptional profile of CD34+ AML stem/progenitors derived from newly diagnosed AML patients at diagnosis and after treatment with the anti-CD70 antibody cusatuzumab as a monotherapy on a single cell level. Methods: Barcoded cDNA from at least 977 CD34+ cells from patients C8 and C10 was prepared using the Chromium Single Cell 3′ Library (v2 Chemistry) & Gel Bead Kit on a Chromium Controller according to the manufacturer’s recommendations (10XGenomics). The barcoded cDNA was further processed into scRNA-seq libraries and sequenced on a NovaSeq 6000 instrument using NovaSeq Control Software v1.6 (Illumina). Libraries were sequenced with 100 cycle S1 flow cell kits using the following paired-end configuration: 26 bp Read 1, 91 bp Read 2. Results/Conclusion: Cusatuzumab monotherapy triggers gene signatures related to myeloid differentiation and apoptosis in CD34+ AML stem/progenitor cells

overall_design: Single cell sequencing profile of CD34+ stem/progenitor cells from two newly diagnosed AML patients (C8 and C10) at diagnosis (day -14) and after cusatuzumab monotherapy (C1D1)

first: Adrian

middle: F

last: Ochsenbein


title: The genomic landscape of metastasis in treatment-naïve breast cancer models

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

type: Genome variation profiling by high throughput sequencing

summary: Exome and whole genome sequencing of matched primary tumor and lung metastases was used to identify metastasis-specific genomic events that drive metastasis.

overall_design: Primary and metastastic tumors from PyMT and Her2 genetically engineered mouse models were isolated and sequenced. Recurrent metastasis-specific copy number alterations, single nucleotide variants, and translocations within codiing regions were assessed. The metastatic driving potential of metastasis-specific single nucleotide variants was then tested using allograft models.

first: Christina

middle: R

last: Ross

first: Howard

last: Yang

first: Tinghu

last: Qiu

first: Karol

last: Szczepanek

first: Jack

last: Sanford

first: Kent

last: Hunter


title: A deregulated HOX gene axis confers an epigenetic vulnerability in KRAS mutant lung cancers

first: Stephanie

middle: Louise

last: Guerra

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard University- Brigham Women's Hospital


title: Role of Fragaria FaPRE1 in the plant development [FaPRE1-overexpression]

city: CÓRDOBA

first: Francisco

middle: Javier

last: Molina-Hidalgo

state: Cordoba

address: Edif. Severo Ochoa (C6.) Planta Baja-Ala Norte Campus de Rabanales

department: Biochemistry and molecular biology

country: Spain

institute: University of Cordoba

summary:
The role played by transcription factors in the regulation of strawberry fruit ripening process is scant. We have identified and functionally characterized FaPRE1, a non-DNA-binding  bHLH transcription factor.
FaPRE1 is a ripening-related transcription factor that regulates genes involved in cell architecture in strawberry fruit receptacles.

overall_design:
A custom-made oligo microarray (60-mer length) platform (FraGenomics 35k) containing a total of 35234 singletons corresponding to those sequences published in the strawberry genome project (http://www.strawberry.org). For each sequence, 4 different oligos were printed per block and four blocks were printed per data set. We have analyzed three control samples, a three samples of transgenic floral buds overexpressing FaPRE1.

Please note that experiments were carried out technically as dual channel (eg, Cy3 and Cy5-labeled samples hybridized to the same array) but processed the results as though they are single channel (Cy3 and Cy5 signals are calculated; Cy3/Cy5 ratios are not calculated). Therefore 3 raw data files for total 6 samples are linked as Series supplementary files and the associated raw data file is indicated in the corresponding sample description field.

first: Juan

last: Muñoz-Blanco

first: Laura

last: Medina-Puche


title: A deregulated HOX gene axis confers an epigenetic vulnerability in KRAS mutant lung cancers [HOXC10]

summary:
HOXC10 overexpression modifies the therapeutic response to combined MEK and BRD4 inhibitors
We performed microarray analysis of cells expressing LACZ or HOXC10 treated with MEK and BRD4 inhibition in combination for 24 hours, prior to the induction of cell death, to analyze transcriptional changes that might be mechanistic drivers of the therapeutic effect.

overall_design: 12 samples in triplicate, 3X LACZ + vehicle treatment, 3X HOXC10 + vehicle treatment, 3X LACZ + combo treatment, 3X HOXC10 + combo treatment

first: Karen

last: Cichowski


title: Genetic signature of prostate cancer mouse models resistant to optimized hK2 targeted alpha-particle therapy

status: Public on Apr 01 2020

first: Robert

last: Klein

state: NY

address: 1 Gustave L Levy Pl

summary: We used RNA sequencing to analyze the genomic signatures of prostate cancer that progressed after targeted alpha therapy.

overall_design: Understanding the expression profile of LNCaP-AR prostate cancer tumors that reoccur after hK2 targeted alpha-radioimmunotherapy

first: David

last: Ulmert


title: Glutathione restricts serine metabolism to preserve regulatory T cell function

city: Esch-sur-Alzette

first: Rashi

last: Halder

address: 7, Avenue des Hauts-Fourneaux

country: Luxembourg

institute: Luxembourg Center for Systems Biomedicine

summary: Regulatory T cells (Tregs) maintain immune homeostasis and prevent autoimmunity. Serine can stimulate glutathione (GSH) synthesis and feeds into the one-carbon metabolic cycle essential for effector T cell (Teff) responses. However, serine’s functions, linkage to GSH, and role in stress responses in Tregs are unknown. Here we show, using mice with Treg-specific ablation of the catalytic subunit of glutamate cysteine ligase (Gclc), that GSH loss in Tregs alters serine import and synthesis, and that the integrity of this feedback loop is critical for Treg suppressive capacity. Although Gclc-ablation does not impair Treg differentiation, the mutant mice develop severe spontaneous autoimmunity and show enhanced anti-tumor responses. Gclc-deficient Tregs exhibit increased serine metabolism, mTOR activation and proliferation but FoxP3 was downregulated. Limitation of cellular serine in vitro and in vivo restores FoxP3 expression and suppressive capacity to Gclc-deficient Tregs. Our work reveals an unexpected role for GSH in restricting serine availability to preserve Treg functionality.

overall_design: Here, we freshly isolated Tregs from WT and mutant mice (indicated as nTregs) as well as differentiate naïve CD4+ T cells from both WT and mutant mice into induced Tregs (indicated as iTregs)

first: Henry

last: Kurniawan

first: Dirk

last: Brenner


title: Molecular and genetic regulation of pig pancreatic islet cell development

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

summary: We report the transcriptomic profiling of islet cell subtypes obtained from pigs at different developmental stages

overall_design: Profiling FACS-purified pigs pancreatic islet cells by RNA-Seq.

first: S

first: R

last: Whitener

middle: K


title: Misactivation of multiple starvation responses in yeast by loss of tRNA modifications

city: Madrid

first: Teresa

last: Laguna

address: Ctra. Cantoblanco, 8

department: Precision Nutrition and Personalized Medicine

institute: IMDEA Food Institute

summary: Previously, combined loss of specific anticodon loop modifications was shown to impair the function of distinct tRNAs in Saccharomyces cerevisiae. Surprisingly, each scenario resulted in shared cellular phenotypes, the basis of which is unclear. To investigate how loss of different tRNA modifications can induce overlapping phenotypes, we characterized global transcription patterns of modification mutants with defects in either tRNAGlnUUG or tRNALysUUU function. We observe that the mutants share an inappropriate induction of multiple starvation responses, including derepression of glucose and nitrogen catabolite-repressed genes as well as improper activation of amino acid biosynthesis and autophagy genes, all of which occur prematurely and inadequately in exponential growth phase. We further demonstrate that improper  responses to starvation as well as the propensity of the tRNA modification mutants to form protein aggregates are diminished upon overexpression of tRNAGlnUUG or tRNALysUUU, the tRNA species that lack the modifications of interest. Hence, our data suggest that global alterations in mRNA translation and proteostasis (rather than codon specific defects in translation) account for the transcriptional stress signatures that are commonly triggered by loss of anticodon modifications in different tRNAs.

overall_design: Examination of 4 different yeast mutants compared to WT strain

first: Alexander

last: Bruch


title: Tumor-derived retinoic acid regulates intratumoral monocyte differentiation to promote immune suppression and resistance to immune checkpoint blockade

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

summary: The immunosuppressive tumor microenvironment (TME) is a major barrier to immunotherapy. Within solid tumors, why monocytes preferentially differentiate into immunosuppressive tumor associated macrophages (TAMs) but not immunostimulatory dendritic cells (DCs) remains unclear. Using multiple murine sarcoma models, we found that the TME induced retinoic acid (RA) production by tumor cells, which polarized intratumoral monocyte differentiation towards TAMs and away from DCs via suppression of DC-promoting transcription factor Irf4. Genetic inhibition of RA production by tumor cells or pharmacologic inhibition of RA signaling within TME increased stimulatory monocyte-derived cells, enhanced T cell-dependent anti-tumor immunity and demonstrated striking synergy with immune checkpoint blockade. Further, RA responsive gene signature in human monocytes correlated with an immunosuppressive TME in multiple human tumors. RA has been long considered as an anti-cancer agent, but our work demonstrates its tumorigenic capability via myeloid-mediated immune suppression and provides proof of concept for targeting this pathway for tumor immunotherapy.

overall_design: Cas9 Control or Raldh1/3 DKO tumors (n=4 per group) were harvested on Day 11 to generate single cell suspensions (as described in Materials and Methods) and CD45+ live cells were FACS sorted. Subsequently, 10x Genomics Controller and the v3 Library and Gel Bead kit (10x Genomics) were used to obtain single-cell emulsions. 10x 3’ v3 kit protocol was followed as described to generate RNA sequencing libraries. The generated libraries were sequenced using an Illumina NovaSeq SP.

first: Samir

last: Devalaraja

first: Tsun

last: To

first: Ian

middle: W

last: Folkert

first: Ramakrishnan

last: Natesan

first: Zahidul

last: Alam

first: Minghong

last: Li

first: Yuma

last: Tada

first: Konstantin

last: Budagyan

first: Mai

last: Dang

first: Li

last: Zhai

first: Graham

last: Lobel

first: Gabrielle

last: Ciotti

first: T

last: Eisinger-Mathason

first: Irfan

middle: A

last: Asangani

first: Kristy

last: Weber

first: M

last: Simon

first: Malay

last: Haldar


title: Expression data of metformin treated wild type and parietal cell- specific AMPK-deficient mice

city: Houston.

first: Jason

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

summary:
Genes related to AMPK activation, cellular respiration, and metabolism are enriched in the gastric parietal cell population. Metformin is known activator of AMPK.
We used microarray analysis to identify metformin targets in mature parietal cells and in parietal cell progenitors.

overall_design: RNA from gastric corpus was isolated from wild type BL6 mice that were treated with or without metformin for 14 days to determine mature parietal cell metformin targets. Mice with parietal cell-specific loss of AMPK have significantly decreased parietal cell number and impaired parietal cell maturation. Gastric epithleium from these mutant mice treated with or without metformin was compared to determine metformin targets in parietal cell progenitor and non-parietal cells.

first: Mahliyah

last: Adkins-Threats

first: Zhi-Feng

last: Miao


title: Capability of FDA-EVIR Microarray for Detection of Norovirus and Hepatitis A Virus in Inoculated Tomatoes, Green Onions, and Celery

city: Laurel

first: Christine

middle: Fang

last: Yu

address: 8301 Muirkirk Rd.

department: Center for Food Safety and Applied Nutrition

institute: US Food and Drug Administration

type: Expression profiling by genome tiling array

summary: The capability of the U.S. Food and Drug Administration Enteric Viruses tiling microarray (FDA-EVIR) was assessed for rapid molecular identification of human norovirus (NoV) and hepatitis A virus (HAV) extracted from artificially inoculated fresh produce. Two published viral extraction strategies, total RNA extraction or virus particle isolation, were employed to prepare the viral targets. We also assessed the amount of viral RNA extracted from celery by three commercially-available kits and how well that RNA performed on the FDA-EVIR.  Our results confirm that FDA-EVIR can correctly identify common enteric viruses isolated from fresh produce and is capable of identifying single and mixed species of viruses, as well as distinguishing among genotypes.  Extending microarray methods to other food matrices should provide important support to surveillance and outbreak investigations.

sample_organism:
Apium graveolens
Solanum lycopersicum
Allium fistulosum

platform_organism:
Bacillus subtilis
unidentified adenovirus
Rotavirus
Coxsackievirus
Hepatovirus A
Sapovirus
Norovirus
Astrovirus sp.
Paslahepevirus balayani

overall_design: In total 17 samples; 11 Input files (different produces/viruses/extraction methods) with the corresponding 6 negative control samples

first: Kaoru

last: Hida

first: Efstathia

last: Papafragkou


title: Effects of AEBP1 knockdown on gene expression profiles in HUVEC

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: We identified adipocyte enhancer binding protein 1 (AEBP1) as a novel tumor endothelial marker in colorectal cancer (CRC). To identify target genes of AEBP1 in endothelial cells, we knocked down AEBP1 in human umbilical vein endothelial cells (HUVECs). We found that genes associated with angiogenesis including aquaporin 1 (AQP1) and periostin (POSTN) are downregulated by AEBP1 knockdown in HUVECs, suggesting that AEBP1 may promote tumor angiogenesis through regulating these genes.

overall_design: HUVECs were transfected with a control siRNA (Silencer Select Negative Control No. 1 siRNA, Thermo Fisher Scientific) or siRNAs targeting AEBP1 (Silencer Select Pre-designed siRNA; AEBP1 siRNA1, s1145; AEBP1 siRNA2, s1146; Thermo Fisher Scientific) using HUVEC Nucleofector Kit (Lonza) and incubated for 48h or 72h.

first: Akira

last: Yorozu


title: Comparison of the modes of action of p-dialkoxy chlorobenzenes in rat primary hepatocytes

city: Tochigi

first: shota

last: Nakagawa

address: 2606, Akabane, Ichikai-Machi, Haga-Gun

institute: Kao Corporation

summary: It is considered that read-across based on only structure similarity has a risk of error on risk assessment. Under this circumstances, considering biological similarity based on adverse outcome pathways (AOPs) using in vitro omics technologies is expected to enhance the accuracy and robustness of conclusions in read-across. However, because of a lack of practical case studies, it is not well discussed key considerations and how to use these technologies for data gap filling. In the present case study, we elucidated and compared the mode of action for structural analogs ; p-dialkoxy chlorobenzenes including 1,4-dichloro-2,5-dimethoxybenzene (DDMB), 2,5-dichloro-1,4-diethoxybenzene (DDEB), 2-chloro-1,4-dimethoxybenzene (CDMB), and 1-chloro-2,5-diethoxybenzene (CDEB) using in vitro omics technologies. To reveal the modes of action, we conducted microarray analysis with rat primary hepatocytes.

overall_design: We conducted microarray analysis with rat primary hepatocytes exposed by DDMB, DDEB, CDMB, CDEB. After 24 h pre-culture, the cells were exposed to each compound at 300 µM for 24 h. Three independent experiments were performed at each condition. In this study, the normalization was divided into two group; (DDMB,CDMB,CDEB vs VC_1), (DDEB vs VC_2) because of lot differences on microarray chips.

first: Shota


title: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [Gfi1-R412X-HTZ]

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

summary: Advances in genetics and sequencing have lead to a deluge of disease-associated and disease-causing genetic alterations. Resolving causality between genetics and disease requires generating accurate models for molecular dissection; however, the rapid expansion of single-cell landscapes presents a major challenge to accurate comparisons between mutants and their wild type equivalents. Here, we generated mouse models of human severe congenital neutropenia (SCN) using patient-derived mutations in the Growth factor independent-1 (GFI1) transcription factor. To delineate the impact of SCN mutations, we first generated single-cell references for granulopoietic genomic states with linked epitopes, then developed a new computational approach to align mutant cells to their wild-type equivalent and derive differentially expressed genes. Surprisingly, the majority of differentially expressed GFI1-target genes are sequentially altered as cells traverse successive states. These cell-state-specific insights facilitated genetic rescue of granulocytic specification but not post-commitment defects in the expression of innate-immune effectors, providing regulatory insights into granulocyte dysfunction.

overall_design: Single cell RNA seq of Gfi1-R412X-HTZ GMP subpopulations

first: David

middle: E

last: Muench

first: Kashish

last: Chetal

first: Nathan

last: Salomonis

first: H

middle: L


title: An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA

city: Irvine

first: Whitney

last: England

state: CA

address: 2403 Natural Sciences I

department: Pharmaceutical Sciences

institute: University of California Irvine

summary: We demonstrate that mammalian cells are able to salvage uracil analogs, yielding high background incorporation into cellular RNA. We also discover the enzymatic pathways responsible for this background. To overcome these limitations, we have developed a novel small-molecule/enzyme pair consisting of uridine/cytidine kinase 2 (UCK2) and 2'-azidouridine (2'AzUd).

overall_design: Six total samples, consisting of three biological replicates each of HEK293T-UCK2/NIH3T3 co-culture treated with 2'AzUd 1 mM for 12 h Input and HEK293T-UCK2/NIH3T3 co-culture treated with 2'AzUd 1 mM for 12 h Enriched

first: Sarah

last: Nainar

first: Bonnie

last: Cuthbert

last: Lim

first: Ke

last: Ke

first: Kanika

last: Sophal

first: Robert

last: Quechol

first: Celia

last: Goulding

middle: C

last: Spitale


title: Bcl6 restrains ST2+ Treg cell development through negative regulation of Blimp1 in the context of allergic inflammation

city: Indianapolis

first: Mark

middle: H

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

summary: Bcl6 play a key role in CD4+ T cell development including follicular regulatory T cells. However, the role of Bcl6 in Treg cells in context of allergic inflammation was not fully understood. In this study, we describe the role of Bcl6 in development and function of ST2+Treg cells by analyzing ST2+Treg cell RNA seq.

overall_design: ST2 positive or negative regulatory T cells were sorted from two wildtype mice. ST2- Treg cells were used as a control.

first: Byunghee

last: Koh


title: High-throughput, Microscope-based Sorting to Dissect Cellular Heterogeneity

city: Seattle

first: Douglas

middle: M

last: Fowler

state: WA

address: Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

summary: Microscopy is a powerful tool for characterizing complex cellular phenotypes, but linking these phenotypes to genotype or RNA expression at scale remains challenging. Here, we present Visual Cell Sorting, a method that physically separates hundreds of thousands of live cells based on their visual phenotype. Automated imaging and phenotypic analysis directs selective illumination of Dendra2, a photoconvertible fluorescent protein expressed in live cells; these photoactivated cells are then isolated using fluorescence-activated cell sorting. First, we use Visual Cell Sorting to assess hundreds of nuclear localization sequence variants in a pooled format, identifying variants that improve nuclear localization and enabling annotation of nuclear localization sequences in thousands of human proteins. Second, we recover cells that retain normal nuclear morphologies after paclitaxel treatment, then derive their single cell transcriptomes to identify pathways associated with paclitaxel resistance in cancers. Unlike alternative methods, Visual Cell Sorting depends on inexpensive reagents and commercially available hardware. As such, it can be readily deployed to uncover the relationships between visual cellular phenotypes and internal states, including genotypes and gene expression programs.

overall_design: Sequencing of cells with varying degrees of nuclear localization reporter activity; or sequencing of cells with nuclear lobulation or normal nuclei

first: Nicholas

last: Hasle


title: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [Gfi1-R412X-Irf8]

last: Grimes

overall_design: Single cell RNA seq of Gfi1-R412X mutant GMP subpopulations


title: NFI Transcription Factors Govern Stem Cell Chromatin Accessibility and Guard Against Irreversible Hair Loss [ChIP-seq]

first: Hanseul

last: Yang

address: 1230 York Avenue

institute: Rockefeller University

summary: Tissue homeostasis and regeneration rely upon resident stem cells (SCs), whose behavior is regulated through niche-dependent crosstalk. The mechanisms underlying SC maintenance are still unfolding. Here, using hair follicles (HFs) as model and spatiotemporal gene ablation in mice, we uncover transcription factors (TFs) NFIB and NFIX as guardians of the process. Complete NFI ablation causes SC depletion and hair loss which resembles irreversible alopecia in humans, who intriguingly also display reduced NFI. Through single cell transcriptomics, ATAC- and ChIP-seq profiling, we uncover a key role for NFIB/NFIX in governing chromatin accessibility of HFSC master TFs . When NFIB/NFIX are genetically removed, the stemness epigenetic landscape is lost, as enhancers driving HFSC identity are decommissioned and those of epidermal differentiation and wound-repair are de-repressed. Together, our findings expose NFIB/NFIX as crucial rheostats of tissue homeostasis, functioning to safeguard the SC epigenome from a breach in lineage confinement that otherwise triggers irreversible tissue degeneration.

overall_design: Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen. The sorted cells were analyzed by ChIPseq.

first: Rene

last: Adam

first: Elaine

last: Fuchs


title: A transcriptional toolbox for exploring peripheral neuro-immune interactions

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

institute: King's College London

summary: Correct communication between immune cells and peripheral neurons is crucial for the protection of our bodies. Its breakdown is observed in many common, often painful conditions, including arthritis, neuropathies and inflammatory bowel or bladder disease. Here, we have characterised the immune response in a mouse model of neuropathic pain using flow cytometry and cell-type specific RNA sequencing (RNA-seq). We found few striking sex differences, but a very persistent inflammatory response, with increased numbers of monocytes and macrophages up to 3½ months after the initial injury. This raises the question of whether the commonly used categorisation of pain into “inflammatory” and “neuropathic” is one that is mechanistically appropriate. Finally, we collated our data with other published RNA-seq datasets on neurons, satellite glial cells, macrophages and Schwann cells in naïve and nerve injury states. The result is a practical web-based tool for the transcriptional data-mining of peripheral neuroimmune interactions.

overall_design: We have characterised the immune response in a mouse model of neuropathic pain using flow cytometry and cell-type specific RNA sequencing (RNA-seq).

first: Zhi

last: Liang

first: Zoe

last: Hore


title: NFI Transcription Factors Govern Stem Cell Chromatin Accessibility and Guard Against Irreversible Hair Loss

city: New York

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

overall_design: Refer to individual Series


title: NFI Transcription Factors Govern Stem Cell Chromatin Accessibility and Guard Against Irreversible Hair Loss [ATAC-seq]

overall_design: Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen. The sorted cells were analyzed by ATAC-seq.


title: NFI Transcription Factors Govern Stem Cell Chromatin Accessibility and Guard Against Irreversible Hair Loss [bulk RNA-seq]

overall_design: Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and WT littermate mice at P70 2nd telogen. The sorted cells were analyzed by RNAseq.


title: Transient Transcriptome Sequencing (TT-seq) of Nascent Gene Expression upon BRD4-NUT Protein Degradation/Recovery and RNA Polymerase II Inhibition

city: Houston

first: Kyle

last: Eagen

state: TX

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

summary:
Delineating how chromosomes fold at length scales beyond one megabase remains obscure relative to smaller-scale folding into TADs, loops, and nucleosomes. We find that rather than simply unfolding chromatin, histone hyperacetylation results in interactions between distant genomic loci separated by tens to hundreds of megabases, even in the absence of transcription. These hyperacetylated “megadomains” are formed by the BRD4-NUT fusion oncoprotein, interact both within and between chromosomes, and form a specific nuclear subcompartment that has elevated gene activity with respect to other subcompartments. Pharmacological degradation of BRD4-NUT results in collapse of megadomains and attenuation of the interactions between them. In contrast, these interactions persist and contacts between newly acetylated regions are formed after inhibiting RNA polymerase II initiation. Our structure-function approach thus reveals that broad chromatin domains of identical biochemical composition, independent of transcription, form nuclear subcompartments, and also indicates the potential of altering chromosome structure
for treating human disease.

overall_design: Transient transcriptome sequencing (TT-seq) to assess nascent gene expression in TC-797 cells after MZ1 treatment to degrade BRD4-NUT, after MZ1 treatment followed by drug washout to partially restore BRD4-NUT protein levels, and after triptolide treatment to inhibit RNA polymerase II transcription.

middle: P


title: NFI Transcription Factors Govern Stem Cell Chromatin Accessibility and Guard Against Irreversible Hair Loss [scRNA-seq]

overall_design: Mouse hair follicle stem cells were purified from Sox9-CreER;NFIBfl/fl;NFIXfl/fl and Sox9-CreER;NFIBfl/+;NFIXfl/fl (NFIB-cKO) littermate mice at P65-70 2nd telogen. The sorted cells were analyzed by ChIPseq.


title: Chromatin Hyperacetylation Impacts Chromosome Folding by Forming a Nuclear Subcompartment


title: KDM4B regulates alternative splicing in castration resistant prostate cancer

city: Dalals

first: zhi-ping

last: liu

address: 6000 Harry Hines Blvd

department: internal medicine

institute: ut southwestern

summary: We studied the alternative splicing function of KDM4B and found that KDM4B can act as a bona fide trans-acting splicing factor that binds RNA and signal-responsive scaffold protein that binds spliceosome.

overall_design:
We performed RNA-seq for LNCaP cells stably transfected with vector or Flag-KDM4B to identify genomewide alternative splicing events.
In our project, we sequence 6 samples using Illumina Hiseq platform, and on average we generated about 6.59 Gb bases from each sample. After mapping sequenced reads to reference genome and reconstruct transcripts,we finally get 13,160 novel transcripts from all samples, of this, 3,282 are previously unknown splicing event for known gene, 173 are novel coding transcripts without any known features, and the remaining 9,705 are long noncoding RNA .

first: Junhang

last: Luo

first: Zhiping

last: Liu


title: KAP1/TRIM28 maintains the transcriptional state of cancer cells

city: Dallas

first: Ivan

last: D'Orso

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

summary: We report the genome-wide effects of KAP1 loss on the transcriptome, the chromatin state, and on recruitment of various components of the transcription machinery in the colon colorectal cancer cell line HCT116.

overall_design: Genome-wide binding profiles of total and phosphorylated Pol II, CDK9, and NELFE in Ctrl vs KAP1 KO cells. Nascent and steady-state RNA expression levels in Ctrl vs KAP1 KO cells. Nucleosome occupancy profiles (MNase-seq) in Ctrl vs KAP1 KO cells

first: Curtis

last: Bacon

first: Ashwini

last: Challa

first: Iván


title: Hi-C to Identify Interactions between Distant Genomic Loci due to BRD4-NUT-mediated Megadomain Formation

overall_design: in situ Hi-C experiments mapping chromosome contacts after induction of BRD4-NUT expression in 293TRex cells and after MZ1 treatment to degrade BRD4-NUT, after MZ1 treatment followed by drug washout to partially restore BRD4-NUT protein levels, and after triptolide treatment to inhibit RNA polymerase II transcription in TC-797 cells.


title: Inhibition of glycolysis in pathogenic TH17 cells through targeting a miR-21-Peli1-c-Rel pathway prevents autoimmunity

city: Shenzhen

first: Zhijun

last: Han

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

institute: Southern University of Science and Technology

summary: It is well known that some pathogenic cells have enhanced glycolysis, the regulatory network leading to increased glycolysis are not well characterized. Here, we show that CNS-infiltrated pathogenic TH17 cells from diseased mice specifically upregulate glycolytic pathway genes compared to homeostatic intestinal TH17 cells. Bioenergetic assay and metabolomics analyses indicate that in vitro derived pathogenic TH17 cells are highly glycolytic compared to nonpathogenic TH17 cells. Chromatin landscape analyses demonstrate TH17 cells in vivo show distinct chromatin states, and pathogenic TH17 cells show enhanced chromatin accessibility at glycolytic genes with NF-kB binding sites. Mechanistic studies reveal that miR-21 targets the E3 ubiquitin ligase Peli1-c-Rel pathway to promote glucose metabolism of pathogenic TH17 cells. Therapeutic targeting c-Rel-mediated glycolysis in pathogenic TH17 cells represses autoimmune diseases. These findings extend our understanding of the regulation TH17 cell glycolysis in vivo and provide insights for future therapeutic intervention to TH17 cell mediated autoimmune diseases.

overall_design: RNA-seq for ileum and CNS-infiltrated TH17 cells with two replicates. RNA-seq for c-Rel overexpression (Ad-c-Rel) and control (Ad-control) in TH17(β) cells in vitro with two replicates. RNA-seq for miR-21-/- and Control TH17(23) with two replicates. ATAC-seq for ileum and CNS-infiltrated TH17 cells with two replicates. ATAC-seq for TH17(β) and TH17(23) with two replicates.

first: Xiang

last: Yu

first: Li

last: Wang

first: Chao

last: Yao

first: Guojun

last: Hou

first: Dai

last: Dai

first: Wenfei

last: Jin

last: Shen


title: The single cell transcriptional landscape of female primordial germ cell differentiation

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: Female primordial germ cell differentiation undergoes sex determination and meiosis initiation asynchronously. Here we investigate the transcriptional profiles of 20519 single cells collected from E12.5, E14.5 and E16.5 mouse fetal ovaries. Clustering analysis identifies ten clusters and defines dozens of corresponding marker genes and provides a global view of cellular differentiation from undifferentiated primordial germ cells towards meiotic oocytes. We explore the dynamics of gene expression within the differentiation trajectory with special focus on the mechanisms for meiotic initiation.

overall_design: Single cell sequencing on primordial germ cells was performed. Oct4-EGFP+ primordial germ cells were sorted from E12.5, E14.5 and E16.5 fetal gonads through MoFLo XDP.

first: Zhenghui

last: Zhao

first: Junyu

last: Ma


title: IRF5 promotes intestinal inflammation by guiding monocyte differentiation towards pathogenic CD11c+ macrophage phenotype

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology


title: Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human

first: Zheng

last: Zhang

address: No. 29, Bulan Road

institute: Shenzhen 3rd People's Hospital

summary: The liver plays a critical role in both immune defense and tolerance in the body. The liver-resident immune cells (LrICs) determine the immune properties, but the unique composition and heterogeneity of these cells are incompletely understood. Here, we dissect the diversity of LrICs by a comprehensive transcriptomic profiling using the unbiased single-cell RNA-sequencing (scRNA-seq). A total of 70, 706 of CD45+ immune cells from the paired liver perfusion, spleen and peripheral blood as references were profiled. We identified 33 discrete cell populations comprising 14 of T and NK cell, 7 of B cell, 4 of antibody-secreting cell (ASC) and 8 of myeloid cell subsets in human liver and donor-paired spleen and blood, and characterized their tissue distribution, gene expression and functional modules. Especially, four of CXCR6+ T and NK cell subsets were found to be present preferentially in the liver, where they manifested heterogeneity, distinct function and prominent homeostatic proliferation. We propose a universal category system of T and NK cells based on distinct chemokine receptors, confirmed subsequently by phenotype, transcriptional factors and functionality. We also identified adaptive changes by the spleen and liver-resident monocyte and macrophage populations. Finally, we give a global glimpse on B cell and ASC subsets in human spleen and liver. We, therefore, reveal the heterogeneity and functional diversity of LrICs in human. This study presents comprehensively the landscape of LrICs and will enable further study on their roles in various human diseases.

overall_design: Using 10x genomics to measure CD45+ immune cells in healthy human liver and paired spleen and PBMCs from the same donors access to liver transplantation.

first: Juanjuan

first: Yang

first: Xiaomeng

last: He

first: Mengmeng

last: Qu

first: Gang

last: Xu

first: Hongbo

first: Man

last: Huang

first: Jin

last: Pan

first: Zhenwen

first: Zhiwei

last: Li

first: Lei

first: Shuye


title: Microarray transcriptome analysis of primary mouse microglia cells treated with NGF

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

summary: The microarray transcriptome analysis of primary microglia was performed to demonstrate a direct modulation of NGF activity on microglia cells. The three different time points were used to evaluate and describe the time course of genes patwhays. In summary this experiment was crucial to describe for the first time the kind of NGF activity on microglia.

overall_design: A total of n=14 samples were processed: 2 experimental groups (NGF-treated and  untreated control) at 3 different time points (2h, 8h, 24h). Two biological replicates were processed for each experimental point (treatment,time) except controls at 24h (4 replicates).

first: Caterina

last: Rizzi

first: Alexia

last: Tiberi

first: Mara

last: D’Onofrio

first: Rossella

last: Brandi

first: Simona

last: Capsoni

first: Antonino

last: Cattaneo


title: Ischemia/Reperfusion Induces Interferon-Stimulated Gene Expression in Microglia

first: James

middle: William

last: MacDonald

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

summary: Stroke is the fifth leading cause of death in the United States and is a leading cause of serious long-term disability worldwide. Innate immune responses are critical in stroke pathophysiology, and microglia are key cellular effectors in the CNS response to ischemia/reperfusion. Using a transcriptional analysis approach, we identified a robust interferon (IFN)-stimulated gene response within microglia exposed to ischemia/reperfusion. We have demonstrated that these responses are dependent on innate immune signaling components including Toll-like receptor-4 and type I IFNs. We have also elucidated several novel ischemia/reperfusion-induced microglial signaling mechanisms.

overall_design: Transient (15 min) middle cerebral artery occlusion followed by 72 h reperfusion (tMCAO/R) or sham surgery was performed under isoflurane inhalational anesthesia on 12- to 14-week-old male WT or TLR4−/− mice using the transient intraluminal filament method. RNA was extracted from ex vivo sorted microglia from ipsilateral cortex and profiled by microarray. Statistical analysis was performed using Bioconductor limma package. Results were validated by quantitative RT-PCR.

first: Ashley

last: McDonough

first: Richard

middle: V

last: Lee

first: Shahani

last: Noor

first: Chungeun

first: Thu

last: Le

first: Michael

last: Iorga

first: Jessica

last: Phillips

first: Sean

last: Murphy

first: Thomas

last: Möller

first: Jonathan

last: Weinstein


title: Transcriptional regulators of the amino acid response pathway in leukemia

status: Public on Mar 31 2020

first: Robert

middle: T

last: Williams

summary: CRISPR/Cas9-based genetic screening revealed ZBTB1 as a critical mediator of the response of T-ALL cells to asparagine deprivation. ZBTB1 regulates the transcription of ASNS, a transcriptional target of ATF4. Loss of ZBTB1 results in decreased transcription and expression of ASNS. ChIP-Sequencing reveals that both ATF4 and ZBTB1 enrich in the promoter of ASNS. This dataset contains the RNA-Seq, ChIP-Seq and ATAC-Seq data on three different cell lines (WT Jurkat cells, ZBTB1 knockout Jurkat cells and ZBTB1 knockout Jurkat cells expressing ZBTB1 cDNA) in support of these findings.

overall_design:
RNA Sequencing: WT Jurkat cells, ZBTB1 knockout Jurkat cells and ZBTB1 knockout Jurkat cells expressing ZBTB1 cDNA were grown in the presence or absence of asparagine before RNA was isolated.
ChIP Sequencing: ZBTB1 knockout cells and ZBTB1 knockout cells expressing ZBTB1 cDNA were grown in the presence or absence of asparagine before ChIP on ATF4, ZBTB1, H3K27Ac, and H3K4me3.
ATAC-Sequencing: WT Jurkat cells, ZBTB1 knockout Jurkat cells and ZBTB1 knockout Jurkat cells expressing ZBTB1 cDNA were grown in the presence or absence of asparagine and collected for ATAC-Sequencing.

first: Kivanc

last: Birsoy


title: RNAseq of mouse arthritic ankles with over-expression of miR-17-5p

city: Nantes

first: Frederic

last: Blanchard

address: 1 rue Gaston Veil

country: France

institute: INSERM

summary: DBA1 mice with collagen-induced arthritis were injected intra-articularly with miR-17-5p mimic lipoplex. At the peak of inflammation (day 7), ankles were processed for bulk RNAseq using Illumina NextSeq 500.

overall_design: Ankle mRNA profiles of DBA1 mice with collagen-induced arthritis injected with miR-17-5p lipoplex (n=4) or control irrelevant miR lipoplex (n=3) were generated by deep sequencing using Illumina NextSeq 500.

first: Aurelie

last: Najm


title: RNA-seq analysis of Barhl1 locus mutant mouse embryonic stem cell (mESC)-derived hair cell-like cells

city: Hangzhou

first: xiao

last: HUANG

state: zhejiang

address: yuhangtang road 588#

department: College of Life Sciences

institute: zhejiang university

summary: Although Barhl1 has been known to be essential for the maintenance of cochlear hair cells, the precise molecular function of Barhl1 in hair cells has not been well studied. This study examined differentially expressed genes in Barhl1 locus mutant hair cell-like cells relative to wild type hair cell-like cells. We detected the critical expression time and period of Barhl1 in our in vitro hair cell induction system, and used the day 9 cultures during induction of otic progenitors towards hair cell-like cells to perform RNA-seq. The known hair cell-specific genes that were significantly downregulated in Barhl1 locus mutant hair cell-like cells are associated with hair cell functions and development, such as neurotransmitter secretion, calcium ion transport, intermediate filament bundle assembly, synaptic potential and sensory perception of sound.

overall_design: mRNA profiles of induced hair cell-like cells derived from wild type (WT)-, Barhl1 mutant (BM)- and E3 E-box site mutant (BEM)-mESCs were generated by deep sequencing using Illumina HiSeq 4000.

first: C

last: Zhong

first: X

last: Huang


title: Analysis of association between LPHN3 markers and substance use disorder

city: Bethesda

first: Ariel

middle: Fernando

last: Martinez

address: 35 Convent Drive, Room 1B209

institute: National Institutes of Health

summary: Genetic factors are strongly implicated in the susceptibility to develop externalizing syndromes such as attention deficit/hyperactivity disorder (ADHD), oppositional defiant disorder, conduct disorder, and substance use disorder (SUD). Variants in the ADGRL3 (LPHN3) gene predispose to ADHD and predict ADHD severity, disruptive behaviors comorbidity, long-term outcome, and response to treatment. In this study, we investigated whether variants within ADGRL3 are associated with SUD, a disorder that is frequently co-morbid with ADHD. Using family-based, case-control, and longitudinal samples from disparate regions of the world, recruited either for clinical, genetic epidemiological or pharmacogenomic studies of ADHD, we assembled recursive-partitioning frameworks (classification tree analyses) with clinical, demographic, and ADGRL3 genetic information to predict SUD susceptibility. Our results indicate that SUD can be efficiently and robustly predicted in ADHD participants. The genetic models used remained highly efficient in predicting SUD in a large sample of individuals with severe SUD from a psychiatric institution that were not ascertained on the basis of ADHD diagnosis, thus identifying ADGRL3 as a risk gene for SUD. Recursive partitioning analyses revealed that rs4860437 was the predominant predictive variant. This new methodological approach offers novel insights into higher order predictive interactions and offers a unique opportunity for translational application in the clinical assessment of patients at high risk for SUD

overall_design: Genomic DNA samples were genotyped using the Infinium® Human Exome-12 v1.2 BeadChip kit, which covers putative functional exonic variants selected from over 12,000 individual exome and whole-genome sequences. SNP markers harbored at the LPHN3 gene were filtered in from this dataset

middle: F

first: Maria

last: Acosta

first: Maximilian

last: Muenke


title: miRNA expression data from bulls with high and low intramusclar fat (IMF) content

status: Public on Mar 28 2020

city: Rostock

first: Steffen

last: Maak

state: Mecklenburg-Vorpommern

address: Wilhelm-Stahl-Allee 2, 18196 Dummerstorf

department: Institute of Muscle Biology and Growth

institute: Leibniz Institute for Farm Animal Biology (FBN)

summary:
Intramuscular fat content is a known trait that attributes to meat quality, taste and juiciness. MicroRNAs have been reported to play key role in lipid metabolism, hence in fat deposition. There is little understanding of miRNA regulation of IMF content and identification of these non-coding factors is important for further understanding of pathways involved in intramuscular fat deposition
Differentially expressed miRNAs were identified and their gene targets predicted.

overall_design: pairwise comparison of Affymetrix GeneChip microarray (miRNA) expression profiles of Musculus longissimus dorsi samples derived from crossbred bulls with high and low IMF content  Type: paired t-test

first: S

first: K

last: Wimmers

last: Ponsusili

last: Komolka

first: B

last: Mir


title: Distinct oncogenic roles of protein arginine methyltransferases (PRMTs) in mammary gland tumorigenesis using transgenic overexpression mouse models

city: Smithville

first: Jianqiang

last: Bao

state: Texas

address: 1808 Park Road 1C (P.O. Box 389), Smithville  TX 78957

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

summary: DEGs in the mammary epithelical cells between NIC and NIC-Prmt

overall_design: DEGs in the mammary epithelical cells upon Prmt overexpression

first: Mark

last: Bedford


title: PfMAP2 is essential for male gametogenesis in the malaria parasite Plasmodium falciparum

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

institute: Swiss Tropical and Public Health Institute

summary: Transcriptional profiling of transgenic P. falciparum stage V gametocytes of the strain NF54/MAP-2GFPDD before and after activation for gametogenesis. The DD (FKBP destabilisation domain) allows for the conditional expression of fusion proteins: DD fusion proteins are rapidly degraded or stably expressed in absence or presence of the stabilising ligand Shield-1, respectively (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in PFMAP-2GFPDD-expressing compared to PfAMP-2GFPDD-depleted stage V gametocytes.

overall_design: Four condition experiment using RNA extracted from mature stage V gametocytes (day 13) of the strain NF54/MAP-2GFPDD expressing PfMAP-2GFPDD from the endogenous locus. Gametocytes were cultured in presence of Shield-1 (ON) (stable PfMAP-2GFPDD expression) or had Shield-1 removed from the culture medium one day prior to sample harvesting (OFF) (PfMAP2-GFPDD protein degraded). Each population was split and one half was activated for gametogenesis by treatment with xanthurenic acid for 10 minutes (ON act. and OFF act.) while the other half was not (ON and OFF). Two biological replicates were performed (eight samples in total).

first: Eva

last: Hitz

first: Aurelia

last: Balestra

first: Mathieu

last: Brochet

middle: S


title: Epigenetic footprint of hepatoblastoma defines a novel integrative molecular classification with clinical implications [RNA-seq]

status: Public on Mar 23 2020

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: Crta Can Ruti; cami de les escoles, S/N

institute: Germans Trias i Pujol Health Research Institute

summary: Hepatoblastoma (HB) is the predominant pediatric liver cancer with limited therapeutic options for patients with aggressive tumors. Nevertheless, it is a rare disease. Here, we performed a high-throughput molecular study of 32 patients with HB and major findings were validated in additional 80 cases. We unveiled an epigenetic footprint including downregulation of RNA-editing, hyperediting of the tumor suppressor BLCAP,14q32 DLK1-DIO3 locus overexpression, DNA hypomethylation and CpG island hypermethylation. Based on these findings, we defined an integrative molecular classification of HB that improve current clinical stratification, and identified CHKA as a therapeutic target for the poor prognostic subclass.

overall_design: 66 RNA samples sequenced from 32 patients with hepatoblastoma.

first: Juan

last: Carrillo-Reixach

first: Laura

last: Torrens

first: Marina

last: Simon-Coma

last: Royo

first: Montserrat

last: Domingo-Sàbat

first: Jordi

last: Abril-Fornaguera

first: Nicholas

last: Akers

first: Margarita

last: Sala

first: Sonia

last: Ragull

first: Magdalena

last: Arnal

first: Núria

last: Villalmanzo

first: Stefano

last: Cairo

first: Alberto

last: Villanueva

first: Roland

last: Kappler

first: Marta

last: Garrido

last: Guerra

first: Constantino

last: Sábado

first: Gabriela

last: Guillén

first: Mar

last: Mallo

first: David

last: Piñeyro

first: María

last: Vázquez-Vitali

first: Olga

last: Kuchuk

first: María Elena

last: Mateos

first: Gema

last: Ramírez

first: Manuel

last: López-Santamaría

first: Yasmina

last: Mozo

first: Aroa

last: Soriano

first: Michael

last: Grotzer

first: Sophie

last: Branchereau

first: Nagore

last: García de Andoin

first: Blanca

last: López-Ibor

first: Ricardo

last: López-Almaraz

first: José Antonio

last: Salinas

first: Bárbara

last: Torres

first: Francisco

last: Hernández

first: José Javier

last: Uriz

first: Monique

last: Fabre

first: Julià

last: Blanco

first: Claudia

last: Paris

first: Viera

last: Bajčiová

first: Geneviève

last: Laureys

first: Helena

last: Masnou

first: Ariadna

last: Clos

first: Cristina

last: Belendez

first: Catherine

last: Guettier

first: Lauro

last: Sumoy

first: Ramón


title: Analysis of NSL knockout brains

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: In the current study, we analyse the function of MOF-NSL complex in neural cells. We find that the NSL complex regulates metabolic networks in the brain.

overall_design: Knockout of NSL complex members Mof, Kansl2 and Kansl3 was induced using the Nestin Cre. Neural cells, endothelial cells, pericytes and microglia were isolated by FACS. Gene expression analysed by RNA seq. and chromatin landscape via ChIP seq.

first: Bilal

last: Sheikh

first: Gina

last: Reschler