title: Whole transcriptome analysis and functional studies reveal that senescence plays a pivotal role in Myotonic Dystrophy type 1

status: Public on Dec 21 2021

city: Muenster

first: Marcos

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

institute: Max Planck Institute for Molecular Biomedicine

summary:
Myotonic dystrophy type 1 (DM1, MIM #160900) is an autosomal dominant disorder,
clinically characterized by progressive muscular weakness and multisystem degeneration.
The broad phenotypes observed in DM1 patients resemble the appearance of a multisystem accelerated aging process.
However, the molecular mechanisms underlying these phenotypes remain largely unknown.
Transcriptomic analysis of fibroblasts derived from DM1 patients and healthy individuals revealed a decrease in cell cycle activity,
cell division, and DNA damage response in DM1, all of which were required for the accumulation of cellular senescence.
Serial passage studies in vitro confirmed the accelerated increase in senescence and the acquisition of a senescence-associated secretory phenotype in DM1 fibroblasts.
Moreover, functional studies highlighted the impact of BMI-1/p16INK4a pathway dysregulation in DM1-associated cellular phenotypes.
Importantly, treatment with the senolytic compounds, quercetin, dasatinib, or navitoclax, reversed the accelerated aging phenotypes in both DM1 fibroblasts in vitro and in fruit flies in vivo.
Our results identified the accumulation of senescence-related processes as a major driver of DM1 pathophysiology and therefore,
demonstrated the efficacy of senolytic compounds in a pre-clinical setting.
This approach warrants further assessment as a novel therapeutic strategy for DM1.
Cell isolation and culture:
For the isolation of primary fibroblasts from healthy donors and DM1 patients (age range, 34 to 71),
punch skin biopsies were cut into 2–3 mm3 fragments and placed on a surface moistened with modified Eagle’s medium, containing 13% newborn calf serum,
0.4% penicillin/streptomycin (Gibco, Waltham, MA, USA) and 2 mM L-glutamine (Gibco).
Flasks were incubated vertically for 3–6 h at 37ºC under 5% CO2 and then returned to the horizontal position.
Human fibroblasts were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco) containing 10% fetal bovine serum (Sigma-Aldrich, St Louis, MO, USA),
1% L-glutamine (Gibco), and 1% penicillin–streptomycin (Gibco).
Fibroblasts were tested regularly for mycoplasma contamination.
Seven cultures from different DM1 patients and five from healthy controls were established.
Transcriptomic study and data analysis:
RNA was extracted from the fibroblasts from six DM1 patients and four age- and sex-matched controls at an early passage using TRIzol
(Life Technologies, Carlsbad, CA, USA).
Large-scale gene expression analysis was performed using the Human Clariom D microarray (Affymetrix, Santa Clara, CA, USA).
RNA integrity was confirmed using an RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA).
Those samples with an RNA integrity value above 9 were used in the analysis.
A total of 300 ng of RNA from each sample was used for microarray analysis, following the manufacturer's instructions.
Microarray data analysis:
The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina).
Background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model.
Variance stabilization was performed using the log2 scaling,
and gene expression normalization was calculated with the method implemented in the lumi package of R-Bioconductor.
Data post-processing and graphics were performed with in-house developed functions in Matlab (MathWorks™).
The GO terms were taken from the AMIGO gene ontology database.
The significance of the GO terms of the DEGs was addressed calculating the P-values using an enrichment approach based on the hypergeometric distribution.
All the sets of GO terms were back-propagated from the final term appearing in the gene annotation to the root term of each GO.

overall_design: 10 samples were analyzed

first: Mikel

first: Ander

last: Saenz-Antoñanzas

first: Gorka

last: Gerenu

first: Alex

last: Arrieta

first: Roberto

last: Fernández-Torrón

first: Miren

last: Zulaica

last: Arauzo-Bravo

last: Matheu

first: Adolfo

middle: L

last: de Munain


title: LncReader: identification of dual functional long non-coding RNAs using multi-head self-attention mechanism [RNA-seq]

status: Public on Nov 25 2021

city: Guangzhou

first: Tianyuan

last: Liu

address: Shatai South Road, Baiyun District

department: Bioinformatics Department

country: China

institute: Sourthern Medical University

type: Expression profiling by high throughput sequencing

summary: The dual functional lncRNAs have been intensively studied and identified to be involved in various fundamental cellular processes recently. It is essential to understand in which context when a dual functional lncRNA serves as a non-coding RNA or a template for coding peptide, particularly in some pathological conditions. However, apart from time consuming and cell type specific experiments, there is virtually no in-silico method for predicting the identity of dual functional lncRNAs. Here, we developed a deep-learning model with multi-head self-attention mechanism, LncReader, to identify dual functional lncRNAs based on their sequence, physicochemical and secondary structural features. Our data demonstrated that LncReader showed multiple advantage compared to various classical machine learning methods. Moreover, to obtain independent in-house datasets for robust testing, mass spectrometry proteomics combined with RNA-seq were applied in four leukemia cell lines. Remarkably, LncReader achieved the best performance among all these datasets. Therefore, LncReader provides a sophisticated and practical tool that enables fast dual functional lncRNAs identification.

overall_design: RNA-seq of four leukemia cell lines (HL60, MOLM13, K562, THP_1), one repulicate of each cell line.

first: Dong

last: Wang

first: Bohao

last: Zou


title: STUB1 regulates antiviral RNAi through inducing ubiquitination and degradation of Dicer and AGO2 in mammals

status: Public on Nov 22 2021

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

type: Non-coding RNA profiling by high throughput sequencing

summary: RNA interference (RNAi) is a cell-intrinsic antiviral defense conserved in diverse organisms. However, the mechanism by which mammalian antiviral RNAi is regulated is largely unknown. Herein, we uncover that STUB1, an E3 ubiquitin ligase, interacts with and ubiquitinates AGO2, the core component of RNAi pathway, resulting in the degradation of AGO2 via ubiquitin-proteasome system. Additionally, STUB1 can induce the degradation of the other mammalian AGO proteins including AGO1, AGO3, and AGO4. Our further study reveals that STUB1 also interacts with and mediates the ubiquitination of Dicer, the endoribonuclease responsible for siRNA or miRNA biogenesis, via K48-linked poly-ubiquitin, which induces the degradation of Dicer and its specialized form, termed antiviral Dicer (aviDicer) that usually expresses in stem cells. Loss of STUB1 upregulated Dicer and AGO2, thereby enhancing antiviral RNAi to effectively inhibit viral RNA replication in mammalian cells. In vivo, the STUB1 deficiency markedly enhanced the production of virus-derived siRNAs and elicited a potent antiviral effect against Enterovirus-A71 (EV-A71) infection in newborn mouse. Our findings demonstrate STUB1 as a novel negative regulator of RNAi by mediating the ubiquitination and degradation of Dicer and AGO proteins, and provide novel insights into the regulatory mechanism of antiviral RNAi in mammals.

sample_organism:
Mus musculus
Enterovirus A71

platform_organism:
Mus musculus
Enterovirus A71

overall_design: Small RNA profile of virus-infected mice.

first: Shumin

last: Zhang

first: Xuhua

first: Yuanyuan

last: Bie

first: Jing

last: Kong

first: An

first: Xi

last: Zhou


title: Gene perturbation after PPARG expression in  basal UMUC6 cells

status: Public on Dec 31 2021

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

country: France

institute: Institut Curie

summary: To better understand the molecular mechanisms underlying PPARG tumor suppressor role in basal cells, we studied the effect of PPARG expression on gene expression levels in UMUC6 cells that express low endogeneous expression levels of PPARG

overall_design: UMUC6 cells were transently transfected by a plasmid encoding WT PPARG or by the backbone plasmid as control. Three independant biological replicat were performed

first: Laure

last: Coutos-Thévenot

first: Isabelle

last: Bernard-Pierrot


title: Active eosinophils regulate host defense and immune responses during intestinal inflammation

status: Public on Oct 22 2021

city: Basel

first: Costanza

last: Borrelli

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zürich

summary: In the past decade, single-cell transcriptomics has helped uncover new cell types and states and led to the construction of a cellular compendium of health and disease1. Still, some difficult-to-sequence cell types remain absent from cell atlases. Eosinophils, elusive granulocytes implicated in a plethora of human pathologies2,3, are among these uncharted cell types. To date, the heterogeneity of eosinophils and the gene programs underpinning their pleiotropic functions remain poorly understood4. In the present study, we provide the first comprehensive single-cell transcriptomic profiling of murine eosinophils. We identify an active and a basal population of intestinal eosinophils, differing in their transcriptome, surface proteome and spatial localization. By means of genome wide CRISPR inhibition screen and functional assays, we dissect a mechanism by which IL-33 and IFN-? induce active eosinophil accumulation in the inflamed colon. Active eosinophils are endowed with bactericidal and T cell regulatory activity, and express the co-stimulatory molecules CD80 and PD-L1. Notably, active eosinophils are enriched in the lamina propria of a small cohort of inflammatory bowel disease patients and tightly associate with CD4+ T cells. Our findings provide novel insights into the biology of this elusive cell type and highlight its crucial contribution to intestinal homeostasis, immune regulation and host defence. Furthermore, we lay a framework for the characterization of eosinophils in human gastrointestinal diseases.

overall_design: ScRNASeq profiling of eosinophils magnetically enriched from different mouse organs, at steady state or upon bacterial infection, pool of 3 Il5-tg or B6 mice per condition

first: Gurtner

last: Alessandra

first: Borrelli

last: Costanza

first: Andreas

middle: E

last: Moor

middle: C

last: Arnold


title: Human dermal fibroblasts (HDF), BRAF-V600E positive (MaMel21 and MaMel63a), and BRAF-WT malignant melanoma cell lines (SBcl2 and WM3438) after vemurafenib or DMSO treatment

status: Public on Dec 11 2021

city: Freiburg

first: Eyleen

last: Corrales

address: Breisacherstr. 153

department: Medizinische Fakultät

country: Germany

institute: Institut für Medizinische Bioinformatik und Systemmedizin

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Glutamine attenuates renal ischemia-reperfusion injury and prevents acute kidney damage

status: Public on Nov 13 2021

city: Münster

first: Jan

last: Rossaint

address: Albert-Schweitzer-Campus 1, Bldg. A1

department: Dpt. of Anesthesiology

institute: University of Münster

summary: Our study investigates how the systemic administration of glutamine modulates the transcriptomic profile of neutrophils and renal tubular epithelial cells in the kidney during acute kidney injury.

overall_design: Acute kidney injury was induced by ischemia-reperfusion injury (IRI) in mice. Single neutrophils were isolated from the blood and renal tubular epithelial cells were isolated from the kidney 24 hours after induction of AKI.

first: Tobias

last: Tekath


title: Expression data of in vitro co-cultures comparing PKCa-KR- vs MIEV-transduced B lineage cells

status: Public on Oct 02 2021

city: Glasgow

first: Alison

last: Michie

address: 21 Shelley Road

department: Paul O'Gorman Leukaemia Research Centre

country: United Kingdom

institute: University of Glasgow

summary:
We performed Affymetrix microarray gene chip analysis on PKCa-KR- vs MIEV retrovirally transduced mouse B lineage cells that had been co-cultured for 17-23 days (late co-culture) to establish B cell transformation.
Expression analysis was performed between PKCa-KR and MIEV samples.

overall_design: Total RNA was isolated for 5 biological replicates of each condition (PKCaKR or MIEV-control).

middle: M

first: Jodie

last: Hay


title: DNA methylome evolution and reprogramming in recurrent glioblastoma

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

country: USA

institute: Geisel School of Medicine at Dartmouth

summary: Recurrent glioblastoma (GBM) has a grim prognosis, though MGMT promoter methylation and IDH mutation provide a significant survival advantage.  The product of IDH mutation, 2-hydroxyglutarate, increases global DNA methylation by inhibiting demethylases.  While lower-grade IDH-mutant gliomas demonstrate increased methylation as a result of this process, DNA becomes relatively hypomethylated during progression from low-grade glioma to secondary (IDH-mutant) GBM.  Here we show that global DNA hypomethylation also occurs  during primary (IDH-wild type) GBM recurrence.  Moreover, in a phase I trial of 14 patients with recurrent (IDH-wild type) GBM, we targeted DNA hypomethylation using a methyl donor treatment.  In autopsied tumors from patients treated, we observed a global increase in DNA methylation compared to initial tumor.  These results suggest that hypomethylation is a marker for recurrence, and its reprogramming represents a potential therapeutic vulnerability.

overall_design: glioblastoma tumors

middle: A

first: Thomas

middle: G

last: Stewart

first: Bret

last: Mobley

first: Chengwei

last: Peng

first: Sudan

middle: N

last: Loganathan

first: Yanjun

last: Ma

first: Jialiang

last: Wang

first: Mitchell

middle: S

last: Berger

first: Devin

last: Absher

first: Paul

last: Moots

first: Brock

last: Christensen

first: Stephen

middle: W

last: Clark


title: Identification of differentially expressed lncRNAs and coding mRNAs in SNAI1/2 overexpression cell line

status: Public on Oct 01 2021

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: The oncogene SNAI2 is known to be a master transcription factor that regulates a broad range of cellular processes, including epithelial-mesenchymal transition (EMT). As a transcription factor, there is no doubt that SNAI1/2 could directly regulate the expression of thousands of genes, including lncRNAs. In this study, we took SNAI1/2 as a breakthrough point to screen and identify lncRNAs regulated by SNAI2 in GC. Our data showed that overexpression of SNAI2 caused a 1.5-fold change in the expression of about 654 lncRNAs (|Log2FC| >0.5), and a 2-fold change in the expression of about 123 lncRNAs (|Log2FC| >1).

overall_design: Examination of the lncRNAs that regulated by SNAI2 and SNAI1 through RNA sequencing studies.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: Knockdown of ILF2/ILF3 (NF45/NF90) in the gastric cancer cell line SGC7901

summary: Our data showed that lncRNA ELF3-AS1 could bind on the exon1 of ELF3-201 to form a double-stranded RNA molecule. This double-stranded RNA could interact with ILF2/ILF3 complex. To explore the biofunction of the interaction between ELF3-AS1 and ILF2/ILF3 complex, loss-of-function studies regarding ILF2 and ILF3 were performed in SGC7901 cell line. RNA sequencing studies showed that knockdown of ILF3 significantly decreased ELF3-AS1, while knockdown of ILF2 significantly increased ELF3-AS1 and NF90 expression. Our data revealed that ILF2/ILF3 complex interacted with ELF3-AS1/ELF3 double-stranded RNA and regulated their transcripts stability.

overall_design: The biofunction of the interaction between ELF3-AS1 and ILF2/ILF3 complex, loss-of-function studies regarding ILF2 and ILF3 were performed in SGC7901 cell line. The potent ILF2/ILF3 target genes were identified by deep sequencing, using Illumina HiSeq 4000.


title: Knockdown of lncRNA ELF3-AS1 in two gastric cancer cell lines

summary: Our data showed that ELF3-AS1 was a nuclear lncRNA, and its biofunction in cancers is largely unknown to date. To explore the function of lncRNA ELF3-AS1 in gastric cancer, loss-of-function study was performed in SGC7901 and AGS cell lines. RNA sequencing studies showed that the expression of almost all the histone coding genes were significantly increased after knocking down of ELF3-AS1 in SGC7901 and AGS cell lines.

overall_design: To reveal the possible target genes of ELF3-AS1 in gastric cancer, we transfected ELF3-AS1-targeted siRNAs and corresponding negative control siRNAs in the SGC7901 and AGS cell lines. The potent ELF3-AS1 target genes were identified by deep sequencing, using BGIseq500.


title: Monitoring CAR T cell generation with a CD8-targeted lentiviral vector by single cell transcriptomics

city: Langen

first: Christian

middle: J.

last: Buchholz

state: Hessen

address: Paul-Ehrlich-Strasse 51-59

institute: Paul Ehrlich Institut

summary: Quantifying gene expression in individual cells can substantially improve our understanding about complex genetically engineered cell products such as chimeric antigen receptor (CAR) T cells. Here we designed a single-cell RNA sequencing (scRNA-seq) approach to monitor the delivery of a CD19-CAR gene via lentiviral vectors (LVs), i.e. the conventional VSV-LV and the CD8-targeted CD8-LV. LV exposed human donor PBMC were evaluated for a panel of 400 immune-response related genes including LV-specific probes. The resulting data revealed a trimodal expression for the CAR and CD8A demanding for a careful distribution-based identification of CAR T cells and CD8+ lymphocytes in scRNA-seq analysis. The fraction of T cells expressing high CAR levels was in concordance with flow cytometry results. More than 97% of the cells hit by CD8-LV expressed the CD8A gene. Remarkably, the majority of the potential off-target cells were in fact on-target cells resulting in a target cell selectivity of above 99%. Beyond that, the differential gene expression analysis revealed the upregulation of restriction factors in CAR-negative cells thus explaining their protection from CAR gene transfer. In summary, we provide a workflow and subsetting approach for scRNA-Seq enabling reliable distinction between transduced and untransduced cells during CAR T cell generation.

overall_design: Analysis of lentiviral vector generated products

first: Filippos

middle: T

last: Charitidis

first: Elham

last: Adabi

first: Frederick

middle: B

last: Thalheimer

first: Colin

last: Clarke

middle: J


title: Submergence-responsive genes in Col-0

status: Public on Aug 27 2021

city: DAEJEON

first: Hyo-Jun

last: Lee

state: DAEJEON

address: 125 GWAHAK-RO YUSEONG-GU

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Col-0 seedlings were submerged or left in air for 1 h and then RNA-sequencing was performed.

overall_design: Three biological replicates for Air and Sub samples were analyzed. Control: Air

first: Seung

middle: Y

last: Shin

first: Su-Jin

last: Park

first: Ji-Sun

first: Ki-Beom

last: Moon

first: Hyun-Soon

last: Kim

first: Jae

middle: H

last: Jeon

first: Hye

last: Cho


title: ecDNA hubs drive cooperative intermolecular oncogene expression [RNA-Seq]

status: Public on Sep 22 2021

city: Stanford

first: Howard

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

summary: Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.

overall_design: RNA-seq of ecDNA-containing cell line COLO320-DM.

first: King

last: Hung

first: Kathryn

last: Yost

first: Liangqi

last: Xie

first: Quanming

last: Shi

first: Konstantin

last: Helmsauer

first: Jens

last: Luebeck

first: Robert

last: Schöpflin

first: Joshua

last: Lange

first: Rocio

last: Chamorro

first: Natasha

last: Weiser

first: Celine

last: Chen

first: Maria

last: Valieva

first: Ivy

last: Tsz-Lo Wong

first: Sihan

last: Wu

first: Siavash

middle: R

last: Dehkordi

first: Connor

middle: V

last: Duffy

first: Katerina

last: Kraft

first: Jun

last: Tang

first: Julia

last: Belk

first: John

last: Rose

first: M

last: Corces

first: Jeffrey

last: Granja

first: Utkrisht

last: Rajkumar

first: Jordan

last: Friedlein

first: Anindya

last: Bagchi

first: Ansuman

last: Satpathy

last: Tijan

first: Stefan

last: Mundlos

first: Vineet

last: Bafna

first: Anton

last: Henssen

first: Paul

last: Mischel

first: Zhe

last: Liu


title: Inflammatory Conditions Promote Resistance to Immune Checkpoint Inhibitors in High Microsatellite Instability Colorectal Cancer

status: Public on Jul 09 2021

city: Shenzhen

first: Chao

last: Chen

state: Outside the US or Canada

address: Shenzhen,china

institute: Peking University Shenzhen Hospital

summary: Inflammatory conditions caused by obstruction or perforation are common complications in colorectal cancer (CRC) and play important roles in tumor progression and immunosuppression. However, the significance of inflammatory conditions in the tumor response to immune checkpoint inhibitors (ICIs) remains unclear. We found a high microsatellite instability (MSI-H) CRC patient (Patient 1) whose primary tumor progressed and liver metastasis regressed during PD-1 blockade after having inflammatory conditions. Then, in 73 MSI-H CRCs, inflammatory conditions during ICI treatment were correlated with a poor tumor response, and an elevated NLR was associated with a poor immune status and resistance to ICIs. An organoid-T cell coculture model demonstrated an inhibited local immune response to treatment instead of systemic immunosuppression in Patient 1. Single-cell RNA sequencing suggested that neutrophils suppress the immune microenvironment mostly through CTLA-4-associated pathways. Therefore, inflammatory conditions in MSI-H CRCs correlate with resistance to ICIs through neutrophil-associated immunosuppression. Additional CTLA-4 blockade may improve the sensitivity to PD-1 blockade.

overall_design:
Single-cell RNA sequencing (scRNA-seq) was conducted using the primary tumor of Patient 1. An scRNA-seq library was prepared using the DNBelab C4 system as previously described. Briefly, the single-cell suspension was transformed into the scRNA-seq library of barcodes through the steps of droplet encapsulation, emulsification and fragmentation, mRNA capture bead collection, reverse transcription, cDNA amplification and purification. An indexed sequencing library was constructed according to the manufacturer's instructions. The sequencing library was quantified using the Qubit SSDNA Assay Kit (Thermo Fisher Scientific). DIPSEQ T1 was used for sequencing libraries at the National Gene Bank (CNGB).
--------------------------------------------------------------
Authors state "raw data are not available for this Series due to patient privacy concerns and human genetic resources policy in China".

first: Qiaoqi

last: Sui

first: Jianhui

last: Yue

first: Jinghua


title: Dynamic genome-wide interaction patterns elucidate the roles of Ki67 in chromatin organization

status: Public on Oct 20 2021

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: Gene Regulation

country: Netherlands

institute: Netherlands Cancer Institute

summary: Ki67 is a widely-used proliferation marker with functions in chromosomal organization. It forms a protective layer around mitotic chromosomes and is involved in genome positioning in interphase. However, a detailed understanding of how Ki67 organizes the genome was still lacking, partially because genome-wide interaction profiles were missing. Here, we generate DNA-Ki67 interaction profiles using our pA-DamID method, and show that Ki67 interacts with the genome in a domain-like pattern that partially overlaps with lamina-associated domains.

overall_design: DNA-Ki67 interactions were profiled with pA-DamID in three human cell lines, throughout the cell cycle and following various nucleolar perturbation experiments. Additionally, Ki67 interactions were compared to Lamin B1 interactions and H3K27me3 and H3K9me3 in normal and perturbed conditions. Finally, the functional role of Ki67 was determined by profiling gene expression data (RNA-seq), replication timing (Repli-seq) and genome interactions (Hi-C).

first: Tom

last: van Schaik

first: Athanasios

middle: E

last: Vouzas

first: David

last: Gilbert


title: Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in lewy body diseases

status: Public on Aug 15 2021

city: London

first: Rahel

last: Feleke

address: Ducane Road

institute: Imperial College

summary: Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of diseasemodifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs  that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular “window” of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.

overall_design: Single-nucleus RNA sequencing of anterior cingulate cortex in 28 individuals, including non-neurological control individuals and individuals with Lewy body disease.

first: Prashant

last: Srivastva

first: Michael

last: Johnson


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and osmads58-/- Panicles Transcriptomes

status: Public on Aug 12 2021

city: Beijing

first: Liping

last: Shen

address: Yanyuan

institute: Peking University

summary:
Purpose: The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Conclusions: Our study represents the detailed analysis of panicles transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: 1cm long panicles mRNA profiles of wild type (WT) and osmads58-/-

first: Feng

last: Tian


title: Evaluation of intestinal response to zinc restriction and zinc sources in pigs

status: Public on Aug 05 2021

city: Falcon Heights

first: Ramya Lekha

last: Medida

state: MN

address: 1216 Fifield Ave

institute: University of Minnesota

summary: We evaluated the intestinal responses of pigs under zinc restriction and under different zinc sources through RNA-seq of ileal samples. We identified changes in genes related to zinc transport, immune response, cell proliferation, DNA damage and stress resposne. Our findings demonstrate that swine intestine is responsive to zinc restriction and can be a model sentinel tissue for human zinc deficiency. Further research is needed to define the intestinal responses to organic and inorganic zinc sources.

overall_design:
RNA seq of ileum of zinc restricted pigs and pigs supplemented with 100 ppm and 50 ppm of zinc by organic and inorganic zinc sources. n=7 for ZnR group, n=8 ZnCl100, ZnCl50, LQ100 groups, n=9 for LQ50 group
Finisher pigs (77.5± 2.5 kg) were randomly assigned to one of the five diets: a diet without added zinc (ZnR), ZnR with either 50 ppm or 100 ppm of zinc supplemented from organic (LQ100, LQ50) and inorganic sources (ZnCl100, ZnCl50).

first: Ramya

middle: L

first: Ashok

last: Sharma

first: Yue

last: Guo

first: Lee

last: Johnston

first: Pedro

last: Urriola

first: Andres

last: Gomez

first: Milena

last: Saqui-Salces


title: Using RNA-Seq to investigate immune-metabolism features in immunocompromised patients with sepsis

status: Public on Aug 23 2021

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

summary: Sepsis is life-threatening and leads to complex inflammation in immunocompromised subjects, including patients with cancer, those receiving immunosuppressants for autoimmune diseases and organ transplant recipients. Increasing evidence have shown that RNA-Sequencing (RNA-Seq) can be used to define subendotype in patients with sepsis; therefore, we aim to use RNA-Seq to identify transcriptomic features among immunocompromised patients with sepsis.

overall_design: A case-control study. A total of 18 immunocompromised subjects with sepsis and 18 sequential organ failure assessment (SOFA) score-matched immunocompetent control subjects were enrolled.

first: Po

last: Cheng

first: Hsin

last: Chen

first: Yu

last: Jiang

first: Tzu

last: Hsiao

first: Jen

last: Wang

first: Chieh

last: Wu

first: Tai

middle: M

last: Ko

first: Wen

middle: C

last: Chao


title: Loss of macrophage miR-146b with aging contributes to inflammation and mitochondrial dysfunction

status: Public on Aug 24 2021

city: Saint Louis

first: Andrea

last: Santeford

state: MO

address: 660 S. Euclid Ave.

department: Opthalmology

institute: Washington University School of Medicine

summary: Macrophages undergo programmatic changes with age leading to altered cytokine polarization and immune dysfunction, shifting these critical immune cells from protective sentinels to disease promoters. The molecular mechanisms underlying macrophage inflammaging are poorly understood. Using an unbiased RNA-seq approach, we identified miR-146b as the only microRNA whose expression progressively and unidirectionally declined with age in murine macrophages. miR-146b deficiency led to altered macrophage cytokine expression and reduced mitochondrial metabolic activity, two hallmarks of cellular aging. Single-cell RNA sequencing identified patterns of altered inflammation and interferon gamma signaling in miR-146b deficient macrophages. Identification of miR-146b as a potential regulator of macrophage aging provides novel insights into immune dysfunction associated with aging.

overall_design: Peritoneal macrophages were harvested from 3-, 6-, 12-, 18-, 24- and 30-month-old C57Bl/6 mice or Lyz2; miR-146b macrophage/monocyte conditional knockout and littermate control mice.

first: Rajendra

last: Apte

first: Alexey

last: Sergushichev

first: Philip

middle: A

last: Ruzycki


title: Characterizing the invasive tumor front of aggressive uterine adenocarcinoma and leiomyosarcoma

status: Public on Jun 28 2021

city: Santiago de Compostela

first: Angel

last: Diaz-Lagares

state: A Coruña

address: C/ Choupana s/n

department: ONCOMET

country: Spain

institute: Health Research Institute of Santiago (IDIS)

type: Methylation profiling by genome tiling array

summary: Invasive tumor front (the tumor-host interface) is vitally important in malignant cell progression and metastasis. Tumor cell interactions with resident and infiltrating host cells and with the surrounding extracellular matrix and secreted factors ultimately determine the fate of the tumor. In this study we focus on the invasive tumor front, making an in-depth characterization of reticular fiber scaffolding, infiltrating immune cells, gene expression and methylation profiles of classified aggressive primary uterine adenocarcinomas and leiomyosarcomas.

overall_design: Total genomic DNA from formalin-fixed paraffin-embedded (FFPE) tissue sections of microdissected invasive tumor front (ITF) of uterine adenocarcinomas (uADC) and leiomyosarcomas  (uLMS) were processed on the Infinium MethylationEPIC array (850K). Samples that passed the quality controls (ADC=21, LMS=9) using GenomeStudio and BeadArray Controls Reporter (Illumina), were analyzed to asses their DNA methylation profile.

first: Rafael

last: Lopez-Lopez


title: Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer and nominates potential therapeutic targets

status: Public on Jun 29 2021

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Global profiling of tumor expression revealed increased RING-PHD-Bromodomain protein TRIM24 levels in numerous human cancers. Conditional over-expression of Trim24 was sufficient to drive murine mammary tumor development, 70% of which were ER, PR and HER2-negative carcinosarcomas with coexisting malignant epithelial and mesenchymal compartments, offering a unique model of human triple-negative, metaplastic breast cancer (MpBC). Both in vivo and in cellulo, TRIM24 induced EMT, repressing CDH1 and activating EMT factors.  Whole exome sequencing of human MpBC tumors and Trim24-driven carcinosarcomas defined a TRIM24-like subclass of MpBC patients with worse overall and relapse-free survival.  Among 40 MpBC patients, 43% had robust expression of TRIM24.  These studies implicate TRIM24 as a potential biomarker and therapeutic target for a subset of MpBC.

overall_design: To determine the transcriptional changes in mammary specific CRE driven TRIM24 overexpressing tumor versus control Cre expressing mammary glands, we performed RNA sequencing. There are 4 control samples which are mammary glands of Cre exprssing FVB/129 mice. The tumors are obtained from TRIM24 COE mice in a similar background.

first: Vrutant

last: Shah

first: Aundrietta

middle: D

last: Duncan

first: Shiming

first: Sabrina

last: Stratton

first: Kendra

last: Allton

first: Clinton

last: Yam

first: Abhinav

last: Jain

first: Patrick

last: Krause

first: Yue

last: Lu

first: Shirong

last: Cai

first: Yizheng

last: Tu

first: Xinhui

last: Zhou

first: Xiaomei

last: Zhang

first: Yan

first: Christopher

last: Carroll

first: Zhijun

last: Kang

first: Bin

last: Liu

first: Jianjun

last: Shen

first: Mihai

last: Gagea

first: Sebastian

last: Manu

first: Lei

last: Huo

first: Michael

last: Gilcrease

first: Reid

last: Powell

last: Guo

first: Clifford

last: Stephan

first: Peter

last: Davies

first: Jan

last: Parker-Thornburg

first: Guillermina

last: Lozano

first: Richard

last: Behringer

first: Helen

last: Piwnica-Worms

first: Stacy

last: Moulder

first: Michelle

last: Barton


title: Immune landscape of genetically-engineered murine models of glioma relative to human glioma by single-cell sequencing

status: Public on Jul 21 2021

first: Daniel

middle: Bernard

last: Zamler

state: TX

department: Genomic Medicine

institute: M.D. Anderson Cancer Center

summary: This work lays the foundation for the intratumoral immune infiltrates of glioma patients analyzed at a single cell level with the dual purpose of establishing the relevance of a new mouse model of GBM with regard to the patient disease. The aim of this study was to determine the level of concordance between the spontaneous and implanted Qk/trp53/Pten (QPP) triple-knockout mouse GBM model and human glioma samples in regard to their immune infiltrates.We analyzed a cohort of fifteen spontaneous QPP mice, nine implanted QPP mice and 10 glioma patients histopathologically. Furthermore, we analyzed three spontaneous QPP mice, thee implanted QPP mice, and 10 glioma patients by single cell RNA sequencing. We found that the QPP model recapitulates human GBM regarding the major immune components including a predominantly myeloid cell population of monocytes, macrophages, and resting dendritic cells, with minor populations of T, B, and NK cells. In addition, the complexity of the myeloid cell populations is preserved between the QPP model and the human disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single Cell Sequencing of 10 glioma patients, 3 spontaneous QPP Mouse GBM, and 3 implanted QPP#7 mouse GBM

first: Jian

last: Hu

first: Giulio

last: Draetta

first: Amy

last: Heimberger


title: The Ewing Sarcoma Cell Line Atlas - Systematic analysis of genome-wide EWSR1-ETS binding and histone marks in 18 Ewing sarcoma cell lines by ChIP-seq

status: Public on Jun 09 2021

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary: Cell lines have been essential for major discoveries in cancer including Ewing sarcoma (EwS). EwS is a highly aggressive pediatric bone or soft-tissue cancer characterized by oncogenic EWSR1-ETS fusion transcription factors converting polymorphic GGAA-microsatellites (mSats) into neo-enhancers. However, further detailed mechanistic evaluation of gene regulation in EwS have been hindered by the limited number of well-characterized cell line models. Here, we present the Ewing Sarcoma Cell Line Atlas (ESCLA) comprising 18 EwS cell lines with inducible EWSR1-ETS knockdown that were profiled by whole-genome-sequencing, DNA methylation arrays, gene expression and splicing arrays, mass spectrometry, and ChIP-seq for EWSR1-ETS and histone marks. Systematic analysis of these multi-dimensional data illuminated hundreds of new potential EWSR1-ETS target genes, the nature of EWSR1-ETS-preferred GGAA-mSats, and potential indirect modes of EWSR1-ETS-mediated gene regulation. Moreover, we identified putative co-regulatory transcription factors and heterogeneously regulated EWSR1-ETS target genes that may have implications for the clinical heterogeneity of EwS. Collectively, our freely available ESCLA constitutes an extremely rich resource for EwS research and highlights the power of leveraging multidimensional and comprehensive datasets to unravel principles of heterogeneous gene regulation by dominant fusion oncogenes.

overall_design: ChIP-seq of 18 Ewing sarcoma cell lines, for each cell lines ChIP for FLI1 or ERG (dependent on the fusion oncogene of the respective cell line), histone marks H3K4me3, H3K27me3, and H3K27ac, and ChIP input as control

first: Martin

middle: F

last: Orth

first: Didier

last: Surdez

first: Sandrine

last: Grossetête

first: Olivier

last: Delattre

middle: G

last: Grünewald


title: Identification of differentially expressed miRNAs after knockdown of ELF3-AS1 in gastric cancer

first: Qin

last: Shanshan

summary: In this study, we used miRNA sequencing to analyze and identify possible miRNAs that can be regulated by and ELF3-AS1 in gastric cancer. The results showed that lncRNA ELF3-AS1 knockdown decreased the expression of miR-33a/b and miR-203a. Due to miR-33a/b and miR-203a were able to target SNAI2 expression, and ELF3-AS1 knockdown significantly upregulates SNAI2 expression, we speculated ELF3-AS1 may negatively regulate SNAI2 expression through positively regulating the expression of miR-33a/b and miR-203a in GC.

overall_design: To reveal the possible target miRNAs of ELF3-AS1 in gastric cancer, we knocked down the ELF3-AS1 expression in  AGS cell lines. The potent differential expressed microRNAs after silencing ELF3-AS1 were identified by microRNA sequencing.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: The Ewing Sarcoma Cell Line Atlas (ESCLA) - methylation profiling of 18 Ewing sarcoma cell lines in EWSR1-ETS-high versus -low condition

summary:
Cell lines have been essential for major discoveries in cancer including Ewing sarcoma (EwS). EwS is a highly aggressive pediatric bone or soft-tissue cancer characterized by oncogenic EWSR1-ETS fusion transcription factors converting polymorphic GGAA-microsatellites (mSats) into neo-enhancers. However, further detailed mechanistic evaluation of gene regulation in EwS have been hindered by the limited number of well-characterized cell line models. Here, we present the Ewing Sarcoma Cell Line Atlas (ESCLA) comprising 18 EwS cell lines with inducible EWSR1-ETS knockdown that were profiled by whole-genome-sequencing, DNA methylation arrays, gene expression and splicing arrays, mass spectrometry, and ChIP-seq for EWSR1-ETS and histone marks.
Systematic analysis of these multi-dimensional data illuminated hundreds of new potential EWSR1-ETS target genes, the nature of EWSR1-ETS-preferred GGAA-mSats, and potential indirect modes of EWSR1-ETS-mediated gene regulation. Moreover, we identified putative co-regulatory transcription factors and heterogeneously regulated EWSR1-ETS target genes that may have implications for the clinical heterogeneity of EwS. Collectively, our freely available ESCLA constitutes an extremely rich resource for EwS research and highlights the power of leveraging multidimensional and comprehensive datasets to unravel principles of heterogeneous gene regulation by dominant fusion oncogenes.

overall_design: 18 established Ewing sarcoma cell lines were stably transduced with inducible shRNA expressing constructs targeting the respective EWSR1-ETS fusion oncogene. EWSR1-ETS knockdown was induced by 1 µg/ml doxycycline in culture medium for 96 h. Genomic DNA was isolated with a membrane based approach from three replicates after EWSR1-ETS-knockdown induction and three control replicates per cell line. DNA was processed and hybridized according to Illumina protocols to Illumina Infinium MethylationEpic BeadChip arrays. Data were processed using Illumina Genome Studio Software.


title: The Ewing Sarcoma Cell Line Atlas (ESCLA) - expression profiling of 18 Ewing sarcoma cell lines in EWSR1-ETS-high versus -low condition

overall_design:
18 established Ewing sarcoma cell lines were stably transduced with an inducible shRNA expressing construct targeting the EWSR1-ETS fusion of the respective cell line. EWSR1-ETS knockdown was induced by the addition of 1 µg doxycycline to growth medium for 96 h. Total RNA was isolated from three replicates treated with doxycycline and three controls. The transcriptome was profiled on Affymetrix Clariom D Human microarrays. Raw data were processed using the Transcriptome Analysis Console (version 4.0) by ThermoFisher, the SST-RMA analysis algorithm and the manufacturer's array description file (version 2).

Please note that the sample data tables (containing normalized data) and GSM5359685 CEL file have been updated on June 9th, 2022.


title: The Ewing Sarcoma Cell Line Atlas (ESCLA)

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

overall_design: Refer to individual Series


title: CXCR2 may serve as a useful index of disease activity in interstitial lung disease associated with primary Sjögren’s syndrome

status: Public on Jun 02 2021

city: Wenzhou

first: Xiaofang

last: Zhu

state: Zhejiang Province

address: Nan Bai Xiang Street

department: Rheumatology

institute: First Affiliated Hospital of Wenzhou Medical University

summary: Primary Sjögren’s syndrome (pSS) is a chronic systemic autoimmune disease characterized by typical autoantibody production and lymphocytic-mediated exocrine gland damage. Interstitial lung disease (ILD) is a common complication of pSS and can be associated with a poor prognosis. However, the pathogenesis of ILD in pSS is still unclear. In this study, we used RNA sequencing to investigate the gene-expression profile of the minor salivary glands (MSGs) from 36 patients with ILD-pSS and 128 patients with non-ILD-pSS. In the remarkably enriched chemokine-mediated signaling pathway, CXCR2 was found to be significantly elevated in both MSG and plasma from pSS patients with versus without ILD (p < 0.001). Furthermore, the CXCR2 expression level in MSG and plasma was significantly associated with the diffusing capacity of the lungs for carbon monoxide, erythrocyte sedimentation rate, and EULAR Sjögren’s Syndrome Disease Activity Index in ILD-pSS. Therefore, with its potential role in ILD progression in patients with pSS and its strong association with clinical manifestations of the disease, CXCR2 may serve as a useful index for disease activity in ILD associated with pSS.

overall_design: **The submitter states that the 'disease state' characteristic and fastq files for some of the Samples might by inaccurate. Corrections are in progress. [Dec 06, 2022]**

first: Saisai

last: Lu

first: Lixia

first: Mengjiao

last: Yu

first: Tingting

last: Wei

first: Xiaochun

first: Dan

last: Chen

first: Chengshui


title: Genome-wide distribution of AR, Sp1, H3K27Ac, H3K4me1 in E16.5 embryonic external genitalia (eExG)

status: Public on May 18 2021

city: Wakayama

first: Gen

last: Yamada

address: 811–1 Kimiidera

department: Institute of Advanced Medicine

country: Japan

institute: Wakayama Medical University

summary: ChIP-seq analysis of AR, Sp1, H3K27Ac, and H3K4me1; The genime-wide distribution of AR, Sp1, H3K27Ac, and H3K4me1 druing murine embryonic external genitalia (eExG) sex differentiation was shown.

overall_design: 20-30 eExG were collected for ChIP-seq. Each ChIP analysis was performed  in 2 independent biological replicates (Sp1 for the single analysis).

first: Daiki

last: Kajioka

first: Tetsuya

last: Sato

first: Shoko

last: Matsushita

first: Kentaro

last: Suzuki


title: ecDNA hubs drive cooperative intermolecular oncogene expression [Hi-C]

status: Public on May 24 2021

first: Howard

last: Chang

summary: Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.

overall_design: Hi-C of ecDNA-containing cell line TR-14.

first: King

last: Hung

first: Kathryn

last: Yost

first: Liangqi

last: Xie

first: Quanming

last: Shi

first: Konstantin

last: Helmsauer

first: Jens

last: Luebeck

first: Robert

last: Schöpflin

first: Joshua

middle: T

last: Lange

first: Rocio

last: Chamorro

first: Natasha

last: Weiser

first: Celine

first: Maria

last: Valieva

first: Ivy

last: Wong

first: Sihan

last: Wu

first: Siavash

last: Dehkordi

first: Connor

last: Duffy

first: Katerina

last: Kraft

first: Jun

last: Tang

first: Julia

last: Belk

first: John

last: Rose

first: M

last: Corces

first: Jeffrey

last: Granja

first: Utkrisht

last: Rajkumar

first: Jordan

last: Friedlein

first: Anindya

last: Bagchi

first: Ansuman

last: Satpathy

last: Tijan

first: Stefan

last: Mundlos

first: Vineet

last: Bafna

first: Anton

last: Henssen

first: Paul

middle: S

last: Mischel

first: Zhe

last: Liu


title: ecDNA hubs drive cooperative intermolecular oncogene expression [ATAC-Seq]

first: Howard

last: Chang

overall_design: ATAC-seq of ecDNA-containing cell line SNU16.

first: King

last: Hung

first: Kathryn

last: Yost

first: Liangqi

last: Xie

first: Quanming

last: Shi

first: Konstantin

last: Helmsauer

first: Jens

last: Luebeck

first: Robert

last: Schöpflin

first: Joshua

last: Lange

first: Rocio

last: Chamorro

first: Natasha

last: Weiser

first: Celine

last: Chen

first: Sihan

last: Wu

first: Siavash

last: Dehkordi

last: Duffy


title: RNA landscape of the emerging cancer-bug Fusobacterium nucleatum

status: Public on May 03 2021

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered much attention for its newly discovered prevalence in colorectal and breast cancer tissue. The growing interest in this emerging cancer-associated bacterium sharply contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. Post-transcriptional networks are also unknown, for fusobacteria lack all established small RNA-associated proteins. Here, we present high-resolution global RNA maps for two clinically relevant F. nucleatum subspecies for different growth conditions, and use these to uncover fundamental aspects of fusobacterial gene expression architecture and a previously unknown suite of noncoding RNAs. Developing a new vector for functional analysis of fusobacterial genes, we identify a conserved oxygen-induced small RNA as a post-transcriptional repressor of major porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum to colonize different compartments of the human body.

sample_organism: Fusobacterium nucleatum subsp. nucleatum ATCC 25586

overall_design: Samples of different growth stages were taken for RNA extraction. Isolated RNA was used for cDNA library generation following the dRNA-seq protocol.

first: Caroline

last: Tawk

first: Yan

last: Zhu

first: Lars

last: Barquist

first: Franziska

last: Faber

first: Jörg

last: Vogel


title: Blood and Brain Gene Expression Signatures of Chronic Intermittent Ethanol Consumption in Mice

status: Public on Jun 04 2021

city: Austin

first: Laura

last: Ferguson

address: 1601 Trinity St Bldg. B, Rm 5.222

department: Waggoner Center for Alcohol and Addiction Research

institute: Dell Medical School, University of Texas at Austin

summary: Alcohol Use Disorder (AUD) is a chronic, relapsing syndrome diagnosed by a heterogeneous set of behavioral signs and symptoms. There are no laboratory tests that provide direct objective evidence for diagnosis. Microarray and RNA-Seq technologies enable genome-wide transcriptome profiling at low costs and provide an opportunity to identify biomarkers to facilitate diagnosis, prognosis, and treatment of patients. Brain gene expression patterns can discriminate alcohol-dependent and non-dependent people and predict drugs that reduce drinking in rodents. However, access to brain tissue in living patients is not possible. Blood contains cellular and extracellular RNAs that provide disease-relevant information for some brain diseases. We hypothesized that blood gene expression profiles can be used to diagnose AUD. We profiled brain (prefrontal cortex, amygdala, and hypothalamus) and blood gene expression levels in C57BL/6J mice using RNA-seq one week after chronic intermittent ethanol (CIE) exposure, a mouse model of alcohol dependence. To determine the preservation of gene expression levels between blood and brain, we calculated the Spearman correlation coefficient between blood and brain mean gene expression levels across all subjects and found a high degree of preservation (rho range: [0.50, 0.67]) with hundreds of transcripts in blood correlated with their brain transcript levels. To determine whether the transcriptional response to alcohol dependence was similar in blood and brain, we studied the overlapping differentially expressed genes (DEGs) and gene coexpression networks. Although there was small overlap between blood and brain DEGs, there was considerable overlap of gene networks perturbed after CIE related to cell-cell signaling (e.g., GABA and glutamate receptor signaling, endocannabinoid signaling, synaptogenesis), immune responses (e.g., antigen presentation, communication between innate and adaptive immune systems), and protein processing / mitochondrial functioning (e.g., ubiquitination, unfolded protein responses, oxidative phosphorylation). To determine whether blood gene expression can predict alcohol dependence status, blood gene expression data were used to train classifiers (logistic regression, random forest, and partial least squares discriminant analysis), which were highly accurate at predicting alcohol dependence status (maximum AUC for females: 90.1%; males: 80.5%). These results suggest that gene expression profiles from peripheral blood samples contain a biological signature of alcohol dependence that can discriminate between alcohol-dependent and non-dependent subjects.

overall_design: Alcohol dependence was induced using chronic intermittent ethanol (CIE) treatment with voluntary alcohol drinking tests (two bottle choice drinking in the dark 2BC DID) N = 40 C57Bl/6J mice; 10 per group; male and female; alcohol-dependent (ethanol vapor) and non-dependent (air vapor). CIE was implemented as described in previous studies. Thirty minutes before the dark cycle, mice were singly housed for two hours with access to two drinking tubes, one containing 15% ethanol and the other containing water. Ethanol and water consumption during these 2-hour periods was recorded. Following this baseline period of two-bottle choice (2BC) drinking, which lasted 20 days (5 days per week for 4 weeks), mice were divided into two balanced groups with similar distributions of ethanol and water consumption. One group was exposed to intermittent ethanol vapor and the other to control air in identical chambers. The ethanol vapor group was administered 1.75 g/kg ethanol plus 68.1 mg/kg pyrazole to inhibit alcohol dehydrogenase, and then was placed in the chambers to receive intermittent vapor for 4 days (16 hours vapor on, 8 hours vapor off). Once per week, immediately following a 16-hour bout of vapor, mice were removed, and tail blood was sampled for blood alcohol determination. Target blood alcohol levels were 175-250 mg%. Following the fourth day of exposure, mice were allowed 72 hours of undisturbed time. The mice were then given 5 days of 2BC drinking. The control group was injected with 68.1 mg/kg pyrazole in saline and placed in chambers delivering air for the same periods as the ethanol vapor group and then received 2BC testing at the same time as the vapor groups. Mice were subjected to four cycles of vapor or air exposure followed by 5 days of 2BC drinking. All mice then received one final 4-day vapor or air exposure. One week later, mice were euthanized and tissue collected for RNA sequencing.

middle: B


title: Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response

status: Public on Apr 03 2021

city: Bryan

first: Kristin

last: Patrick

state: Texas

address: 8447 Riverside Pkwy, MREB 3102

department: Microbial Pathogenesis and Immunology

institute: Texas A&M University, College of Medicine

summary:
Purpose: The goal of this study is to measure how steady state RNA and alternatively spliced transcript abundance levels are impacted by loss of specific RNA-binding proteins as part of macrophage transcriptional activation upon pathogen sensing.
Methods: SRSF 1, 2, 6, 7, 9, and hnRNP C, F, K, U were knockdown using shRNA in RAW 264.7 macrophages. Macrophages were collected as uninfected (resting) cells and infected with Salmonella Typhimuirum for 4HR. mRNA profiles of uninfected (UN) and Salmonella infected (SAL) hnRNP C, F, K, U and SRSF 1, 2, 6, 7, 9 were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the gene expression and transcript expression level with CLC Genomics Workbench. qRT–PCR validation was performed using SYBR Green assays.
Results: We identified thousands of transcripts whose abundance is increased or decreased by SR/hnRNP knockdown in macrophages. We observed that different SR/hnRNPs control the ex-pression of distinct gene regulons in uninfected and Salmonella-infected macrophages, with sev-eral key innate immune genes (Nos2, Mx1, Il1a) relying heavily on multiple SR/hnRNPs to main-tain proper induction and/or repression. Knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for a number of key immune sensors and signaling molecules and many of these splicing changes were distinct in uninfected and Salmonella-infected macrophages. After observ-ing a surprising degree of similarity between the differentially expressed genes (DEGs) and DIUs in hnRNP K and U knockdown macrophages, we found that these cells are better able to restrict vesicular stomatitis virus repli-cation than control cells, supporting a role for these hnRNPs in controlling infection outcomes in macrophages ex vivo. Based on these findings, we conclude that many innate immune genes have evolved to rely on one or more splicing regulatory factors to ensure the proper timing and magnitude of their induction, bolstering a model wherein pre-mRNA splicing is a critical regulatory node in the innate immune response.
Conclusions: SR and hnRNP proteins have profound impacts on the abundance of innate immune transcripts and seem to contribute to macrophage gene expression via distinct mechanisms

overall_design: RAW 264.7 macrophage mRNA profiles of SCR (control) and hnRNP or SR shRNA knockown cells

first: Kelsi

middle: O

last: West

last: Watson


title: Transcriptome profile of M.tb treated/untreated host cells

status: Public on May 16 2021

city: Wuhan

first: Xiaojian

last: Cao

address: No.1095 Jiefang Avenue

department: Department of Rehabilination Medicne

institute: Tongji Hospital

summary: Transcriptome profile of M.tb uninfected or infected 0 d.p.i or 3 d.p.i Raw264.7, bEnd.3, THP1, A549, hBMEC cells

overall_design: Each condition have 2 replicates which make up 12 samples from mouse cells and 18 samples from human cells

first: Weize

last: Xu

first: Xi

first: Gang


title: RNA sequencing of isolated lung endothelial cells from Wildtype (WT) and PRR(Atp6ap2) endothelial cell-specific mutants

status: Public on Jul 07 2021

city: New Orleans

first: Stryder

last: Meadows

state: LA

address: 6400 Freret

department: Cell and Molecular Biology

institute: Tulane University

summary:
Purpose: ATP6AP2 is a single transmembrane protein that has been implicated in regulating various biological process including vascular angiogenesis. However, the exact role of ATP6AP2 during blood vessel development remains largely undefined. Here, we use an inducible endothelial cell (EC)-specific mouse to investigate the role of murine Atp6ap2 gene during both physiological and pathological angiogenesis of the postnatal retina, a well-established model system of angiogenesis. In this study we aimed to Identify what genes are differentially expressed upon loss of PRR(Atp6ap2) in ECs.
Methods: ECs were isolated from lungs of both WT and PRR mutant mice at postnatal day 7 (P7). Total RNA was extracted from isolated lung ECs and quantified using Qubit RNA High Sensitivity Assay Kit. RNA integrity was determined using the Bioanalyzer RNA 6000 Nano assay kit. RNA library construction was performed with the TruSeq RNA Library Prep Kit v2 from Illumina. The resulting mRNA library was quantified using Qubit dsDNA High Sensitivity Assay Kit and verified using the Bioanalyzer DNA1000 assay kit. Verified samples were sequenced using the NextSeq 500/550 High Output Kit v2.5 (150 Cycles) on a Nextseq 550 system. Sequenced reads were aligned to the mouse (mm10) reference genome with RNA-seq alignment tool (version 2.0.1). The aligned reads were used to quantify mRNA expression and determine differentially expressed genes using the RNA-seq Differential Expression tool (version 1.0.1). Both alignment and differential expression analysis were performed using the tools in the BaseSpace Sequence Hub.
Results: We found 1876 differentially expressed genes of which 823 genes were upregulated while 1053 genes were downregulated. Downregulated genes were enriched in biological processes such as angiogenesis, cell migration and extracellular matrix remodelling, while upregulated genes were enriched in DNA and cell cycle regulation.
Conclusions: We identify PRR (ATP6AP2) to play an important role in regulation of the angiogenesis process.

overall_design: Isolated lung ECs mRNA profiles of postnatal day 7 WT and PRR(Atp6ap2) endothelial-cell specific mutant mice.

first: Nehalkumar

last: Patel


title: Genome-wide DNA methylation study in bladder cancer

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

institute: Genomictree

summary: Methylation profiling in Bladder cancer : adjacent normal tissue vs bladder tumor tissue

overall_design: indirect comparison experiment : CRD(common reference DNA) vs tumor-adjacent normal, CRD vs Bladder tumor

first: Sungwhan

last: An

first: TaeJeong

last: Oh

first: Ju

middle: H

last: Shin

first: Jae

last: Lim


title: Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans

status: Public on Apr 30 2021

city: Xiamen

first: Huifen

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

institute: Huaqiao University

summary: Majority of the human genome is transcribed in a form of long non-coding (lnc) RNAs. While these transcripts attracted considerable interest, their molecular mechanisms of function and biological significance remain controversial. Here, we present a genome-wide functional annotation strategy for lncRNAs based on integration of three distinct types of approaches: co-expression analysis, mapping of lncRNA-chromatin interactions and assaying molecular effects of lncRNA knockdowns obtained using an inducible and highly specific CRISPR/Cas13 system. We apply the strategy to annotate 407 vlincRNAs belonging to a novel widespread subclass of lncRNAs. We show that vlincRNAs appear to regulate, positively and negatively and both in trans and cis, multiple genes encoding proteins predominantly involved in RNA- and development-related functions, cell cycle and cellular adhesion via a potential mechanism involving proximity in nucleus. Finally, we show vlincRNAs and their regulatory networks potentially represent novel components of DNA damage response.

overall_design: Regulatory networks for vlincRNAs were established based on co-expression analysis using 64 RNA-seq samples obtained using single-molecule sequencing (SMS, Helicos/SeqLL platform) from total RNA isolated from K562 cells perturbed with various drug treatments.

first: Philipp

last: Kapranov


title: The conserved sex regulator/pioneer factor DMRT1 recruits SOX9 in sexual cell fate reprogramming

status: Public on May 20 2021

city: Minneapolis

first: Micah

last: Gearhart

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

department: Genetics, Cell Biology and Development

summary: Mammalian sexual development commences when fetal bipotential progenitor cells adopt male Sertoli (in XY) or female granulosa (in XX) gonadal cell fates.  Differentiation of these cells involves extensive divergence in chromatin state and gene expression, reflecting distinct roles in sexual differentiation and gametogenesis.  Surprisingly, differentiated gonadal cell fates require active maintenance through postnatal life to prevent sexual transdifferentiation and female cell fate can be reprogrammed by ectopic expression of the sex regulator DMRT1.  Here we examine how DMRT1 reprograms granulosa cells to Sertoli-like cells in vivo and in culture.  We define postnatal granulosa- and Sertoli-biased gene expression programs and identify cell type-biased three-dimensional chromatin contacts and differentially accessible chromatin regions (DARs) associated with differentially expressed genes.  Using a conditional transgene we find DMRT1 only partially reprograms the ovarian transcriptome in the absence of SOX9 and its paralog SOX8, indicating that these factors functionally cooperate with DMRT1.  ATAC-seq and ChIP-seq show that DMRT1 induces formation of many DARs that it binds with SOX9, and DMRT1 is required for binding of SOX9 at most of these sites.  We suggest that DMRT1 can act as a pioneer factor to open chromatin and allow binding of SOX9, which then cooperates with DMRT1 to reprogram sexual cell fate.

overall_design: RNA-seq (78 samples), ChIP-seq (21 samples), ATAC-seq (16 samples) and Hi-C (4 samples) on gonads and purified granulosa and Sertoli cells.

first: David

last: Zarkower


title: Characterizing the invasive tumor front of aggressive uterine adenocarcinoma and leiomyosarcoma

status: Public on Apr 15 2021

city: Seville

first: Juan

last: Diaz-Martin

address: Av Manuel Siurot

institute: IBiS

summary: Invasive tumor front (ITF, the tumor-host interface) is vitally important in malignant cell progression and metastasis. Tumor cell interactions with resident and infiltrating host cells and with the surrounding extracellular matrix and secreted factors ultimately determine the fate of the tumor. Herein we focus on the invasive tumor front, making an in-depth characterization of reticular fiber scaffolding, infiltrating immune cells, gene expression and epigenetic profiles of classified aggressive primary uterine adenocarcinomas (uADC)  and leiomyosarcomas (uLMS).

overall_design: Transcriptomic profiling of invasive tumor front of aggressive primary uterine adenocarcinomas (n=19) and leiomyosarcomas (n=11) using HTG EdgeSeq Precision Immuno-Oncology Panel, which interrogates 1,392 genes involved in tumor/immune interaction.

first: Carmen

last: Salguero-Aranda

first: Enrique

last: de Alava


title: Growth enhancement of obligate anaerobic archaeon, Thermococcus onnurineus NA1 by the addition of oxygen

status: Public on Mar 10 2021

city: Busan

first: LEE

middle: SEONG

last: HYUK

address: Haeyang-ro

department: Department of Marine Biotechnology

institute: Korea Institute of Ocean Science and Technology

summary: Hyperthermophilic archeaon, Thermococcus onnurineus NA1 has known as a strict anaerobe. To date, a few of studies have been reported that strict anaerobe can grow using oxygen. However, the research of the growth enhancement of strict anaerobic archaeon belonging to the order of Thermococcales using the oxygen, in which has never been reported so far. In this study, we showed that the growth of T. onnurineus NA1 strain increased under various oxygen concentrations and we observed that oxygen was decreased in the headspace during the growth of cell. Genome-wide transcriptomic analysis was carried out to evaluate alterations in gene expression induced by O2 and to explain the physiological effects of oxidative stress on the growth of T. onnurineus NA1.

overall_design: RNA expreesion profile of T. onnurineus NA1 genes in the absence or presence of 20 % O2-containing media, using Illumina HiSeq 2500

first: Seong

last: Lee

first: Hyun

first: Sung

last: Kang


title: Soluble Sema4D in plasma as an immune biomarker of non-inflamed head and neck squamous cell carcinoma profile.

status: Public on Mar 09 2021

city: Baltimore

first: Rania

middle: Hassan

last: Younis

state: MD

address: 650 W Batimore St

department: Oncology and Diagnostic Sciences

institute: University of Maryland School of Dentistry

summary: This work demonstrates the potential of soluble Semaphorin 4D (sSema4D) as an immune biomarker in plasma of patients with head and neck squamous cell carcinoma (HNSCC) that can read the histological immune subtype (HIS) and IFN-γ signature of the paired tumor tissue. Advanced analysis of 10 HNSCC tumor tissue using the IO-360 nanoString platform, showed that tumors with high sSema4D in plasma (HsS4D) clustered as negative IFN-γ immune signature and were most of histologically immune Excluded (HIS‐IE). 2/3 of the tumors with low sSema4D (LsSema4D) were IFN-γ positive, and histologically inflamed as scored using Sema4D in the tumor bed.  Advanced custom analysis showed the myeloid immune cell type, Wnt and TGF-beta signaling and hypoxia to predominate in the paired tumor tissue of HsS4D, while the lymphoid compartment and costimulatory signaling was more in the low sSema4D (LsS4D) with high Treg component.

overall_design:
Under an Institutional Review Board (IRB) approved protocol and patient consent at the University of Maryland School of Medicine (UMSOM) (HP-00073603), paired blood samples and whole excision tumor tissues were collected prospectively. Blood was drawn pre-operatively at the day of surgery. 10 samples were used for RNA extraction for nCounter Human Pan Cancer IO-360  nanoString Technology .

Please note that the sample characteristics for the Age, gender and race have been updated on Nov 14, 2022.

first: Vasileios

middle: I

last: Theofilou


title: Downregulation of TGR5 (GPBAR1) in biliary epithelial cells is characteristic of sclerosing cholangitis and may contribute to disease pathogenesis

status: Public on Mar 12 2021

city: Tuebingen

first: Gisela

last: Gabernet

state: BW

address: Auf der Morgenstelle 10

department: University of Tuebingen

institute: Quantitative Biology Center (QBiC)

summary: Primary sclerosing cholangitis (PSC) is characterized by chronic inflammation and progressive fibrosis of the biliary tree. The bile acid receptor TGR5 is found on biliary epithelial cells (BECs), where it promotes secretion, proliferation and tight junction integrity. Thus, we speculated that changes in TGR5 expression in BECs may contribute to PSC pathogenesis.

overall_design: PSC mouse models with genetic background Abcb4-/-, Abcb4-/-/Tgr5Tg and wt mice were generated (N=4 per group). Liver bile ducts enriched on BECs by FACS sorting with EpCAM were isolated. BEC gene expression was analysed by single cell transcriptomics (scRNAseq) from the different mouse models.

first: Verena

last: Keitel

first: Maria

last: Reich

first: Karl-Erich

last: Koehrer

first: Tobias

last: Lautwein

first: Marina

last: Vogel

first: Jan-Philipp

last: Mallm


title: Identification of VIMP/SELS as a gene inhibiting cytokine production in human CD4+ effector T cells

status: Public on Mar 01 2021

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Many players regulating the CD4+ T cell-mediated inflammatory response have already been identified. However, the critical nodes that constitute the regulatory and signaling networks underlying CD4 T cell responses are still missing. Using a correlation-network-guided approach, here we identified VIMP (VCP-interacting membrane protein, also known as SELS), one of the 25 genes encoding selenoproteins in humans, as a gene regulating the effector functions of human CD4 T cells, especially production of several cytokines including IL2 and CSF2. We identified VIMP as an endogenous inhibitor of cytokine production in CD4 effector T cells via both, the E2F5 transcription regulatory pathway and the Ca2+/NFATC2 signaling pathway. Our work not only indicates that VIMP might be a promising therapeutic target for various inflammation-associated diseases, but also shows that our network-guided approach can significantly aid in predicting new functions of the genes of interest.

overall_design: We performed transcriptomic analysis in human primary CD4 Teffs (CD4+CD25- cells). The Teffs were transfected with specific siRNA against VIMP/SELS or the scrambled control siRNA (si_NS) for 1 day followed by 1 day stimulation using Dynabeads Human T-activator CD3/CD28 for T cell expansion and activation (11131D, ThermoFischer Scientific) (for details, see the section 'Protocols'). The Affymetrix human Gene 2.0 ST Arrays were used and analyzed at EMBL Genomics core facilities (Heidelberg. Germany). Array data was processed by Affymetrix Expression Console v1.4 using Exon-level analysis. No technical replicates were performed. But the results were obtained from 3 different healthy donors.

first: Christophe

last: Capelle

first: Ni

last: Zeng

first: Egle

last: Danileviciute

first: Markus

last: Ollert

first: Rudi

last: Balling

middle: Q

last: HeFeng


title: The human brain vasculature at single-cell resolution

status: Public on Apr 24 2021

city: Palo Alto

first: Andrew

last: Yang

address: 3801 Miranda Ave

institute: Stanford University

summary: 10x single-cell RNA-sequencing to profile human cerebrovascular cells in health and disease

overall_design: Single-cell profiling of hippocampus and superior frontal cortex from 25 hippocampus and cortex samples across 17 control and Alzheimer’s disease (AD) patients

middle: C

first: Tony

last: Wyss-Coray


title: Singlet oxygen induced RNA oxidation and translational arrest [RB]

status: Public on Feb 28 2021

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

country: Israel

institute: Weizmann Institute of Science

summary: Effect of various concentrations of RB on gene expression in Arabidopsis

overall_design: Total RNA obtained from 2-week old Arabidopsis seedlings subjected to 0, 10, 100, 400 µM of RB for 2 hours in light (30 µE)

first: Eugene

last: Koh

first: Robert

last: Fluhr


title: Singlet oxygen induced RNA oxidation and translational arrest [CHX]

summary: Effect of various concentrations of CHX on gene expression in Arabidopsis

overall_design: Total RNA obtained from 2-week old Arabidopsis seedlings subjected to 0, 1, 10, 100 µM of CHX for 2 hours in light (30 µE)


title: Singlet oxygen induced RNA oxidation and translational arrest [DCMU]

summary: Effect of various concentrations of DCMU on gene expression in Arabidopsis

overall_design: Total RNA obtained from 2-week old Arabidopsis seedlings subjected to 100 µM of DCMU for 0, 1, 2, 4 hours in light (30 µE)


title: The critical role of chondroitin sulfate proteoglycan interactions with receptor PTPσ in the inhibition of neural repair after stroke

status: Public on Mar 16 2021

city: Cincinnati

first: Lei

middle: Frank

last: Huang

state: Ohio

address: 2600 Clifton Ave

institute: Uiversity of Cincinnati

summary: We used RNAseq to compare transcriptome of peri-infarct cortex in stroke mice that received vehicle or ISP treatment (which blocks the PTPsigma receptor signaling) at 14 days post stroke. The purpose of this project is to identify genes that are differentially expressed in control stroke mice and ISP treated stroke mice that might mediated the behavioral improvement in ISP treated stroke mice.

overall_design: RNA was extracted from peri-infarct cortical region at 14 days post stroke in control or ISP treated mice and subjected to RNAseq.

first: Yu

last: Luo

first: Jerry

last: Silver

first: Frank

first: Zhen

last: You


title: Differential miRNA expression of healthy and inflammatory periodontal ligament stem cells-derived exosomes

status: Public on Apr 01 2021

city: Xi'an

first: zheng

middle: ya

last: wang

address: Changle West Road

institute: The Fourth Military Medical University

summary: To further explore the specific expressed miRNA in healthy and inflammatory periodontal ligament stem cells (PDLSCs)-derived exosomes, we extracted their exosomal RNA for miRNA microarray assay.

overall_design: The culture supernatants of healthy PDLSCs (H-PDLSCs, obtained from healthy periodontal ligament tissue) and inflammatory PDLSCs (P-PDLSCs, obtained from periodontitis periodontal ligament tissue; L-PDLSCs, H-PDLSCs treated with lipopolysaccharide for 7 days) were used for exosomes extraction (H-Exo, P-Exo and L-Exo) by using ultracentrifuge. The supernatants used for exosomes extraction mixed equal amounts of 5 individuals H-PDLSCs or P-PDLSCs culture supernatants and the source of cells used for L-Exo extraction was the same as H-Exo; n=5. P-EXO vs H-EXO; L-EXO vs H-EXO; P-EXO vs L-EXO.

first: Qintao

last: Wang

first: Yazheng


title: A Resource of Gene Expression Data from a Multiethnic Population Cohort of Induced Pluripotent Cell–Derived Cardiomyocytes

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: Induced pluripotent stem cells (iPSCs), upon differentiation into somatic cell types, offer the ability to model the genetic states of tissues in the individuals from whom the iPSCs were derived. A recent study used a multiethnic cohort of healthy individuals to derive iPSCs and iPSC-hepatocytes and perform gene expression and expression quantitative trait locus analyses, identifying causal genes and variants linked to blood lipid levels.2 We sought to use the same cohort of iPSC lines to generate a similar resource with iPSC-cardiomyocytes and make the results available to the community.

overall_design: Mononuclear cells isolated from peripheral blood samples of 91 healthy individuals were used to generate iPSC lines.We differentiated the various cell lines (one per individual) into iPSC-CMs using an established 2-dimensional differentiation protocol. We found that a total of 71 iPSC-CM lines (34 from individuals self-identified as African-Americans and 37 from individuals self-identified as European-Americans; 44 from women, 32 from men) were 80% positive for troponin T staining (AB-8295, abcam) using flow cytometry. We performed next generation RNA-seq analysis on these cell lines and create a transcriptome repository

first: Apoorva

last: Babu

middle: P

first: Wenjian

last: Lv

first: Kiran

last: Musunuru


title: Singlet oxygen induced RNA oxidation and translational arrest [flu mutant]

summary: Effect of various dark incubation times on gene expression in Arabidopsis flu mutant

overall_design: Total RNA obtained from 2-week old flu Arabidopsis seedlings incubated for 0, 4h in the dark before exposure to light (30 µE) for 30min


title: Singlet oxygen induced RNA oxidation and translational arrest

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

overall_design: Refer to individual Series


title: Serpina3 modulates neuronal cell fate determination (scRNA sequencing)

status: Public on Jan 26 2021

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose: To better understand how Serpina3 modulate cortex enpansion and folding. We performed single cell sequencing to reveal the change of cell types in single cell level.
Method: Single cell isolation was prepared from P0 telencephalic tissue of wild-type (WT) and serpina3f/+;Nestin-Cre mice. The fragmented cDNAs containing barcode and UMI sequences was built the library. Agilent 2100 Bioanalyzer was used to quality controlled and quantified. Single cell RNA-sequencing analysis was used by the Illumina platform in Annoroad Genomics.
Results: Clustering and labeling of these cells visualized on a t-SNE plot between the wild-type (WT) and Serpina3f/+;Nestin-Cre mice brain cortex. Specific layer neurons were increased in Serpina3 knock in mice.
Conclusions: Single cell RNA-seq data would provide an overall understanding how SERPINA3 gene contribute to generation of cortical expansion and folding in mice.

overall_design: Single cell isolation of P0 wild type (WT) and SERPINA3f/+;Nestin-Cre mice were generated by deep sequencing, in triplicate, using Illumina.

first: Jinyue

last: Zhao

first: Chao

last: Feng


title: Single nucleus sequencing of SOX2+ glioma stem nuclei from IDH1/TP53-mutant and wild-type glioma samples

status: Public on Jan 12 2021

city: Vladivostok

first: Valeriia

last: Gulaia

address: 10 Ajax Bay

department: School of Biomedicine

country: Russia

institute: Far Eastern Federal University

summary: Understanding the glioma stem cell (GSC) heterogeneity within IDH1 and TP53 mutant tumors may elucidate possible targets for astrocytoma treatment. We performed single-nucleus transcriptomics of 6 mutant and wild-type glioma samples sorted for Sox2 stem cell marker. Malignant states of different clusters were evaluated by the expression of the normal and hematopoietic markers. We found that mutant GSCs were characterized by collagen synthesis and CD44-high phenotype prone to migration, while wild-type GSCs had vulnerability points in ATP synthesis. Additionally, mutant GSCs displayed altered lipogenesis probably attributed to the low NADPH consumed by mutant IDH1. The collagen and lipid biosynthesis represent possible target pathways for prospective tackling GSCs with IDH1 R132H and TP53 point mutations, uncouplers of oxidative phosphorylation are promising to address wild-type GSC proliferation

overall_design: Examination of SOX2+ sorted nuclei in mutant glioma samples (IDH1 R132H and TP53 point mutation) compared to wild type glioma samples (IDH1 and TP53 wild type).

first: Vadim

last: Kumeyko


title: Human serpina3 modulates cortex expansion and folding

status: Public on Jan 23 2021

summary:
Purpose:To gain a deeper insight into how Serpina3 regulates neurogenesis and further controling cortex folding  in mice brain, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by TCF20 deletion at E15.
Methods: Total RNA was extracted from E15 telencephalic tissue of WT and serpina3 cKI  mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately approximately one thousand transcripts showed differential expression between the WT and Serpina3 knock-in brain cortex, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the up-regulated genes were enriched in the terms related to neurogenesis, neuronal specification, neural differentiation and secretion by cells. Up-regulated genes showed a significant enrichment of terms involved in up regulation of hypersensitivity and down regulation of inflammatory response. These results reflected the importance of serpina3 in cortical neurogenesis and cortex folding.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how serpina3 contribute to brain cortical development.

overall_design: serpina3 conditional knock-in mice vs. wild type


title: Differential transcriptomics in sarcoidosis lung and lymph node granulomas with comparisons to pathogen-specific granulomas

status: Public on Dec 09 2020

city: Oro Valley

first: Manuel

middle: Leonardo

last: Gonzalez-Garay

state: Arizona

address: 13560 N Vistoso Reserve

department: Medicine

institute: UA

summary: Rationale: Despite the availability of multi-“omics” strategies, insights into the etiology and pathogenesis of sarcoidosis have been elusive. This is partly due to the lack of reliable preclinical models and a paucity of validated biomarkers. As granulomas are a key feature of sarcoidosis, we speculate that direct genomic interrogation of sarcoid  tissues, may lead to identification of dysregulated gene pathways or biomarker signatures.  Objective: To facilitate the development sarcoidosis genomic biomarkers by gene expression profiling of sarcoidosis granulomas in lung and lymph node tissues (most commonly affected organs) and comparison to infectious granulomas (coccidiodomycosis and tuberculosis).

overall_design:
Transcriptomic profiles of immune-related gene from micro-dissected lungs and mediastinal lymph nodes sarcoidosis granulomas was compared to infectious granulomas. Differentially-expressed genes (DEGs) were profiled, compared among the three granulomatous diseases and analyzed for functional enrichment pathways.

Grant ID: CDA22
Grant title: University of Arizona Career Development
Funding source: The University of Arizona
Grantee: Nancy Casanova

Grant ID: NA
Grant title: Sarcoidosis Mini-grant
Funding source: Foundation for Sarcoidosis Research
Grantee: Nancy Casanova

first: Nancy

last: Casanova

middle: L

first: Belinda

last: Sun

first: Christian

last: Bime

first: Kenneth

last: Knox

first: Elliot

last: Crouser

first: Xiaoguang

first: Nora

last: Sammani

first: Taylor

last: Gregory

first: Bhupinder

last: Natt

first: Sachin

last: Chaudhary

first: Yves

last: Lussier

first: Joe

last: Garcia


title: TOR targets an RNA processing network to regulate facultative heterochromatin, developmental gene expression and cell proliferation

status: Public on Dec 22 2020

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

type: Genome binding/occupancy profiling by genome tiling array


title: TOR targets RNA elimination machinery to govern facultative heterochromatin assembly and mitosis to meiosis developmental switch [RNA-seq]

summary: RNA sequencing in Schizosaccharomyces pombe

overall_design: RNA sequencing of mitotic or meiotic cells

first: Yi

last: Wei

first: Nathan

middle: N

last: Lee

first: David

last: Wheeler

first: Li-Xia

last: Pan

first: Jothy

last: Dhakshnamoorthy

first: Ling-Ling


title: A longitudinal m6A epi-transcriptome profile during porcine development of prenatal skeletal muscles

status: Public on Dec 01 2020

city: shenzhen

first: Xin

middle: xin

last: Zhang

state: china/guangdong

address: No.7 pengfei road Dapend

department: agricultural genomics institute at shenzhen

institute: chinese academy of agricultural science

summary: By comparative epigenomics, our study has revealed the critical role of m6A in prenatal skeletal muscle development.

overall_design: To study the regualtion of m6A for prenatal myogenesis, we profile the 6 stages transcriptome-wide m6A of prenatal skeletal muscle in pig.

first: Fei

last: Gao

first: Xinxin


title: Effects of dermatan sulfate from marine invertebrates in wound healing pathway: a natural resource applied to regenerative therapy

status: Public on Nov 30 2020

city: Rio de Janeiro

first: Vanessa

last: Rizzo

state: Rio de Janeiro

address: Cezar Zama St. 185

department: Biomedical Research Institute

country: Brazil

institute: Marcilio Dias Naval Hospital

summary:
The aim of this study was to identify the biological mechanisms involved in the effects of natural compounds such as heparin analogues obtained from marine invertebrates in wound healing
We performed the obtaining, purifying and chemical characterization of the dermatan sulfate extracted from Styela plicata, an ascidian species. DS was used in wound healing in vitro assay and was analyzed for its effect in the toxicity, proliferation and cellular migration of murine fibroblasts. In addition, a gene expression test was performed to determine which genes responsible for the healing process were being modulated.

overall_design: All experiments was performed in biological triplicates (control group - untreated, and test group - DS treated).

last: Rizzo-Valente

first: Renata

last: da Cruz

first: Rachel

middle: A

last: Santos

first: Lucas

middle: S

last: Silva

first: Mauro

last: Pavão

first: Shana

last: Barroso

first: Daniel

middle: F

last: Schulz

first: Roberta

last: Escaleira

first: Bruno

last: Miranda

first: Daniela

middle: Z

first: Rodrigo

middle: J

last: Guerra


title: ecDNA hubs drive cooperative intermolecular oncogene expression [HiChIP]

status: Public on Nov 25 2020

city: Stanford

first: Howard

middle: Y

last: Chang

state: CA

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

summary: Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.

overall_design: H3K27ac HiChIP of ecDNA-containing cell lines COLO320-DM and SNU16.

first: King

last: Hung

first: Kathryn

middle: E

last: Yost

first: Liangqi

last: Xie

first: Quanming

last: Shi

first: Konstantin

last: Helmsauer

first: Jens

last: Luebeck

first: Robert

last: Schöpflin

first: Joshua

middle: T

last: Lange

first: Rocio

last: Chamorro

first: Natasha

last: Weiser

first: Celine

last: Chen

first: Sihan

last: Wu

first: Siavash

middle: R

last: Dehkordi

first: Connor

middle: V

last: Duffy

first: Katerina

last: Kraft

first: Jun

last: Tang

first: Julia

last: Belk

first: John

last: Rose

first: M

last: Corces

first: Jeffrey

middle: M

last: Granja

first: Rui

last: Li

first: Utkrisht

last: Rajkumar

first: Jordan

last: Friedlein

first: Anindya

last: Bagchi

first: Ansuman

last: Satpathy

last: Tijan

first: Stefan

last: Mundlos

first: Vineet

last: Bafna

first: Anton

middle: G

last: Henssen

first: Paul

last: Mischel

first: Zhe

last: Liu


title: TOR targets a nuclear RNA processing network to support cell proliferation and control developmental gene expression [ChIP-chip]

first: Shiv

last: Grewal

summary:
Occupancy profiling of lysine 9 dimethylated histone H3 in fission yeast.
Occupancy profiling of MYC-tagged or GFP-tagged Pir1 protein in fission yeast.
Occupancy profiling of FLAG-tagged Rec12-DNA linkages during meiosis of fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of K9-dimethylated histones or Pir1 proteins from asynchronous culture of fission yeast.

first: Yi

last: Wei

first: Nathan

last: Lee

first: David

last: Wheeler

first: Li-Xia

last: Pan

first: Jothy

last: Dhakshnamoorthy

first: Ling-Ling

last: Sun

middle: I


title: Novel LncRNA and mRNA expression profiles of peripheral blood mononuclear cells in patients with systemic lupus erythematosus and healthy controls

status: Public on Jan 06 2021

city: HANGZHOU

first: Qi

last: Cheng

state: Zhejiang

address: 88 Jiefang Road

department: rheumatology

institute: the Second Affiliated Hospital of Zhejiang University School of Medicine

summary: The multi-system involvement and high heterogeneity lead to great challenge in the diagnosis and treatment of systemic lupus erythematosus (SLE). Long non-coding RNA is a type of RNA greater than 200 nucleotides that does not encode proteins. LncRNA is a key regulator of gene expression in the immune system and is involved in the pathogenesis of a variety of autoimmune diseases, including SLE. In this work, we performed transcriptome sequencing and microarray analysis of peripheral blood mononuclear cells (PBMC) from freshly isolated healthy controls (n=5) and SLE patients (n=5) to analyze the expression of novel lncRNAs and mRNAsand explore their potential as biomarkers and their correlation with clinical features.

overall_design:
PBMCs were isolated from 5 healthy controls and 5 patients with SLE, and total RNA was extracted for transcriptome sequencing

[Dec-28-2022] The submitter corrected the annotation of GSM4962537-GSM4962541 from healthy controls to SLE patients and of GSM4962542-GSM4962546 from SLE patients to healthy controls.

first: Xiaochan

last: Chen

first: Huaxiang

last: Wu

first: Yan

last: Du


title: ecDNA hubs drive cooperative intermolecular oncogene expression [ChIP]

first: Howard

last: Chang

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) for BRD4 and H3K27ac in COLO320-DM, COLO320-HSR and SNU16 cell lines, with or without JQ1 treatment.

first: King

last: Hung

first: Kathryn

last: Yost

first: Liangqi

last: Xie

first: Quanming

last: Shi

first: Konstantin

last: Helmsauer

first: Jens

last: Luebeck

first: Robert

last: Schöpflin

first: Joshua

last: Lange

first: Rocio

last: Chamorro

first: Natasha

last: Weiser

first: Celine

first: Sihan

first: Siavash

last: Dehkordi

first: Connor

last: Duffy

first: Katerina

last: Kraft

first: Jun

last: Tang

first: Julia

last: Belk

first: John

middle: C

last: Rose

first: M

last: Corces

first: Jeffrey

last: Granja

first: Rui

last: Li

first: Utkrisht

last: Rajkumar

first: Jordan

last: Friedlein

first: Anindya

last: Bagchi

first: Ansuman

last: Satpathy

last: Tijan


title: ecDNA hubs drive cooperative intermolecular oncogene expression [scRNA and scATAC-Seq]

first: Howard

last: Chang

summary: Extrachromsomal DNA (ecDNA) are prevalent in human cancers and are associated with high oncogene expression as well as altered chromatin. Here we show that multiple ecDNAs cluster in the nucleus during interphase to form ecDNA hubs, where oncogene transcription preferentially occurs. Single-cell multiomics, single-molecule sequencing, and 3D enhancer connectome reveal MYC ecDNAs are heterogenous in primary sequence and that ecDNA hubs support ectopic and intermolecular enhancer-promoter interactions. Bromodomain-containing protein 4 (BRD4) extensively occupies ecDNA regulatory elements, and inhibition by JQ1 disperses ecDNA hubs and preferentially reduces ecDNA oncogene transcription. Two amplified oncogenes can intermix in ecDNA hubs, engage in intermolecular enhancer-promoter interactions, and transcription is uniformly sensitive to JQ1. Thus, ecDNA hubs – nuclear bodies of many ecDNAs tethered by proteins – are platforms for cooperative oncogene transcription. The recognition of ecDNA hubs as units of oncogene function and diversification has potentially broad implications for cancer cell evolution and therapy.

overall_design: Single cell multiome ATAC + gene expression profiling of COLO320-DM and COLO320-HSR cell lines.

first: King

middle: L

last: Hung

first: Kathryn

last: Yost

first: Liangqi

last: Xie

last: Wu

first: Joshua

last: Lange

first: Quanming

last: Shi

first: Robert

first: Vineet

last: Bafna

first: Paul

last: Mischel

first: Zhe

last: Liu