title: Expression data from global miR-100 overexpressing mice

status: Public on Feb 27 2021

city: Freiburg

first: Christian

last: Smolka

state: Baden Württemberg

address: Breisacher Strasse 33

department: Department of Cardiology and Angiology I

institute: Heart Center Freiburg University

summary:
Excessive supernutrition can lead to metabolic syndrome, liver steatosis and NAFLD. To find genes involved in metabolic regulation might be helpfull in treating metabolic diseases.
We used microarray analysis to identify possible new targets of microRNA-100 in liver tissue.

overall_design: Liver tissue samples from 6 months old, male, untreated wildtype (4x) and global microRNA-100 overexpressing mice (4x) was used for RNA extraction and hybridization on Affymetrix microarrays.


title: Next-generation sequencing of human snoRNA molecules associated with human cytomegalovirus virus.

status: Public on Mar 05 2021

city: Los Angeles

first: David

last: Strugatsky

state: CA

address: 615 CHARLES E YOUNG DR S

department: MIMG

country: USA

institute: UCLA

type: Non-coding RNA profiling by high throughput sequencing

summary: Using Next-generation sequencing of total RNA isolated from human cytomegalovirus virions we have analyzed host (human) snoRNA molecules.

overall_design: Next-generation sequencing of snoRNA molecules associated with virions of human cytomegalovirus

first: Yun-Tao

last: Liu

first: Wei

first: Z

middle: H

last: Zhou


title: Somatic mutation of the cohesin complex subunit confers therapeutic vulnerabilities in human cancer

status: Public on Feb 22 2021

city: Indianapolis

first: Xiongbin

last: Lu

state: Indiana

address: 980 W. Walnut Street, R3-C218D	MMGE

institute: Indiana University School of Medicine

type: Expression profiling by high throughput sequencing

summary: Synthetic lethality-based strategy has been developed to identify therapeutic targets in cancer harboring tumor suppressor gene mutations, as exemplified by the effectiveness of poly(ADP)-ribose polymerase (PARP) inhibitors in BRCA1/2-mutated tumors. However, many synthetic lethal interactors are less reliable due to the fact that such genes usually do not perform fundamental housekeeping functions in the cell. Here we explore an approach to identify the “essential lethality” arose from these mutated/deleted essential genes, which are largely tolerated in cancer cells due to genetic redundancy. In additional to the known synthetic-lethal interactions, this approach uncovered the cohesion subunit SA1 as a putative synthetic-essential target in cancers carrying inactivating mutations of its paralog, SA2. In SA2-deficient Ewing sarcoma and bladder cancers, further depletion of SA1 profoundly and specifically suppressed cancer cell proliferation, survival and tumorigenic potential. Mechanistically, inhibition of SA1 in the SA2-mutated cells leads to premature chromatid separation and dramatic extension of mitotic duration, which is accompanied by lethal failure of cell division. More importantly, depletion of SA1 renders those SA2-mutated cells not only more susceptible to DNA damage, especially double-strand breaks (DSBs), but also defective in DNA repair. Furthermore, inhibition of SA1 sensitizes the SA2-deficient cancer cells to PARP inhibitors in vitro and in vivo, providing a potential therapeutic strategy for patients with SA2-deficient tumors. This study provides a framework for the discovery of therapeutic targets in cancers that harbor specific essential gene deficiency.

overall_design: Both TC71 and TC32 Ewing sarcoma cell lines were treated with doxycycline to induce SA1 knockdown and then the total RNAs, in triplicate,  were used for RNA-seq. Deep sequence data were mapped, normalized and the differentially expressed genes were collected for pathway analysis. The HRD score was defined by comparing those DEGs with the published HRD signature.

first: Yunhua

first: Hanchen

last: Xu

first: Kevin

last: Van der Jeught

first: Yujing

last: Li

first: Sheng

first: Lu

last: Zhang

first: Yuanzhang

last: Fang

first: Xinna

first: Milan

last: Radovich

first: Bryan

middle: P

last: Schneider

first: Xiaoming

last: He

first: Cheng

last: Huang

first: Chi

first: Jun

last: Wan

first: Guang

last: Ji


title: Thyroid hormone receptor beta is required for thyrotrpin regulation and thyroid hormone production.

status: Public on Feb 20 2021

first: Kailtyn

middle: Yan-Yun

address: 10833 Le Conte Ave

department: Medicine

institute: UCLA/VA

summary: Thyroid hormone receptor beta (THRB) is post-translationally modified by small ubiquitin-like modifier (SUMO). To investigate the biological role of THRB sumoylation, we generated a mouse model with a mutation that disrupts sumoylation at lysine 146 (K146Q). The THRB K146Q mutant mice had normal serum thyroxine (T4), markedly elevated serum thyrotropin (TSH) (81-fold above control), and enlargement of both the pituitary and the thyroid gland. The marked elevation in TSH, despite a normal serum T4 concentration, indicated blunted feedback regulation of TSH. TH profuction was 10-fold lower (per mg of thyroid tissue) in mutant mice compared to Wt mice.

overall_design:
Generated a THRB mutant mouse model that disrupted sumoylation at lysine K146 of THRB. The mutaiton is located in the 2nd zinc finger area. The funcitonal test and sturcture analysis indicated that the K146Q mutation did not alter THRB binding to a consensus DR4-TRE.
Age-matched 3 months old males of wt and TRbK146Q mutant mice were used in the studyies. Thyroid hormone and pituitary thyoroid stimulating hormone (TSH) were analyzed.
The hypothalamus-pituitary-thyroid axis regulation was examined by RNA-seq.
Tissues from 3 mice of each genotype were desected and used in RNA-seq.

first: Kaitlyn

middle: Y

first: Gregory

middle: A

last: Brent


title: Frontal Cortex whole transcriptome sequencing in COVID-19 elderly patients

status: Public on Mar 09 2021

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

summary: SARS-Cov-2 infection is frequently associated with Nervous System (NS) manifestations. However, it is not clear how SARS-CoV-2 can cause neurological dysfunctions and which molecular processes affects. In this work, we examined the frontal cortex tissue of patients who died of COVID-19 for the presence of SARS-CoV-2, comparing qRT-PCR with ddPCR. We also investigated the transcriptomic profile of frontal cortex from COVID-19 patients and matched controls by RNA-seq analysis to characterize the transcriptional signature.

overall_design: Frontal cortex from 9 COVID-19 patients and 7 age- and sex-matched healthy controls (CTRL) were deep-sequenced and included in Real Time PCR experiments.

first: Stella

last: Gagliardi

first: Emanuele

middle: T

last: Poloni

first: Cecilia

last: Pandini

first: Francesca

last: Dragoni

first: Valentina

last: Medici

first: Annalisa

last: Davin

first: Silvia

last: Visonà

first: Matteo

last: Moretti

first: Orietta

last: Pansarasa

first: Antonio

last: Guaita

first: Livio

last: Tronconi

first: Mauro

last: Ceroni

first: Cristina

last: Cereda


title: Expression data for dSTING mutant vs. wild type flies

city: Birmingham

first: Katarina

last: Akhmetova

state: AL

address: 720 20th St S, Kaul 548

institute: University of Alabama at Birmingham

summary:
STING is a protein that plays important role in innate immune response. However, it also has functions not related to immunity. We studied role of STING in fruit fly Drosophila melanogaster. We used microarray to detect gene expression changes in dSTING knockout fruit flies.
We studied role of STING in fruit fly Drosophila melanogaster. To detect gene expression changes in dSTING-knockout flies microarray assay was used.

overall_design: 5-day-old male flies, wild type (w1118) or with the knockout of dSTING gene, fed or 24 hour starved (3 replicates per condition) were analysed for gene expression changes.

first: Adam

middle: C

last: Gower


title: Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast.

status: Public on Feb 19 2021

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

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: A burned-out CD8+ T-cell subset expands in the tumor microenvironment and curbs cancer immunotherapy

status: Public on Feb 23 2021

city: New Haven

first: Miguel

middle: F

last: Sanmamed

state: CT

address: 300 George Street 203A

institute: Yale University

summary: Tumor-infiltrating lymphocytes (TILs) are considered to be exhausted, lacking proliferative and effector functions, which impairs cancer immunity. We employed single-cell mass cytometry and tissue imaging technologies to dissect TILs in 25 resectable and 35 advanced non-small cell lung cancer (NSCLC) patients. We identified a phenotypically burn-out CD8 TIL subset (Ebo), specifically accumulated within the tumor microenvironment (TME). In contrast to exhausted T-cells, Ebo appears to be the most proliferative TIL subset. Furthermore, Ebo showed the highest expression of activation markers, but it was more apoptotic and produced less IFNg than other CD8 TIL subsets. Using a humanized patient-derived tumor xenograft model, we demonstrated that Ebo expansion occurred within the TME in a PD-pathway dependent manner. Importantly, Ebo abundance in baseline tumor tissues was associated with resistance to anti-PD therapy in NSCLC patients. Our study identified a dysfunctional TIL subset, distinct from exhausted T-cells, and implies strategies to overcome resistance in cancer immunotherapy.

overall_design: There are 3 groups, 3 samples in each group, overall 9 samples analyzed

first: Xinxin

last: Nie

first: Dejian

last: Zhao

first: Lieping

last: Chen


title: Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [ChIP-Seq]

summary: RNAse III is an evolutionarily conserved family of endoribonuclease that cleaves dsRNA structures. Here we studied RNAse III homolog Pac1 In fission yeast to shed light on underappreciated roles of Drosha. We found that Pac1 co-transcriptional cleavage of nascent hairpin RNA structures trigger transcriptional termination by creating an entry point for “torpedo” exonucleases – that is, exonuclease that degrade the nascent RNA until they bump into the transcribing polymerases. As such termination pathway decouple termination from pre-mRNA polyadenylation, the nascent transcript are destabilized upon Pac1 cleavage, therefore expending the paradigm of post-transcriptional regulation of gene expression.

overall_design: ChIP assays of Pac1-TAP in wild-type and of of Pol II occupancy (8WG16 antibody) in wild-type and Pac1-Anchor-Away strain.

first: François

last: Bachand


title: A Competing Endogenous RNA Network in Circulating Extracellular Vesicles Reveals Differentially-expressed Functional lncRNA in Human Subjects with Metabolic Syndrome

status: Public on Feb 10 2021

city: Rochester

first: xianfeng

last: chen

state: MN

address: 1216 2nd St SW

department: Biochem & Molecular Biology

institute: Mayo Clinic

summary: The metabolic syndrome (MetS), a collective cluster of disease risk factors that includes dyslipidemia, obesity, inflammation, hypertension, and insulin resistance, affects numerous people worldwide.  Accumulating studies have shown that long-noncoding RNAs (lncRNA) serve as competing endogenous RNA (ceRNA) to play essential roles in regulating gene expression in various diseases. To explore the role of lncRNAs as ceRNAs in MetS, we examined a MetS-associated network in circulating extracellular vesicles (EVs) collected from systemic blood of MetS and control patients (n=5 each). MetS patients showed elevated body-weight, glucose, blood pressure, insulin, liver injury and inflammatory markers levels. In total, 191 differentially-expressed (DE) lncRNAs, 1389 mRNAs, and 138 miRNAs were selected for further analysis. Biological processes and pathway functional enrichment analysis were performed based on the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. LncRNA/mRNA/miRNA ceRNA network was constructed by Cytoscape v3.8 based on the DE-RNAs, and included 13 lncRNAs, 8 miRNAs, and 64 mRNAs. We found that the lncRNA-associated ceRNA network members potentially serve as regulators of central cellular processes and complications of MetS, including cancer. These findings suggest that MetS alters the interactions among the ceRNA network components in circulating EV-specific ceRNA network, and implicate the cargo of circulating EVs in ramifications of MetS.

overall_design: Circulating extracellular vesicles (EVs) collected from systemic blood of metabolic syndrome (MetS) and control patients (n=5 each)

first: Lilach

middle: O

last: Lerman


title: ScRNAseq of human IEL and LPL T lymphocytes

city: Cambrdge

first: Ramya

last: Gamini

state: MA

address: 1 Portland st

institute: Pfizer Inc.,

summary:
We sequenced T cells from 2 control and 2 Crohn's disease patients
We determined that in human Th17 T cells are highly enriched in the IEL compartment
We identified discrete populations of CD8 and CD4 T cells, which are differently represented in IEL and LP

overall_design: The IEL and LP compartments were separately extracted and T cells sorted and sequenced on the 10X genomics platform

first: Natalia

last: Jager

first: Marina

last: Cella

first: Jorge

middle: L

last: Schettini

first: Mattia

last: Bugatti

first: Shanrong

first: Charles

middle: V

last: Rosadini

first: Ekaterina

last: Esaulova

first: Blanda

last: Di Luccia

first: Baylee

last: Kinnet

first: William

last: Vermi

first: Maxim

middle: N

last: Artyomov

first: Thomas

last: Wynn

first: Ramnik

middle: J

last: Xavier

first: Scott

last: Jelinsky

first: Marco

last: Colonna


title: Impact of TNRC6 isoforms on gene expression and splicing

city: DALLAS

first: David

middle: Reid

last: Corey

state: TX

address: 6001 Forest Park Road

department: Pharmacology

institute: UT-Southwestern Medical Center at Dallas

summary: Through the RNA interference (RNAi) pathway, small RNAs can influence translation, splicing, transcriptional activation, and transcriptional repression. RNAi is carried out by the targeting Argonaute (Ago) effector protein and the facilitating TNRC6 (also known as GW182) scaffolding protein. Here, we use a suite of gene knockout cell lines and high-throughput sequencing to gather definitive answers about the TNRC6 paralogs, their roles in the cell, and their relation to Ago knockout cell lines. Each subsequent TNRC6 paralog knockout caused more gene changes and few genes overlapped between the single TNRC6 paralog knockouts. In addition, TNRC6 knockout and Ago knockout cell lines’ gene expression profiles are highly correlated with one another, indicating the important regulatory functions these proteins share. Overall we found that in spite of less than 40% sequence identity, TNRC6 paralogs are functionally redundant and can replace one another for core RNAi functions.

overall_design: Total 24 samples, all standard transcriptome-type RNA-seq

first: Samantha

last: Johnson

first: Yongjun

last: Chu

middle: R


title: Sites for Argonaute Binding within Human Nuclear RNA and their Impact on Alternative Splicing

summary: Mammalian RNA interference (RNAi) is often linked to regulation in the cytoplasm. While synthetic RNAs regulate transcription and splicing, endogenous functions for nuclear RNAi have been obscure. Using enhanced crosslinking immunoprecipitation (eCLIP), we mapped AGO2 binding sites within nuclear RNA. The strongest AGO binding sites mapped to miRNAs. The prevalence of individual miRNAs was similar in the cytoplasm and the nucleus. Most statistically-significant AGO2 binding was within intron boundaries. RNAseq comparing AGO1, AGO2, AGO1/2, and AGO1/2/3 knockout to wild-type cells revealed that binding was associated with both up- and down-regulation of gene expression. We observed changes of splicing at genes with significant AGO binding at exon/intron junctions or within introns. Splicing changes were confirmed by RT-PCR and could be recapitulated by synthetic duplex RNAs that target the sites of AGO binding. Inhibition of miRNA action by addition of an anti-miR reversed miRNA-mediated control of splicing. We conclude: 1) That AGO binding sites occur throughout nuclear RNA but are often within introns; 2) The distribution of miRNAs is similar in the nucleus and cytoplasm; and 3) miRNAs can control gene splicing. Nuclear RNAi has the potential to be a natural regulatory mechanism but careful study will be necessary to identify critical RNA drivers of normal physiology and disease.

overall_design: Total 23 samples, including 15 for standard transcriptome-type RNA-seq and 8 for eCLIP-seq

first: Shinnichi

last: Yakota

first: Jing

last: Liu

first: Audrius

last: Kilikevicius

first: Krystal


title: Induction of gastric cancer by successive oncogenic activation in the corpus

status: Public on Feb 17 2021

city: Singapore

first: Daisuke

last: Douchi

address: 14 Medical Drive

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

summary:
Background & Aims: Metaplasia and dysplasia in the corpus are reportedly derived from dedifferentiation of chief cells. However, the cellular origin of metaplasia and cancer remained uncertain. Therefore, we investigated whether pepsinogen Ctranscript expressing cells (PGC-transcript expressing cells) represent the cellular origin of metaplasia and cancer using a novel Pgc-specific CreERT2 recombinase mouse model.

Methods: We generated a Pgc-mCherry-IRES-CreERT2 (Pgc-CreERT2) knock-in mouse model. Pgc-CreERT2/+ and Rosa-EYFP mice were crossed to generate PgcCreERT2/Rosa-EYFP (Pgc-CreERT2/YFP) mice. Gastric tissues were collected, followed by lineage-tracing experiments, histological and immunofluorescence staining. We further established Pgc-CreERT2;Kras G12D/+ mice and investigated whether PGCtranscript expressing cells are responsible for the precancerous state in gastric glands. To investigate cancer development from PGC-transcript expressing cells with activated Kras, inactivated Apc and Trp53 signaling pathways, we crossed Pgc-CreERT2/+ mice with conditional KrasG12D , Apcflox , Trp53 flox mice.

Results: Expectedly, mCherry mainly labeled chief cells in the Pgc-CreERT2 mice. However, mCherry was also detected throughout the neck cell and isthmal stem/progenitor regions, albeit at lower levels. In the Pgc-CreERT2;Kras G12D/+ mice, PGC-transcript expressing cells with Kras G12D/+ mutation presented pseudopyloric metaplasia. The early induction of proliferation at the isthmus may reflect the ability of isthmal progenitors to react rapidly to Pgc-driven Kras G12D/+ oncogenic mutation. Furthermore, Pgc-CreERT2;KrasG12D/+ ;Apc flox/flox mice presented intramucosal dysplasia/carcinoma, while Pgc-CreERT2;KrasG12D/+ ;Apcflox/flox ;Trp53 flox/flox mice presented invasive and metastatic gastric carcinoma.

Conclusions: The Pgc-CreERT2 knock-in mouse is an invaluable tool to study the effects of successive oncogenic activation in the mouse corpus. Time-course observations can be made regarding the responses of isthmal and chief cells to oncogenic insults. We can observe stomach-specific tumorigenesis from the beginning to metastatic development.

overall_design: RNA expression profile of stomach corpus of PGC;Ras;APC FF mice or Control (Ras;APC FF) mice. Total RNA was extracted from the corpus tissue.  Triplicate samples are shown.

first: Akihiro

last: Yamamura

first: Junichi

last: Matsuo

first: Yi

last: Lim

first: Napat

last: Nuttonmanit

first: Mitsuhiro

last: Shimura

first: Kazuto

last: Suda

first: Sabirah

last: Chen

first: ShuChin

last: Pang

first: Kazuyoshi

last: Kohu

first: Takaya

last: Abe

first: Go

last: Shioi

first: Guowei

last: Kim

first: Asim

last: Shabbir

first: Supriya

last: Srivastava

first: Michiaki

last: Unno

first: Jimmy

middle: B

last: So

first: Ming

last: Teh

first: Khay

middle: G

last: Yeoh

first: Linda

middle: S

last: Chuang

first: Yoshiaki

last: Ito


title: Cotranscriptional RNA cleavage by Drosha homolog Pac1 triggers transcription termination in fission yeast. [RNA-Seq]

first: Carlo

last: Yague-Sanz

overall_design: RNA-seq of Pac1 deficient cells (Pac1-AA or pac1-ts) and of exonuclease mutants.

first: François

last: Bachand


title: Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave

status: Public on Feb 04 2021

city: Irvine

first: Kim

last: Green

address: 3208 Biological Sciences 3

department: Neurobiology and Behavior

institute: University of California, Irvine

summary:
28d Regular Repop Study: Two-month-old male C57BL/6 (Jax 000664) were maintained on control diet for 35 days (control) or treated for 7 days with PLX3397 (600 ppm) diet, then to stimulate repopulation PLX3397 placed with control diet for 28 days (28d Recovery). Mice were sacrificed and myeloid cells were extracted from whole hemispheres. RNA was extracted from single-cell suspensions generated from fluorescence-activated cell sorting (FACS) gating for CD11b+CD45int cells.
SVZ Study: Two-month-old male C57BL/6 (Jax 000664) were maintained on control diet for 19 days (control), treated for 14 days with PLX3397 (600 ppm) diet (microglial elimination), or treated for 14 days with PLX3397 (600 ppm) diet and then placed on control diet for 5 days (5d recovery). Mice were sacrificed and the subventricular zone was micro-dissected for RNA isolation.
28d Alt Repop +/- LPS Study: Two-month-old male C57BL/6 (Jax 000664) were maintained on control diet for 35 days (control) or treated for 14 days with PLX3397 (600 ppm) diet and then placed on control diet for 28 days (28d Recovery). At 6 or 24 hours (hr) prior to sacrifice, lipopolysaccharide (LPS; 0.33 mg/kg body weight) was administered via intraperitoneal injection. Some mice did not receive an LPS injection and serve as controls (0 hr). Mice were sacrificed and myeloid cells were extracted from whole hemispheres. RNA was extracted from single-cell suspensions generated from fluorescence-activated cell sorting (FACS) gating for CD11b+CD45int cells.

overall_design: Temporal repopulation study

first: Lindsay

last: Hohsfield

first: Neelakshi

last: Soni


title: Integrated multi-omics analysis of RB-loss identifies widespread cellular programming and synthetic weaknesses.

status: Public on Feb 15 2021

city: Columbus

first: Wayne

last: Miles

state: OH

address: 460 West 12th Avenue

department: Molecular Genetics

institute: The Ohio State University

summary: To assess how cells adapt to RB-loss, we quantitatively measured transcriptional, changes in diploid non-tumorigenic human cells transiently depleted of RB.

overall_design: Examing transcriptomic changes from pRB depletion via doxycycline

first: Miles

last: Wayne

first: Siddiqui

last: Jalal


title: Colorectal Cancer DNA Methylation

status: Public on Feb 05 2021

first: Darryl

last: Shibata

address: 1441 Eastlake Ave NOR2424

institute: USC Keck School of Medicine

type: Methylation profiling by genome tiling array

summary: Methylation is measured from opposite tumor sides of human colorectal cancers

overall_design: DNA is isolated from hundreds of tumor glands released after EDTA washout

first: Marc

middle: D

last: Ryser


title: Binding site identification for the Epstein-Barr virus transcription factor Zta in epithelial cells

city: Brighton

first: Alison

middle: Jane

last: Sinclair

state: E. Sussex

address: University of Sussex

department: School of Life Sciences

country: United Kingdom

institute: University of Sussex

summary: Epstein-Barr virus (EBV) is present in a state of latency in infected memory B-cells and EBV-associated lymphoid and epithelial cancers. Cell stimulation or differentiation of infected B-cells and epithelial cells induces reactivation to the lytic replication cycle. In each cell type, the EBV transcription and replication factor Zta (BZLF1, EB1) plays a role in mediating the lytic cycle of EBV. Zta is a transcription factor that interacts directly with Zta response elements (ZREs) within viral and cellular genomes. Here we undertake chromatin-precipitation coupled to DNA-sequencing (ChIP-Seq) of Zta-associated DNA from cancer-derived epithelial cells. The analysis identified over 14,000 Zta-binding sites in the cellular genome. We assessed the impact of lytic cycle reactivation on changes in gene expression for a panel of Zta-associated cellular genes. Finally, we compared the Zta-binding sites identified in this study with those previously identified in B-cells and reveal substantial conservation in genes associated with Zta-binding sites.

overall_design: Input and duplicate Zta ChIP Seq


title: Preclinical characterization of antagomiR-218 as a potential treatment for Myotonic Dystrophy

status: Public on Jan 31 2021

city: Burjassot

first: Ruben

last: Artero

state: Valencia

address: C/ Doctor Moliner, 50

department: Genetics

country: Spain

institute: Universidad de Valencia

summary: Myotonic Dystrophy (DM1) is a rare neuromuscular disease caused by the expansion of unstable CTG repeats in a non-coding region of the DMPK gene. CUG expansions in mutant DMPK transcripts fold into hairpins that sequester MBNL1 proteins in ribonuclear foci, depletion of MBNL1 being a chief contribution to disease symptoms such as muscle weakness and atrophy, and myotonia. Thus, the upregulation of endogenous MBNL1 levels may compensate for the sequestration. We have demonstrated that antisense oligonucleotides against miR-218 boost expression of MBNL1 and rescue phenotypes in disease models. Here we provide a preclinical characterization of an antagomiR-218 molecule using the HSALR mouse model and patient-derived myoblasts. In HSALR, antagomiR-218 rescued molecular and functional phenotypes in a dose-dependent manner, showed a good toxicity profile, and lasted some 15 days after a single subcutaneous injection. In muscle tissue, the antagomiR rescued the normal subcellular distribution of Mbnl1 and did not alter the percentage of myonuclei containing CUG foci. In patient-derived cells, antagomiR-218 improved defective fusion and differentiation and rescued up to 34% of the gene expression alterations found in the transcriptome of patient myoblasts. Importantly, miR-218 was found upregulated in DM1 muscle biopsies, which makes this miRNA a relevant therapeutic target.

overall_design: We compare 3 replicas of healthy myoblasts, DM1 myoblasts and DM1 myoblasts treated with antagomiR-218

first: Estefanía

last: Cerro-Herreros

first: Jorge

last: Espinosa-Espinosa

first: Rubén


title: The repressor C protein, Pf4r, controls superinfection of Pseudomonas aeruginosa PAO1 by the Pf4 filamentous phage and regulates host gene expression

first: Muhammad Hafiz

last: Ismail

state: Singapore

address: Nanyang Technological University, 60 Nanyang Drive, SBS-01N-27

institute: Nanyang Technological University / Singapore Centre for Environmental Life Sciences Engineering (SCELSE)

summary: It has been shown that the filamentous phage, Pf4, plays an important role in biofilm development, stress tolerance, genetic variant formation and virulence in Pseudomonas aeruginosa PAO1. These behaviours are linked to the appearance of superinfective phage variants. Here, we have investigated the molecular mechanism of superinfection as well as how the Pf4 phage can control host gene expression to modulate host behaviours. Pf4 exists as a prophage in PAO1 and encodes a homolog of the P2 phage repressor C. Through a combination of molecular techniques, ChIPseq and transcriptomic analyses, we show that repressor C (Pf4r) is the minimal factor for immunity against reinfection by Pf4 possibly through Pf4r binding to its putative promoter region, and that Pf4r also functions as a transcriptional regulator for expression of host genes. A binding motif for Pf4r was also identified. In wild type P. aeruginosa and Pfr4 complemented Pf4 deficient mutant strains, virulence factor related genes including phenazine and type VI secretion system effectors were upregulated, potentially explaining the reduced virulence of Pf4-deficient P. aeruginosa PAO1. X-ray crystal structure analysis shows that Pf4r forms symmetric homo-dimers homologous to the E.coli bacteriophage P2 RepC protein. A mutation associated with the superinfective Pf4r variant, found at the dimer interface, suggests dimer formation may be disrupted, which derepresses phage replication. This is supported by MALS analysis where the Pf4r* protein only shows monomer formation. Collectively, these data suggest the mechanism by which filamentous phages play such an important role in P. aeruginosa biofilm development.

overall_design: For the ChIPseq, we aim to identify the potential regulon and DNA binding motif of Pf4r. For the RNAseq, we examine if Pf4r causes the differential expression of any genes to see if it also regulates other genes in the PAO1 genome.

first: Scott

last: Rice


title: Expression profiling of circular RNA in human tetralogy of

status: Public on Feb 01 2021

city: Shanghai

first: Xinrui

last: Wang

address: 197 Ruijin Rd II

country: China

institute: Rui-Jin Hospital affiliated to Shanghai Jiao Tong University School of Medicine

summary: By the high sensitive cricular RNA microarray, we commpared 13617 circular RNAs abundant in the human TOF heart tissues and health control heart tissues, and the functional role of differentially expressed circular RNAs were analyzed by bioinformatics. The enrichment results indicated that these circular RNAs may involevd in the occurrence and progression process of heart development.

overall_design: TOF heart tisuues and health control heart tissues were used to acquire the circular RNAs expression profiling, and qPCR was performed to confirm the results of circular RNA chip.

first: Hua

last: Cao


title: A global analysis of photoreceptor-mediated transcriptional changes reveals the intricate relationship between central metabolism and DNA repair in the filamentous fungus Trichoderma atroviride

status: Public on Feb 02 2021

city: Irapuato

first: Manuel

last: Villalobos-Escobedo

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: Ingeniera Genetica

country: Mexico

institute: cinvestav

summary: Light provides critical information for the behavior and development of basically all organisms. Filamentous fungi sense blue light through a unique transcription factor complex that activates its targets in a light-dependent manner. In Trichoderma atroviride, the Blr-1 and Blr-2 proteins constitute this complex, which triggers the light-dependent formation of asexual reproduction structures (conidia). Using transcriptomics, we identified the genes regulated by the photoreceptors Blr-1, Blr-2, Cry-1, Cry-DASH, and Envoy. The evaluation of the transcriptional response to blue light of the Δblr-1 and Δblr-2 mutants showed that the BLR proteins have common targets, which indicates that these proteins act as a complex in gene regulation. Nevertheless, the severe alteration in the transcriptional profile of the Δblr-2 strain indicates that Blr-2 provides target specificity to the protein complex, while Blr-1 central role is as a transcriptional activator. The Δenv-1 mutant phenotypic characterization showed that Envoy functions as a growth and conidiation checkpoint, preventing excessive light responses. Similarly, we observed that Cry-1 and Cry-DASH contribute to the typical light-induced conidiation response. In the env-1 mutant, we observed, at the transcriptomic level, a general induction of DNA metabolic processes and strong repression of central metabolism. An analysis of the expression level of DNA repair genes showed that they increase their expression in the absence of Envoy. Photoreactivation experiments showed that Δenv-1 had increased DNA repair capacity, which is consistent with the transcriptomic data. Our results indicate that light perception in T. atroviride is far more complex than originally thought.

overall_design:
Transcriptomes of the wild-type strain and the photoreceptor mutants (Envoy, Cry, Cry-DASH, Blr1 and Blr2) were sequenced. All strains were grown on PDA and pulsed with blue light and as a control the strains were grown in complete darkness. Three biological replications were made for each treatment and sequenced.

*Although we have and present here the Blr2 transcriptomes, the data obtained in this mutant background were not used for the present work.

**On the other hand, the library of Envoy-mutant in darkness condition biological replicate 3 presents a greater variation than the other libraries, so we decided not to include it for the final differential expression analysis.

first: Enrique

last: Pola-Sánchez

first: José

middle: M

first: Pedro

last: Martínez-Hernández

first: Emma

last: Beltrán-Hernández

first: Alfredo

last: Herrera-Estrella


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix

status: Public on Feb 03 2021

city: Grand Rapids

first: Peipei

last: Li

state: MI

address: 333 Bostwick Ave N.E.

department: Center for Neurodegenerative Science

institute: Van Andel Research Institute

type: Methylation profiling by high throughput sequencing

overall_design: Refer to individual Series


title: Transcriptional Signatures Predict Phenotypic Variations of Candida auris

status: Public on Jan 30 2021

city: Vienna

first: Sabrina

last: Jenull

address: Dr. Bohrgasse 9/2

country: Austria

institute: Max Perutz Labs

summary: Transcriptomic analysis of different Candida auris clinical isolates with distinct antifungal susceptibility profiles.

overall_design: RNA-sequencing was performed of the following C. auris clinical isolates: 470140, 4710147, 470154 and CBS10913 provided by Rajendra Prasad and Arunoloke Chakraborti. Cells were grown to the exponential phase in YPD at 37 °C. Cultures were then harvested for RNA isolation. Three biological replicates for each isolate were sequenced.

first: Karl

last: Kuchler

first: Raju

last: Shivarathri

first: Neeraj

last: Chauhan


title: Transcriptional comparison of ptpn2-deficient and competent effector and memory precursor cells in acute HSV infection

city: Melbourne

first: Katharina

last: Hochheiser

state: Victoria

address: 792 Elizabeth Street

department: Department of Microbiology & Immunology

country: Australia

institute: The University of Melbourne

summary: We compared the transcriptional profile of FACS-purified total effector, KLRG1+ effector and KLRG1- effector Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells from spleens of acutely infected mice. As expected, we found a large number of differentially expressed genes (DEG; |log2(fold-change)| >1; false discovery rate <0.05) between KLRG1– and KLRG1+ subsets of both Lck-Cre;Ptpn2fl/fl (712 DEG) and Ptpn2fl/fl (528 DEG) OT-I cells. Furthermore, we found 190 DEGs between total populations of Ptpn2-deficient and control OT-I cells. Considerably fewer genes were differentially expressed between Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells amongst the KLRG1– (93 DEG) and KLRG1+ (59 DEG) subsets. Hierarchical clustering analysis further revealed clustering of KLRG1– cells of both genotypes with total Ptpn2fl/fl OT-I cells, whereas KLRG1+ cells of both genotypes clustered with total Lck-Cre;Ptpn2fl/fl OT-I cells. Gene set enrichment analysis further showed that differential gene profiles between Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells for all subfractions (total, KLRG1+, KLRG1–) were enriched significantly for previously identified effector versus memory CD8+ T cell signature genes. Taken together, these findings indicate that after in vivo priming following HSV infection, Ptpn2 deficiency resulted in the preferential generation of OT-I cells with a transcriptional profile biased towards more terminally differentiated KLRG1+ effector cells with restricted memory potential.

overall_design: mRNA sequencing of FACS-purified total effector, KLRG1+ effector and KLRG1- effector Lck-Cre;Ptpn2fl/fl and Ptpn2fl/fl OT-I cells from spleens of acutely infected mice (day 8 after HSV skin infection).

first: Moshe

last: Olshansky

first: Brendan

last: Russ

first: Stephen

last: Turner

first: Thomas

last: Gebhardt


title: Identification of human tRNA molecules bound to human cytomegalovirus capsid using cryoEM and Next-generation sequencing

city: Los Angeles

first: David

last: Strugatsky

address: 615 CHARLES E YOUNG DR S

institute: UCLA

summary: Using Next-generation sequencing of total RNA isolated from human cytomegalovirus virions we have identified host (human) tRNA molecules.

overall_design: Next-generation sequencing of tRNA molecules associated with capsid of human cytomegalovirus

first: Yun-Tao

last: Liu

first: Wei

first: Z

middle: H

last: Zhou


title: Gene expression changes in gastric and colon cancer cell lines after RHOA knockdown.

city: Shinjukuku, Tokyo

first: Naoki

last: Ikari

address: 8-1 Kawadacho

department: Department of Surgery

country: Japan

institute: Institute of Gastroenterology, Tokyo Women's Medical University

summary:
RHOA is a recurrently mutated gene in diffuse-type gastric cancer, whose molecular influence in gastric cancer has not been well uncovered. We aimed to clarify the contribution of RHOA to pro-oncogenesis to improve the understanding of the role of RHOA as a therapeutic target.
We performed microarray analysis after RHOA knockdown for HGC-27, AGS, CCK-81, and SW948.

overall_design: To investigate the effects of mutant and wild-type RHOA functions, microarray analysis was performed on the following cell lines in which RHOA was knocked down using RNA interference; HGC-27 which harbored wild-type RHOA, AGS which harbored heterozygous RHOA^p.E64del, CCK-81 which harbored trans-compound heterozygous RHOA^p.R5Q and RHOA^p.Y42C, and SW948 which harbored heterozygous RHOA^p.G17E.  The data were normalized to the cells underwent RNA interference using negative control RNA. The experiments were performed twice.

first: Akiko

last: Serizawa

first: Etsuko

last: Tanji

first: Masakazu

last: Yamamoto

first: Toru

last: Furukawa


title: Transcriptional control of CALMODULIN by CAMTA regulates neural excitablity

status: Public on Jan 13 2021

city: Klosterneuburg

first: Thanh

middle: TK

last: Vuong-Brender

address: Am Campus 1

institute: Institute of Science and Technology Austria

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


title: Creatine mediated crosstalk between adipocytes and cancer cells regulates obesity-driven breast cancer

status: Public on Jan 22 2021

city: New York

first: Sarah

last: Ackerman

address: 1230 York Ave

institute: Rockefeller University

summary: Obesity is a major risk factor for adverse outcomes in breast cancer. Maguire, Ackerman et al. reveal Gatm and Acsbg1 as molecular regulators of obesity-driven breast cancer progression. They further show that in obesity creatine is a key metabolite in the crosstalk between adipocytes and breast tumors.

overall_design: Examining 4th mammary subcutaneous adiose tissue in lean and obese mice, near and far from the breast tumor

first: Paul

last: Cohen


title: Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states

status: Public on Jan 21 2021

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

summary: The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generated a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and developed a network-graph approach to examine the atlas at multiple spatial scales. We uncovered highly connected promoter hubs that changed substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merged to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identified widespread state-specific differences in enhancer activity and interactivity that corresponded with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide new, multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.

overall_design: We generated Hi-C (one replicate) and PCHi-C (two replicates) data sets for naïve and primed human pluripotent stem cells (hPSCs). We also generated ChIP-seq data sets in naïve hPSCs including NANOG (two replicates), SOX2 (two replicates) and input (two replicates). We also generated CUT&RUN datasets for H3K4me1 in naive (two replicates) and primed hPSCs (three replicates).

first: Peter

last: Chovanec

first: Amanda

last: Collier

first: Csilla

last: Varnai

first: Christel

first: Claudia

last: Semprich

first: Stefan

last: Schoenfelder

first: Anne

last: Corcoran

last: Rugg-Gunn


title: RIP1 perturbation induces chondrocyte necroptosis and promotes osteoarthritis pathogenesis

city: beijing

first: cheng

last: jin

address: 49 Huayuan Bei Lu

institute: Peking University Third Hospital

summary: Receptor-interacting protein kinase 1 (RIP1)-mediated necroptosis plays a vital role in various diseases, but the involvement of RIP1 and its functional mechanism in osteoarthritis pathogenesis remains largely unknown. To identify molecular targets of RIP1 in chondrocytes, RNA sequencing was performed in chondrocytes treated with adenovirus expressing RIP1 or vector control. We found that 9857 genes were differentially expressed in chondrocytes after RIP1 overexpression. GO analysis indicated that DNA replication, chromosome segregation and regulation of cell cycle process were upregulated, while terms including cartilage development, skeletal system development, extracellular matrix organization, skeletal system morphogenesis, chondrocyte differentiation, collagen fibril organization and limb development were downregulated. Pathway analysis revealed that IL-17 signaling pathway, cell cycle, DNA replication, proteasome, TNF signaling pathway, cellular senescence and p53 signaling pathway were significantly upregulated by RIP1, meanwhile, ECM-receptor interaction, other glycan degradation and glycosaminoglycan degradation were downregulated. These results underscore the importance of RIP1 in OA by perturbing a series of essential events during disease progression such like cell cycle regulation, chondrocyte differentiation, inflammation and ECM remodeling.

overall_design:
chondrocytes treated with adenovirus expressing RIP1 or vector control.

**Please note that both raw and processed data have been replaced on Mar 22, 2021 by the submitter.

first: Jin

last: Cheng

first: Xiaoning

last: Duan

first: Xin

last: Fu

first: Yanfang

last: Jiang

first: Peng

last: Yang

first: Chenxi

last: Cao

first: Qi

last: Li

first: Jiying

last: Zhang

first: Xiaoqing

last: Hu

first: Yingfang

last: Ao


title: PD-1 signaling in intestinal lymphoid tissue inducer cells facilitates gut homeostasis

status: Public on Jan 11 2021

city: Beijing

first: Chao

last: Zhong

address: 38 Xueyuan Rd , Haidian District

department: Institute of Systems Biomedicine

institute: Peking University

summary: PD-1/PD-L1 signaling play inhibiting role in CD4+ effector T cells. Innate lymphoid cells (ILCs) represent the innate counterparts of the CD4+ T helper cells, the role of PD-1/PD-L1 signaling on ILCs is still need more study. We found high PD-1 expression on Lymphoid tissue inducer (LTi) cells by experiment. RNA-sequencing analysis suggests different gene expression feature in the PD-1high and PD-1- LTi cells from Pdcd1hu/+ or Pdcd1hu/- mice. PD-1-expressing LTi are more prominent in cytokine production and Pdcd1 deficit could downregulate LTi cytokine production. In addition, metabolic pathways analysis showed the most dramatic downstream change of PD-1 signaling was from lipid metabolism-related genes. Thus, PD-1/PD-L1 signaling promotes LTi effector function and the mechanism may through regulating lipid metabolism. Meanwhile, the RNA-seq data of LTi cultured in presence or absence of palmitic acid also revealed the regulatory function of fatty acid oxidation on LTi. Meanwhile, the RNA-seq data of LTi cultured in presence or absence of  palmitic acid also revealed the regulatory function of fatty acid oxidation on LTi.

overall_design: We want to identify unique genes expressed by PD-1high LTi  and PD-1- LTi from Pdcd1hu/+ and Pdcd1hu/- mice with RNA-Seq, and to identify gene expression changes between LTi cultured in presence or absence of palmitic acid with RNA-Seq. To further investigate the relationship between activation and metabolism, we conducted sc-RNA-Seq experiment with all ILCs and retained ILC3s (Nkp46+ ILC3 and LTi) for downstream analysis.

first: Di

last: Wu

first: Luni

first: Yimo


title: Transcriptional control of CALMODULIN by CAMTA regulates neural excitablity [RNA-seq]

first: Thanh

last: Vuong-Brender

summary: We profiled different neuronal classes in C. elegans camt-1 mutants and compared it with the control

overall_design: One or more neuronal classes of C. elegans were GFP-abelled at a time. Worms were dissociated. Fluorescent cells were FACS-sorted and RNA libraries were established for sequencing.

first: Sean

last: Flynn

first: Mario

last: de Bono


title: Arabidopsis thaliana cotyledons: ecotype Col-o vs lea13 Ti-DNA line

status: Public on Jan 15 2021

city: Celaya

first: Gerardo

last: Acosta-Garcia

address: Av. García Cubas Pte. # 600, Esquina Av. Tecnológico, Colonia Alfredo V. Bonfil

department: Ingeniería Bioquímica

institute: Instituto Tecnológico de Celaya

summary: Transcriptional profiling of Arabidopsis thaliana cotyledons comparing ecotype Col-0 (Control) with lea13 T-DNA line to elucidate the response mechanism to drought stress conditions that rely on LEA protein function.

overall_design: One-condition experiment, lea13 vs. Col-0. Biological replicates: 1 control, 1 problem, three independently grown and harvested samples were pooled for each condition.

last: Acosta-García

first: Abigael

last: López-Cordova

first: Guillermo

middle: A

last: Silva-Martínez


title: Single-cell sequencing of yolk sac and fetal liver hematopoietic progenitors

city: Paris

first: Laina

last: Freyer

address: 25-28 rue du Dr Roux

department: Developmental and Stem Cell Biology

country: France

institute: Institut Pasteur

summary: Erythro-myeloid progenitors (EMP) and their progeny were labeled with YFP in mouse embryos using genetic fate mapping (constitutive Csf1r-iCre;Rosa26-eYFP or inducible Csf1r-MeriCreMer;Rosa26-eYFP injected at embryonic day E8.5 with 4-hydroxytamoxifen). EMP-derived progenitors (Lin- Kit+ YFP+) were sorted by FACS for single-cell transcriptomic analysis using the MARS-Seq approach. The purpose was to uncover heterogeneity and differentiation trajectories of EMP by comparing their transcriptional status at different developmental timepoints (E9.5, E10.5 and E12.5) and across niches (yolk sac and fetal liver).

overall_design: Single cell mRNA analysis of EMP in Csf1r-iCre;Rosa26-eYFP and Csf1r-MeriCreMer;Rosa26-eYFP mice

first: Elisa

last: Gomez Perdiguero

first: Lorea

last: Iturri

first: Anne

last: Biton


title: Chitin and Biochar in strawberry cultivation

status: Public on Jan 01 2021

city: Ghent

first: Bruno

last: Verstraeten

state: Oost-Vlaanderen

address: Technologiepark 71

institute: Ghent University

summary: Strawberry cultivation is associated with high mineral fertilizer doses and excessive use of chemical plant protection products. Based on previous research, we expected that chitin application to the growing medium will increase the nutrient availability and activate the plant’s systemic defense response, resulting in higher strawberry yields and less disease symptoms. We set up two experiments in which the temporal variability and differences in initial nutrient concentrations of the growing media were taken into account. Chitin induced the plant’s shoot biomass, explained by elevated N concentration in the growing medium and/or the attraction of plant-growth promoting fungal genera towards the plant root, such as Mortierella and Umbelopsis. The over-excessive N concentration and P and K deficiencies in  the chitin treatment led to nutrient disbalances. This may explain the decreased fruit yield and disease resistance of the fruits towards Botrytis cinerea. In contrast, chitin caused a clear defense priming effect of the strawberry leaves, with a strong induction of the jasmonic acid response, resulting in less disease symptoms. Chitin caused positive effects on shoot  growth and disease resistance of the leaves, but caution needs to be taken for nutrient disbalances leading to negative influences on fruit production and disease susceptibly.

overall_design: Strawberry plants were grown and harvested under multiple conditions: grown in peat substrate, mock-inoculated,grown in chitin or biochar-enriched peat substrate, mock-inoculated, grown in peat substrate and B. cinerea inoculated or grown in chitin or biochar-enriched peat substrate and B. cinerea inoculated

first: Caroline

last: De Tender

first: Bart

last: Vandecasteele

first: Sarah

last: Ommeslag

first: Tim

last: De Meyer

first: Jill

last: De Visscher

first: Peter

last: Dawyndt

first: Lieven

last: Clement

first: Tina

last: Kyndt

first: Jane

last: Debode


title: RNAsequencing describing the transcriptional landscape of cancer cells isolated from E0771 tumors from lean or obese animals

last: Ackerman

summary: The goal of this study is to compare the gene expression profiles of cancer cells isolated from tumors arising in lean or obese animals.

overall_design: E0771 Cells expressing mCherry flourescent protein were orthotopically implanted into the mammary fat pad of lean or obese animals. At midpoint (14 days after implantation) or endpoint (21 days after implantation) tumors were dissociated and mcherry positive cancer cells were isolated using FACS. Cancer cells from each tumor were collected and processed.

first: Paul

last: Cohen


title: Retinoic Acid Promotes Endothelial Cell Cycle Early G1 State to Enable Human Hemogenic Endothelial Cell Specification

city: Uppsala

first: Sofia

last: Nordling

address: Dag Hammarskölds väg 20

country: Sweden

institute: Uppsala University

summary: Endothelial cells derived from hESCs were separated into 4 different cell cycle phases via FACS and sequenced (i.e., early G1, late G1, G1/S, S/G2/M)

overall_design: Endothelial cells of different cell cycle phases were sequenced. RNA-seq were performed for 5 replicates per sample.

first: Jingyao

last: Qiu

first: Karen

middle: K

last: Hirschi


title: Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (2: PD_RNASeq)

first: Peipei

last: Li

summary: The gastrointestinal tract may be a site of origin for α-synuclein (α-syn) pathology in idiopathic Parkinson’s disease (PD), and an abundance of aggregated α-syn has recently been demonstrated in both the healthy and PD appendix. However, the molecular changes that enable gut α-syn aggregates to contribute to the development and progression of PD remain unclear. Here, our deep-sequencing of DNA methylation changes at 521 autophagy-lysosomal pathway (ALP) genes in the human appendix and brain in PD and healthy controls indicates a pattern of widespread hypermethylation in the PD appendix that is recapitulated in the PD brain. There is significant overlap in the individual ALP genes affected across the PD appendix and brain, with lysosomal genes specifically downregulated in both regions. Healthy epigenetic aging, which involves a hypermethylation of macroautophagy and selective autophagy genes in the appendix and brain, is disrupted in both areas in PD. In mice, DNA methylation changes at ALP genes induced by chronic gut inflammation are greatly exacerbated by the presence of α-syn pathology. DNA methylation changes at ALP genes induced by α-synucleinopathy are significantly associated with the ALP abnormalities observed in the PD appendix, specifically involving lysosomal genes. Our work, which constitutes an in-depth, unbiased investigation of epigenetic changes in the ALP of the PD gut and brain, identifies the epigenetic misregulation of the ALP, especially a downregulation of lysosomal genes, as a potential culprit for the initiation and spread of α-syn pathology in idiopathic PD.

overall_design: Transcriptomic analysis of the PD and control appendix by RNA-sequencing

first: Juozas

last: Gordevicius

first: Lee

last: Marshall

first: Bryan

last: Killinger

first: Sean

last: Lang

first: Elizabeth

last: Ensink

first: Nathan

last: Kuhn

first: Wei

last: Cui

first: Nazia

last: Maroof

first: Irving

last: Vega

first: Fredric

last: Manfredsson

first: Markus

last: Britschgi

first: Viviane

last: Labrie


title: mRNA expression data in epididymal fat tissues derived from mir342-/- and mir342wt/wt mice

status: Public on Dec 28 2020

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

summary:
mir342-/- and mir342wt/wt C57BL/6J mice were fed with standard diet (STD) and high fat-high sucrose diet (HFHS).
We used microarrays to investigate the mRNA expression profile in the epididymal adipose tissues.

overall_design: mir342-/- and mir342wt/wt C57BL/6J mice were housed in cages and maintained on a 12-hour light-dark cycle. The were fed with STD (NMF; Oriental Yeast) and HFHS chow (D12331; Research Diet, New Brunswick, NJ). The mice were sacrificed at 16 weeks of age and epididymal adipose tissues were used for RNA extraction and applied to GeneChip Mouse Gene 2.0 ST Array.

first: Satoshi

last: Yamaguchi

first: Dongxiao

last: Zhang


title: NGS of sRNA reads in plants

status: Public on Dec 31 2020

city: Madrid

first: Tomas

last: Canto

state: Madrid

address: Ramiro de Maeztu 9

department: Environmental Plant Biology

institute: CSIC

summary: Previous works had found correlation between the association of small RNAs (sRNAs) to Potyvirus HCPro variants in infected plants, and their abilities to suppress silencing.  Moreover, we had shown a preference by HCPro for sRNAs of 21-22 nt with 5´-end adenines, and of viral sequence.  Conformational properties can explain preferences for sRNAs by size and/or 5´-ends, but preference for sRNAs of viral over plant sequence would require their having different accessibilities to the suppressor, or chemical properties.  To investigate this, we expressed suppressor-competent and –deficient HCPro variants by agro-infiltration or from potex- and potyviral vectors and characterized the sRNAs in infiltrated tissues and associated to the purified proteins.  In input infiltrated or virus-infected tissues, methylation levels in selected sRNAs of either T-DNA or plant sequence were assessed, and the former were found significantly less methylated in the presence of suppression-competent HCPro.  In purified preparations of suppression-competent HCPro, sRNAs of non-plant sequence of 21 ntwere selectively enriched in those having 5´-end adenines.  Our data indicate that the ratio of sRNAs of plant vs. non-plant sequence associated to HCPro is influenced by the context in its expression, and suggest that also by a concurrent interference by HCPro on the methylation of newly generated sRNAs of non-plant sequence.

overall_design: 14 different samples analyzed by NGS

first: Francisco

last: del Toro


title: Early removal of senescent cells protects retinal ganglion cells loss in experimental ocular hypertension

status: Public on Dec 01 2020

city: La Jolla

first: Michal

last: Krawczyk

address: 9500 Gilman Dr

department: Ophthalmology

institute: UCSD

summary: Experimental ocular hypertension (IOP) induces senescence of retinal ganglion cells (RGCs) that mimicks events occurring in human glaucoma. An established transgenic p16-3MR mouse model in which the systemic administration of the small molecule ganciclovir (GCV) selectively kills p16INK4a-expressing cells was used to compare  transcriptomes of retinas from IOP and control eyes in GCV-treated and non-treated mice, to investigate how experimental removal of senescent p16INK4a-positive cells impacts retinal cells in conditions resembling glaucoma.

overall_design: All six mice carried the p16-3MR transgene. High IOP was induced in one eye of each of the 6 mice and the other was a normal IOP controls. Three mice were subsequently (the same day) treated with GCV and the other three were mock treated. GCV  injections were repeated daily for a total of three days, at which point the mice were sacrified, retinas were dissected and total RNA was isolated for transcriptomic analyses.

first: Lorena

last: Rocha

first: Qianlan

last: Xu

first: Mary

last: Jabari

first: Dorota

last: Skowronska-Krawczyk


title: Tracheal aspirate RNA sequencing identifies distinct immunological features of COVID-19 ARDS

status: Public on Dec 18 2020

city: San Francisco

first: Aartik

last: Sarma

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: We compared differential gene expression in tracheal aspirates collected mechanically ventilated subjects with COVID-19 ARDS to gene expression in tracheal aspirates from: 1)  subjects with ARDS from other casues and 2) mechanically ventilated controls without evidence of pulmonary disease.

overall_design:
RNASeq from tracheal aspirates in COVID-ARDS compared to Other-ARDS and controls.

*** Raw data submission disallowed by submitter's IRB ***

first: Chaz

last: Langelier

first: Carolyn

last: Calfee


title: Cell-Type-Specific Transcriptome of CD4+, CD8+ T cells and CD14+ monocytes in multiple sclerosis

first: Sergio

middle: E

last: Baranzini

address: 675 Nelson Rising LN, STE 240

department: Neurology

institute: UCSF

summary: Multiple sclerosis (MS) is an autoimmune disease of the central nervous system in which both genetic and environmental factors are thought to be involved. Genome-wide association studies revealed more than 200 risk loci, most of which harbor genes primarily expressed in immune cells. However, whether genetic differences are translated into cell-specific gene expression profiles and to what extent these are altered in MS are not well understood. To assess cell-type-specific gene expression in a large cohort of MS patients, we sequenced the whole transcriptome of sorted T cells (CD4+ and CD8+) and CD14+ monocytes from treatment-naive MS patients (n=122) and healthy subjects (n=22). Next, we performed a comprehensive analysis of the RNA sequencing dataset and identified 612 differentially expressed genes (DEGs) in CD14+ monocytes, 464 in CD4+ T cells, and 93 in CD8+ T cells. Notably, about one third (36.6%) of DEGs were non-coding RNAs, the majority of which (88.2%) were down-regulated in MS. We identified large co-expressed gene modules and cis-eQTLs with key MS genes in each cell subset. Importantly, we discovered dysregulation of NAE1, a subunit of NEDD8 activating enzyme (NAE), in CD4+ T cells which activates the neddylation pathway. Finally, we demonstrated that NAE inhibition using Pevonedistat (MLN4924) dampened disease severity in murine experimental autoimmune encephalomyelitis (EAE). Our findings provide novel insights into MS-associated gene regulation unraveling neddylation as a crucial pathway in MS pathogenesis with implications for the development of tailored disease-modifying agents.

overall_design: Whole transcriptome profile of sorted CD4+ T cells, CD8+ T cells, and CD14+ monocytes in treatment naïve MS patients (n=122) and healthy controls (n=22)

first: Kicheol

last: Kim


title: Poly(A) RNA sequencing of Silencing Defective 2 (SDE2) depletion in HeLa cells via siRNA

city: Boston

first: Adam

last: Labadorf

address: 72 East Concord Street E301

institute: Boston University Medical School

summary: Pre-mRNA splicing is a complex and dynamic process that relies on the intricate coordination between a multitude of cis-elements and trans-acting factors. Here, we identify and characterize Silencing Defective 2 (SDE2) as a human RNA binding protein and trans-acting splicing-associated factor required for efficient mRNA processing. In this study, we use Poly(A) purified RNA sequencing to identify the alternative splicing profile in Hela cells following depletion of SDE2 via siRNA. Our data demonstrate that SDE2 depletion causes widespread changes in alternative splicing (AS), with increased intron retention being the most common event. These retained introns are significantly shorter, have a higher GC content, and overall maintain weaker 5' and 3' splice sites than other introns throughout the genome. Following the depletion of SDE2, increased intron retention causes catastrophic consequences for the cell, including defects in mitotic progression, global loss of protein translation, and ultimately, complete loss of cellular viability.  Taken together, we define SDE2 as a previously uncharacterized RNA binding protein that functions to regulate pre-mRNA splicing and ensure cellular viability.

overall_design: Nine total samples are analyzed, three biological replicates from three separate conditions (Mock transfection, siSDE2-1 siRNA, siSDE2-2 siRNA).

first: Rachel

middle: L

last: Flynn

first: Anqi

last: Dai

first: Jess

last: Floro


title: AIB1 dependent transcriptome in endocrine resistance

status: Public on Dec 30 2020

city: Dublin

first: Leonie

last: Young

state: Dublin

address: York House, York Street,, Dublin 2

country: Ireland

institute: Royal College of Surgeons in Ireland

summary:
Purpose:   AIB1 expression is associated with disease progression in aromastase inhibitor (AI) treated patients in breast cancer. In order to identify genes aberrantly regulated by AIB1 in AI resistance, RNA-seq was carried out in endocrine resistant LetR cells and endocrine sensitive MCF7 cells +/- AIB1 under estrogen deprivation.
Methods:  RNA-seq was carried out in biological triplicate in MCF7 and LetR cells comparing NT  (Scramble siRNA) cells versus cells depleted of AIB1 using a SMARTpool ON-TARGETplus  siRNA. RNA was extracted using Qiagen RNeasy Kit and subjected to 100bp PE sequencing  using the BGISEQ 500 platform. Briefly, clean reads were mapped to reference genome  using Bowtie2 and gene expression was calculated with RSEM. Differentially  expressed genes (DEGs) were detected with DEseq2. With the KEGG pathway analysis,  the pathway functional enrichment was performed using phyper, a function of R.
Results:  61 AIB1 differentially regulated genes were identified as unique to endocrine resistant tumor cells (logfc≥1.5; Padj≤0.05).MSigDB Oncogenic signature analysis of the 61 AIB1-regulated genes revealed enrichment in growth promoting endocrine resistance pathways including LTE2, RAF, ERBB2 and MEK.
Conclusion: In the endocrine resistant setting, aberrant AIB1 expression regulates the expression of genes associated with growth factor signalling.

first: Damir

last: Varešlija


title: Gene expression across 4 and 24 hours of growth modulating paradigms in chicks

status: Public on Nov 16 2020

city: Canberra

first: Regan

last: Ashby

state: ACT

address: University Drive, Bruce

department: Faculty of Science and Technology

institute: University of Canberra

summary: Using RNA-Seq, mRNA from 54 retinae were sequenced from male chicks in which myopia development was inhibited by one of five growth inhibitory treatments.

overall_design: Examination of mRNA levels in 54 retina samples across two timepoints (4 and 24 hours) and seven conditions (untreated, FDM, FDM and Atropine, FDM and Pirenzepine, FDM and ADTN, FDM and TPMPA, and Recovery from FDM).

first: Cindy

last: Karouta

first: Robert

last: Kucharski

first: Kristine

last: Hardy

first: Kate

last: Thomson

first: Ian

last: Morgan

first: Ryszard

last: Maleszka


title: Single-cell RNA sequencing (scRNA-seq) on Treg cells from PBS and STAg treated mice

city: Shanghai

first: Zikai

last: Zhou

state: Shanghai

address: 600 Wan Ping Nan Road

department: Research Center

institute: Shanghai Mental Health Center

summary: To identify cell composition and characterize transcriptional regulation in regulatory T (Treg) cells derived from mice subjected to soluble tachyzoite antigen (STAg) of Toxoplasma gondii treatment, we prepared splenic CD4+CD25+ Treg cells from PBS and STAg treated mice, and performed scRNA-seq using the 10× Genomics method.

overall_design: Using the 10× Genomics to analyze single-cell transcriptome in 2 types of Tregs pooled from PBS and STAg treated mice.

first: Xiaoyun

last: Zhang


title: Next Generation Sequencing Facilitates Quantitative Analysis of dermal Transcriptomes of Imiquimod (IMQ)-Induced Psoriasis-Like Dermatitis Treated by Xiao-Yin-Fang (XYF) Therapy

status: Public on Nov 13 2020

first: Xilin

address: No. 1278#, Baode Rd, Jingan District

department: Dermatology

institute: Shanghai Skin Disease Hospital

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare dermal transcriptomes of control group (wild-type IMQ-untreated C57/BL6 mice), model group (wild-type IMQ-treated C57/BL6 mice) and XYF group (model group mice treated by XYF).
Methods: Dermal mRNA profiles of control group, model group and XYF group mice were generated by deep sequencing. Total RNA samples were prepared from intact dermal ear sheets of mouse ear skin from two mice. Double-strand cDNA was generated from equal amounts of total RNA by following TruSeq8 RNA Library Prep Kit v2 (#RS-122-2001/2002, Illumina). The cDNA libraries were sequenced using Illumina Hi-seq2500. STAR software was utilized for sequence alignment between the preprocessing sequence and reference genome sequence of mice downloaded from the Ensembl database(Mus_musculus.GRCm38.90,ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/ Mus_musculus.GRCm38.90.chr.gtf.gz). Transcript assembly of mRNA sequencing data was performed by StringTie software. The expression levels for each of the genes were normalized to FPKM (fragments per kilobase of transcript per million fragments mapped). DESeq 2 was applied to conduct the analysis of differentially expressed genes (DEG). The cutoffs of DEG method were determined as the P value < = 0.05, the FDR value < = 0.05 and the Fold Change (FC) value > = 2.
Results: Heatmap analysis of differentially expressed genes (DEG) revealed distinct transcriptomes between different groups, which displayed a partial reversal of pathological gene-expressing modifications by the treatment of XYF. Detailed comparison identified shared DEGs of opposite deviations between control group versus model group and model group versus XYF group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis uncovered the dermis from disease-model group was greatly disturbed in cytokine-cytokine receptor interaction, chemokine signaling pathways, IL-17 signaling pathway, TNF signaling pathway, Wnt signaling pathway and PI3K-Akt signaling pathway. As for XYF therapy, several metabolic pathways, Calcium signaling, cAMP signaling pathway and cGMP-PKG signaling pathway were affected within the dermis. Further Gene Set Enrichment Analysis (GSEA) exposed multiple metabolic pathways, which involved ether lipid metabolism, alpha linolenic acid metabolism, arachidonic acid metabolism, linoleic acid metabolism, glycerophospholipid metabolism, glycosaminoglycan biosynthesis heparan sulfate, along with VEGF signaling and cell cycle were considerably suppressed in the dermal tissue when given XYF.
Conclusions: XYF might regulate various inflammatory signaling, metabolic processes and microvascular formation to influence γδT cell biology.

overall_design: Dermal Transcriptomes of IMQ-Induced Psoriasis-Like Dermatitis Treated by XYF Therapy

first: Xiaorui

last: Li


title: Exploring with transcriptomic approaches the underlying mechanisms of essential oils-based phytogenic in the small intestine and liver of pigs

status: Public on Jan 08 2021

city: Tulln

first: Bertrand

last: Grenier

address: Technopark 1

institute: BIOMIN

summary:
Purpose:  The study aims the evaluation by RNA-Seq of the anti-oxidant properties of PFA on ileum and liver of pigs. At day 28, for both tissues, 6 biological replicates per groups
Method : Ileum & liver mRNA profile of 28-day-old pigs were generated by NextSeq sequencing (2*75, 30 Mio per strand). Sequenced reads were trimmed by bbmap, aligned by STAR on the SusScrofa 11.1 reference genome. Quantification was performed by HTSeq-count. RT-qPCR validation was performed using TaqMan and SYBR green assays.
Results: In the ileum, the gene set enrichment analysis showed that the activity of several immune pathways (NF-kB, interferon α/β, antimicrobial peptide, collagen pathways) was reduced in piglets fed PFA compared to the control piglets. In the liver, the addition of OO induced strong effects on the transcriptome, and most likely accounted for the significant growth impairment. The likelihood ratio test across the four diets revealed a global response driven by the oxidative stress challenge with hundreds of genes associated with fatty acid β-oxidation and peroxisome in the liver. The expression levels of those genes in the piglets fed OO+PFA were much less affected by the challenge.
Conclusions : The effects seen at day 28 suggest that substances in the PFA formulation provide anti-inflammatory and -oxidant properties.

overall_design: Ileum & liver mRNA from 28 day old pigs. For each tissue, 6 biological replicates (= 6 pigs) per groups (Control, Phytogenics Feed Additive, Oxidized Oil, Phytogenics Feed Additive+Oxidized Oil).

first: Jérémy

last: Le Coz

first: Suzana

last: Ilic

first: Silvia

last: Fibi-Smetana

first: Gerd

last: Schatzmayr

first: Mathias

last: Zaunschirm

first: Betrand


title: A Budding Yeast Model for Human Disease Mutations in the EXOSC2   Cap Subunit of the RNA Exosome

status: Public on Dec 14 2020

city: Atlanta

first: Anita

last: Corbett

state: Georgia

address: 1510 Clifton Road

department: Biology

institute: Emory University

summary: RNA exosomopathies, a growing family of tissue-specific diseases, are linked to missense mutations in genes encoding the structural subunits of the conserved 10-subunit exoribonuclease complex, the RNA exosome. Such mutations in the cap subunit gene EXOSC2 cause the novel syndrome SHRF (Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies). In contrast, exosomopathy mutations in the cap subunit gene EXOSC3 cause pontocerebellar hypoplasia type 1b (PCH1b). Though having strikingly different disease pathologies, EXOSC2 and EXOSC3 exosomopathy mutations result in amino acid substitutions in similar, conserved domains of the cap subunits, suggesting that these exosomopathy mutations have distinct consequences for RNA exosome function. We generated the first in vivo model of the SHRF pathogenic amino acid substitutions using budding yeast by introducing the EXOSC2 mutations in the orthologous S. cerevisiae gene RRP4. The resulting rrp4 mutant cells have defects in cell growth and RNA exosome function. We detect significant transcriptomic changes in both coding and non-coding RNAs in the rrp4 variant, rrp4-G226D, which models EXOSC2 p.Gly198Asp. Comparing this rrp4-G226D mutant to the previously studied S. cerevisiae model of EXOSC3 PCH1b mutation, rrp40-W195R, reveals that these mutants have disparate effects on certain RNA targets, providing the first evidence for different mechanistic consequences of these exosomopathy mutations. Congruently, we detect specific negative genetic interactions between RNA exosome cofactor mutants and rrp4-G226D but not rrp40-W195R. These data provide insight into how SHRF mutations could alter the function of the RNA exosome and allow the first direct comparison of exosomopathy mutations that cause distinct pathologies.

overall_design: RNA-seq analysis of biological triplicates of rrp4-G226D yeast cells and RRP4 yeast cells

first: Maria

middle: C

last: Sterrett

first: Liz

last: Enyenihi

first: Sara

middle: W

last: Leung

first: Laurie

last: Hess

first: Sarah

last: Strassler

first: Daniela

last: Farchi

first: Richard

last: Lee

first: Elise

last: Withers

first: Isaac

last: Kremsky

last: Baker

first: Munira

last: Basrai

first: Ambro

last: van Hoof

first: Milo

last: Fasken


title: Single-cell sequencing of glioblastoma reveals central nervous system susceptibility to SARS-CoV-2

status: Public on Nov 12 2020

city: Hefei

first: Bingshan

last: Wu

state: Anhui

address: 218 Jixi Road

department: Department of Neurosurgery

institute: First Affiliated Hospital of Anhui Medical University

summary:
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the recent global COVID-19 outbreak, which led to a public health emergency. Entry of SARS-CoV-2 into human cells is dependent on the SARS-CoV receptor, angiotensin converting enzyme 2 (ACE2) receptor, and cathepsin. Cathepsin degrades the spike protein (S protein), which results in the entry of viral nucleic acid into the human host cell.
Methods: We explored the susceptibility of the central nervous system (CNS) to SARS-CoV-2 infection using single-cell transcriptome analysis of glioblastoma.
Results: The results showed that ACE2 expression is relatively high in endothelial cells (ECs), bone marrow mesenchymal stem cells (BMSCs), and neural precursor cells (NPCs). Cathepsin B (Cat B) and cathepsin (Cat L) were also strongly expressed in various cell clusters within the glioblastoma microenvironment. Immunofluorescence staining of glioma and normal brain tissue chips further confirmed that ACE2 expression co-localized with CD31, CD73, and nestin, which confirmed the susceptibility to SARS-CoV-2 of nervous system cells, including ECs, BMSCs and NPCs, from clinical specimens.
Conclusions: These findings reveal the mechanism of SARS-CoV-2 neural invasion and suggest that special attention should be paid to SARS-CoV-2-infected patients with neural symptoms, especially those who suffered a glioma.

overall_design:
Four GBM tissue specimens and their adjacent brain tissues (as described in the metadata_readme.txt)
Transcriptome and SampleTag information of single cells was obtained through BD Rhapsody System. Sample tag 01, 03, 05, 07 was GBM tissues and Sample tag 02, 04, 06, 08 was their adjacent brain tissues respectively. Single cells obtained from eight samples was loaded on two BD Cartridge. Sample tag 01-04 on Cartridge 106 and Sample tag 05-08 on Cartridge 108. Cartridge 106 got two package: * JZsc106*.fastq.gz and * JZsc107*.fastq.gz; while Cartridge 108 got two package: * JZsc108*.fastq.gz and * JZsc109*.fastq.gz. 106 and 108 are single-cell expression matrix. 107 and 109 are tag sequencing data (SampleTag library).  Therefore, each sample records represent mixed tissue sample. Raw sequencing reads of cDNA library and SampleTag library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline. * R1.fastq.gz represents quality-filtered R1 reads and * R2.fastq.gz represents the quality-filtered R2 reads.

first: Xingliang

last: Dai


title: Novel role of miR-18a-5p and Galanin in rat lung ischemia-reperfusion mediated response

status: Public on Nov 19 2020

first: Kun

last: Xiao

address: 28 Fuxing Road, Haidian District

institute: CHINESE PLA GENERAL HOSPITAL

summary: Lung ischemia-reperfusion (IR) is known to occur after lung transplantation or cardiac bypass. IR leads to tissue inflammation and damage, is also associated with increased morbidity and mortality. Various receptors are known to partake in activation of innate immune system, but the downstream mechanism of tissue damage and inflammation is yet unknown. MicroRNAs (miRNA) are in the forefront in regulating ischemia reperfusion injury and are involved in inflammatory response. Here, we have identified by high throughput approach and evaluated distinct set of miRNAs that may play a role in response to IR in rat lung tissue. Top three differentially expressed miRNAs were validated through quantitative PCRs in the IR rat lung model and an in vitro model of IR of hypoxia and reoxygenation exposed type II alveolar cells. Among the miRNAs, miR-18a-5p showed consistent downregulation in both the model systems on IR. Cellular and molecular analysis brought to light a crucial role of this miRNA in ischemia reperfusion. MiR-18a-5p plays a role in IR mediated apoptosis, ROS production and regulates the expression of neuropeptide Galanin. It also influences the nuclear localization of transcription factor: Nuclear factor-erythroid 2 related factor (Nrf2) which in turn may regulate the expression of miR-18a gene. Thus, we have not only established a rat model for lung IR and enumerate the important miRNAs involved in IR but have also extensively characterized the role of miR-18a-5p in the same. This study will have important clinical and therapeutic implications for and during transplantation procedures.

overall_design: The lung tissue of rats in sham operation group and lung ischemia-reperfusion group were conducted, using miRNA sequencing to find some differential expression in miRNA and target genes.

first: Lei

last: Song

first: Ye

last: Hu

first: Wanxue

last: He

first: Fei

last: Hou

first: Peng

last: Yan

first: Jianqiao

last: Xu

first: Kaifei

last: Wang

first: Yi

last: Tao

first: Dan

last: Li

first: Lixin

last: Xie


title: Expression levels of HLA-DRB and HLA-DQ are associated with MHC Class II haplotypes in healthy individuals and rheumatoid arthritis patients

status: Public on Dec 22 2020

city: Solna

first: Leonid

last: Padyukov

address: Visionsgatan 18

department: Division of Rheumatology, Department of Medicine

institute: Karolinska Institutet

summary: HLA-DRB1 alleles have been associated with several autoimmune diseases. In anti-citrullinated protein antibody positive rheumatoid arthritis (ACPA-positive RA), HLA-DRB1 shared epitope (SE) alleles are the major genetic risk factors. In order to investigate whether expression of different alleles of major histocompatibility complex (MHC) Class II genes influence functions of immune cells, we investigated transcriptomic profiles of a variety of immune cells from healthy individuals carrying different HLA-DRB1 alleles. Sequencing libraries from peripheral blood mononuclear cells, CD4+ T cells, CD8+ T cells, and CD14+ monocytes of 32 genetically pre-selected healthy female individuals were generated, sequenced and reads were aligned to the standard reference. For the MHC region, reads were mapped to available MHC reference haplotypes and AltHapAlignR was used to estimate gene expression. Using this method, HLA-DRB and HLA-DQ were found to be differentially expressed in different immune cells of healthy individuals as well as in whole blood samples of RA patients carrying HLA-DRB1 SE-positive versus SE-negative alleles. In contrast, no genes outside the MHC region were differentially expressed between individuals carrying HLA-DRB1 SE-positive and SE-negative alleles. Existing methods for HLA-DR allele-specific protein expression were evaluated but were not mature enough to provide appropriate complementary information at the protein level. Altogether, our findings suggest that immune effects associated with different allelic forms of HLA-DR and HLA-DQ may be associated not only with differences in the structure of these proteins, but also with differences in their expression levels.

overall_design: RNA expression profiling in peripheral blood mononuclear cells, CD4+ T cells, CD8+ T cells, and CD14+ monocytes of healthy individuals with pre-selected HLA-DRB1 types.

first: Miranda

last: Houtman


title: N6-methyladenosine modification in chronic stress response due to social hierarchy positioning of mice

status: Public on Nov 11 2020

city: Mainz

first: Hristo

last: Todorov

address: Hanns-Dieter Hüsch-Weg 15

department: Institute of Human Genetics

country: Germany

institute: Johannes Gutenberg University Mainz

summary: Appropriately responding to stressful events is important for maintaining health and well-being of an organism. With respect to social stress, the response is not always as straightforward as reacting to physical stressors, e.g. extreme heat, and thus has to be balanced subtly. Particularly, regulatory mechanisms contributing to gaining resilience in the face of mild social stress are not fully deciphered yet. We employed an intrinsic social hierarchy stress paradigm in mice of both sex to identify key factors for coping strategies. While global transcriptomic changes could not be observed in male mice, several genes which were previously reported to be involved in synaptic plasticity, learning and anxiety-like behavior were differentially regulated in female mice. Moreover, changes in N6-methyladenosine-modification of mRNA associated with corticosterone level occurred. Further investigation of proteins involved in m6A modification revealed that no significant changes of amount or activity could be detected for male mice. However, METTL3 and WTAP, subunits of the methyltransferase complex, showed elevated levels in female mice. N6-adenosyl-methylation is the most prominent type of mRNA methylation and plays a crucial role in processes such as metabolism, but also response to physical stress. Our findings underpin its important role by attributing it also to social stress evoked by hierarchy building within same-sex groups.

overall_design:
Comparison of brain right hemisphere transcriptomic profile of dominant and submissive male and female mice.

Please note that the processed data columns correspond to the samples as below:
um_endres_2018_01_01_1394-D2_S1 = Dominant male 1
um_endres_2018_01_03_1395-D2_S3 = Dominant male 2
um_endres_2018_01_05_1396-D1_S5 = Dominant male 3
um_endres_2018_01_07_1397-D2_S7 = Dominant male 4
um_endres_2018_01_09_1398-D1_S9 = Dominant male 5
um_endres_2018_01_11_1399-D1_S11 = Dominant male 6
um_endres_2018_01_13_1400-D3_S13 = Dominant male 7
um_endres_2018_01_02_1394-S3_S2 = Submissive male 1
um_endres_2018_01_04_1395-S4_S4 = Submissive male 2
um_endres_2018_01_06_1396-S2_S6 = Submissive male 3
um_endres_2018_01_08_1397-S4_S8 = Submissive male 4
um_endres_2018_01_10_1398-S2_S10 = Submissive male 5
um_endres_2018_01_12_1399-S2_S12 = Submissive male 6
um_endres_2018_01_14_1400-S1_S14 = Submissive male 7
jgu_gerber_2018_01_07_01279-3_dominant_S7 = Dominant female 1
jgu_gerber_2018_01_10_01280-2_dominant_S10 = Dominant female 2
jgu_gerber_2018_01_11_Gr1-4_dominant_S11 = Dominant female 3
jgu_gerber_2018_01_13_Gr2-4_dominant_S13 = Dominant female 4
jgu_gerber_2018_01_08_01279-4_submissive_S8 = Submissive female 1
jgu_gerber_2018_01_09_01280-1_submissive_S9 = Submissive female 2
jgu_gerber_2018_01_12_Gr1-3_submissive_S12 = Submissive female 3
jgu_gerber_2018_01_14_Gr2-2_submissive_S14 = Submissive female 4

first: Malena

last: dos Santos Guilherme

first: Theodora

last: Tsoutsouli

first: Sina

last: Teifel

first: Susanne

last: Gerber

first: Kristina

last: Endres


title: Memory CD8+ T cells mediate early pathogen-specific protection through localized delivery of antigen-dependent chemokines and IFNgamma to clusters of inflammatory monocytes

status: Public on Oct 29 2020

city: Bronx

first: gregoire

last: lauvau

state: New York

address: 1300 morris park avenue

department: microbiology and immunology

institute: AECOM

summary: While cognate antigen-driven clonal expansion is a cardinal feature of memory CD8+ T cell effective response, inflammatory cytokines also orchestrates their rapid activation and production of IFNᵧ, contributing to innate mechanisms of protection. Despite antigen-independent secretion, IFNᵧ accounts for a large part of antigen-dependent protection in a multitude of infections, yet how cognate antigen enables memory CD8+ T cell-derived IFNᵧ to achieve host protection remains unknown. Herein, using distinct models of immunization, we establish that cognate antigen (Ag) recognition by memory CD8+ T cells on conventional CD11chi dendritic cells initiates their coordinated production of a burst of chemokines (CCL3, CCL4, XCL1) under the transcriptional control of IRF4. Using intravital microscopy imaging, we further reveal that memory CD8+ T cells undergo Ag-mediated arrest in splenic red pulp clusters of CCR2+ monocytes to deliver them with IFNᵧ- and Ag-dependent chemokine-potentiating microbicidal activities. These results establish that effective memory CD8+ T cell responses require coordinated stepwise processes that quickly restrict pathogen growth and optimize the local delivery of effector molecules before clonal expansion occurs.

overall_design: We adoptively transferred 2,000 naive OT-I  (ova-specific) and 50,000 gBT-I (HSV2-specific) CD8+ T cells to mice subsequently immunized with 10,000 Listeria monocytogenes expressing the Ova and the gB antigen (Lm-Ova-gB). 6 weeks later, mice were challenged or not with 100,000 Lm-Ova. Spleens were harvested 8 hrs post challenge and OT-I and gBT-I memory cells were enriched by negative selection (dynabeads) and 1,000 OT-I and 1,000 gBT-I were flow-sorted (Aria III) into lysis buffer before proceeding to first strand cDNA synthesis and amplification, and library (Illumina) preparation for sequencing (RNA-seq).

first: Marie

last: Boutet

first: Fabien

last: Delahaye

first: Gregoire

last: Lauvau


title: mRNA profiles of tumor infiltrating macrophage and monocyte derived from C3 wild-type and knock-out mice, subjected to sarcoma transplantable model

status: Public on Nov 24 2020

city: Pieve Emanuele

first: sarah

middle: natalia

last: mapelli

state: Milan

address: Via Rita Levi Montalcini 4

department: Experimental Immunopathology

institute: Humanitas research

summary: Complement has emerged as a component of tumor promoting inflammation. We conducted a systematic assessment of the role of complement activation and effector pathways in sarcomas. C3-/-, MBL1/2-/- and C4-/- mice showed reduced susceptibility to 3-methylcholanthrene sarcomagenesis and transplanted sarcomas, whereas C1q and factor B deficiency had marginal effects. Complement 3a receptor (C3aR), but not C5aR1 and C5aR2, deficiency mirrored the phenotype of C3-/- mice. C3 and C3aR deficiency were associated with reduced accumulation and functional skewing of tumor-associated macrophages, increased T cell activation and response to anti-PD-1 therapy. Transcriptional profiling of sarcoma infiltrating macrophages and monocytes revealed the enrichment of MHC II-dependent antigen presentation pathway in C3-deficient cells. In patients, C3aR expression correlated with a macrophage population signature and C3 deficiency-associated signatures predicted better clinical outcome. These results suggest that the lectin pathway and C3a/C3aR axis are key components of complement and macrophage-mediated sarcoma promotion and immunosuppression.

overall_design: C3 wild-type and C3 knock-out mice were injected with mycoplasma-free MN/MCA1 cells (0.5 milion/100 µl PBS sc into the right flank). Tumors were collected 21 days after tumor cell injection and washed once with physiologic solution. Single-cell suspension were obtained by mechanical and enzymatic dissociation in 0.1 mg/ml Type IV Collagenase for 1h at +37°C. Monocytes (CD45+, CD11b+, Ly6G-, CD11c-, F4/80-, Ly6C+) and macrophages (CD45+, CD11b+, Ly6G-, CD11c-, Ly6C-, F4/80+) were sorted on a FACSAria cell sorter. RNA was purified from cells with the Single Cell RNA Purification Kit and sequenced with Illumina NextSeq 500.

first: Elena

last: Magrini

first: Sarah Natalia

last: Mapelli

first: Cecilia

last: Garlanda


title: Next Generation Sequencing Facilitates Quantitative Analysis of Epidermal Transcriptomes of Imiquimod (IMQ)-Induced Psoriasis-Like Dermatitis Treated by Xiao-Yin-Fang (XYF) Therapy

status: Public on Nov 10 2020

first: Xilin

last: Zhang

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare epidermal transcriptomes of control group (wild-type IMQ-untreated C57/BL6 mice), model group (wild-type IMQ-treated C57/BL6 mice) and XYF group (model group mice treated by XYF).
Methods: Epidermal mRNA profiles of control group, model group and XYF group mice were generated by deep sequencing. Total RNA samples were prepared from intact epidermal ear sheets of mouse ear skin from two mice. Double-strand cDNA was generated from equal amounts of total RNA by following TruSeq8 RNA Library Prep Kit v2 (#RS-122-2001/2002, Illumina). The cDNA libraries were sequenced using Illumina Hi-seq2500. STAR software was utilized for sequence alignment between the preprocessing sequence and reference genome sequence of mice downloaded from the Ensembl database(Mus_musculus.GRCm38.90,ftp://ftp.ensembl.org/pub/release-90/gtf/mus_musculus/ Mus_musculus.GRCm38.90.chr.gtf.gz). Transcript assembly of mRNA sequencing data was performed by StringTie software. The expression levels for each of the genes were normalized to FPKM (fragments per kilobase of transcript per million fragments mapped). DESeq 2 was applied to conduct the analysis of differentially expressed genes (DEG). The cutoffs of DEG method were determined as the P value < = 0.05, the FDR value < = 0.05 and the Fold Change (FC) value > = 2.
Results: Heatmap analysis of differentially expressed genes (DEG) revealed distinct transcriptomes between different groups, which displayed a partial reversal of pathological gene-expressing modifications by the treatment of XYF. Detailed comparison identified shared DEGs of opposite deviations between control group versus model group and model group versus XYF group. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis uncovered the epidermis from disease-model group was highly enriched in multiple inflammatory signaling, involving cytokine-cytokine receptor interaction, PI3K-Akt signaling pathway, IL-17 signaling pathway and cGMP-PKG signaling pathway. As for XYF therapy, PI3K-Akt signaling pathway, Calcium signaling, Hippo signaling pathway and cGMP-PKG signaling pathway were modulated in the epidermis. Further Gene Set Enrichment Analysis (GSEA) exposed downregulations in focal adhesion, ECM receptor interaction, TGF-β signaling pathway and glyoxylate and dicarboxylate metabolism in XYF-treated psoriasis-like epidermis.
Conclusions: XYF might regulate various inflammatory signaling, metabolic processes and microvascular formation to influence γδT cell biology.

overall_design: Epidermal Transcriptomes of IMQ-Induced Psoriasis-Like Dermatitis Treated by XYF Therapy

first: Xiaorui

last: Li


title: KLF10 deficiency in CD4+ T cells triggers obesity and insulin resistance

status: Public on Nov 06 2020

first: Stefan

last: Haemmig

state: MA

address: 77 Avenue Louis Pasteur, NRB-742

department: Medicine

institute: Brigham and Women Hospital / Harvard Medical School

summary: Gene expression profiling of CD4+ T regs from WT and CD4-KLF10-KO mice on a high-fat diet.

overall_design: CD4+ T regs were isolated from spleens of WT and CD4-KLF10-KO mice on a high-fat diet using T reg magnetic bead isolation kit.

first: Mark

last: Feinberg

first: AKM

last: Wara


title: RNA sequencing of Medicago seed tissues under optimal and heat stress conditions

status: Public on Nov 03 2020

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

institute: INRAE

summary: We analysed transcriptome changes between seed devlopement (4 stages corresponding at before (S1) and after (S2) desiccation tolerance acquisition and before (S3) and after (S4) longevity acquisition) in dissected seed tissues (embryo, E; Endosperm Eo and Seed Coat SC)

overall_design: Three replicates of at least 50 dissected embryos at four developmental stages. Two replicates of at least 50 dissected endosperm at 4 developmental stages and dissected seed coat at 2 developmental stages (S1 & S2)

first: Jerome

last: Verdier

first: Zhijuan

last: Chen

first: Benoit

last: LyVu


title: E14 MGE

status: Public on Oct 22 2020

first: Corey

last: Harwell

state: CA

address: 35 Medical Center way

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: Genome wide analysis of mRNA expression and polysome profiling in DDX3 knockdown SAS cells

status: Public on Nov 05 2020

city: Taipei

first: Hung-Hsi

address: N223, IBMS, No. 128, Sec. 2, Academia Rd.

country: Taiwan

institute: Academia Sinica

summary: By analyzing the RNAseq and RIBOseq results, we identified potential pathways for DDX3 to remodel tumor microenviroment.

overall_design: Examination of RNAseq and RIBOseq in control or DDX3-depleted SAS cells

first: Hung-His

first: Sim-Lin

last: Lim

first: Woan-Yuh

last: Tarn


title: ChIP-Seq of PRDM16 binding sites in E14 MGE

summary: Identification of genome-wide PRDM16 binding sites in the medial ganglionic eminence of E14 mice

overall_design: Whole MGE lysates were used in ChIP-seq experiments to identify PRDM16 binding sites (2 replicates)

first: Miguel

last: Turrero Garcia

first: Jose

last: Baizabal


title: Altered gene expression by hsa_circ_0000839 in papillary thyroid cancer cells

city: Shenyang

first: Jiahui

last: Guo

address: No. 155 Nanjing Bei Street

institute: The First Hospital of China Medical University

summary: The expression level of hsa_circ_0000839 was downregulated in papillary thyroid cancer. However, its functions were still unclear. To explore the functions of hsa_circ_0000839, we analyzed the gene expression in TPC1 cells with or without hsa_circ_0000839 silencing.

overall_design: The mRNA profile of TPC1-si-circ_0000839 and TPC1-NC (negative control)  cells were generated by RNA-sequencing

first: J

first: T

last: Liu

first: W

last: Teng


title: Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade

status: Public on Oct 28 2020

first: Cloud

middle: Peter

last: Paweletz

address: 360 Longwood Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: We report results of transcriptional profiling of ex vivo MC38 murine organotypic tumor spheroids following programmed death-1 (PD-1) blockade compared to isotype control IgG treatment by bulk and single-cell RNA-sequencing after 6 days of treatment. Additionally, we report results from single-cell RNA-sequencing of MC38 tumors treated in vivo with PD-1 blockade versus isotype control IgG to validate ex vivo workflow.

overall_design: Transcriptional profiling of residual MC38 tumor cells after PD-1 blockade

first: Kartik

last: Sehgal

first: Andrew

last: Portell

first: Elena

last: Ivanova

first: Patrick

last: Lizotte

first: Juan

last: Miret

last: Pawaletz

first: David

last: Barbie


title: Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces

status: Public on Nov 30 2020

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

type:
Other
Third-party reanalysis

summary: Discovering the interaction mechanism and location of RNA binding proteins (RBPs) on RNA is critical for understanding gene expression regulation. Here, we apply selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) on in vivo transcripts to identify transcriptome-wide footprints (fSHAPE) on RNA when compared to protein-absent transcripts. Structural analyses indicate that fSHAPE precisely detects nucleotides whose base moieties hydrogen bond with protein and that fSHAPE patterns can predict binding sites of RBPs of interest. To illustrate, we demonstrate that fSHAPE correctly identifies known and novel iron response protein RNA elements. Furthermore, we enable selective interrogation of RNA-protein complexes by integrating SHAPE and fSHAPE with crosslinking and immunoprecipitation (eCLIP) of desired RBPs. To demonstrate, histone stem loop elements and their nucleotides that hydrogen bond with stem-loop binding protein were identified by SHAPE-eCLIP and fSHAPE-eCLIP. Together, these technologies greatly expand on strategies for understanding specific cellular RNA interactions in RNA-protein complexes.

overall_design:
Footprinting and SHAPE structure probing of human cells was performed in conjunction with enhanced crosslinking and immunoprecipitation in order to interrogate cellular RNA-protein complexes in a targeted manner. fSHAPE was performed on multiple human cell lines and identifies hydrogen bonds that occur between RNA base moieties and interacting protein residues. fSHAPE-eCLIP was performed on K562 cells with immunoprecipitation for stem loop binding protein (SLBP) and both identifies SLBP transcript binding sites as well as bases that hydrogen bond with protein. SHAPE-eCLIP was performed on K562 cells with immunoprecipitation for SLBP and identifies SLBP transcript binding sites as well as returning RNA structure probing information in these sites.

in vivo click (ic)SHAPE structure probing, performed in parallel with fSHAPE,  produces base pairing probailities (i.e. "reactivities") at each nucleotide across transcripts.

Please note that
[1] each processed data was generated from multiple samples/replicates as indicated in the corresponding sample description field.
[2] the 293T_vitro_icSHAPE.tar.gz files were generated from re-analyzing the samples GSM2075714-GSM2075717. The 293T_vivo_icSHAPE.tar.gz files were generated from re-analyzing the samples GSM2075714-GSM2075715, GSM2075718-GSM2075719 (in GSE74353; third-party re-analysis).
[3] the 293tmaps.tar.gz files were generated from re-analyzing the samples GSM2075716-GSM2075719 (in GSE74353; third-party re-analysis).

first: Meredith

last: Corley

first: Ryan

last: Flynn

first: Byron

last: Lee

first: Steven

last: Blue

first: Howard

middle: Y

last: Chang