title: Chd7-KO transcriptomic analysis

status: Public on Oct 31 2019

city: MONTREAL

first: ERIC

last: SAMARUT

state: QC

address: 900 St DENIS

department: NEUROSCIENCES

institute: CRCHUM

summary: Mutations in the chromatin remodeller CHD7 cause CHARGE syndrome (CS). Importantly, children with CS exhibit moderate to severe neurological and behaviour symptoms including autism. However, the neural substrates underlying these symptoms remain largely unknown. Here we show that zebrafish chd7 mutant display a nighttime hyperactivity behavioural phenotype and exhibit altered number and positioning of GABAergic neurons in brain regions. Using a transcriptomic approach, we identified many genes involved in cell adhesion, migration and receptor signalling that are dysregulated in the chd7 brain. We also show an abnomal hyperactivation of ERK signalling contributing to the GABAergic defects. A phenotype-based screen of 3850 compounds identifies a lead compound, ephedrine that ameliorates GABAergic and behavioural anomalies in chd7 animals. Our study identifies CHD7 as critical regulator of GABAergic network development. Importantly, we provide novel insight into the mechanisms underlying the neurological deficits in CS and identify a new therapeutic for CS-associated neurobehavioural symptoms.

overall_design: 5 dpf dissected larval brains

first: Eric

last: Samarut

first: Kessen

last: Patten


title: Targeted microarray analysis of two symbiotic cyanobacterial diazotroph strains in the western tropical North Atlantic

city: Stockholm

first: Marcus

last: Stenegren

address: Svante Arrhenius vag 20A

department: Ecology Environment and Plant Sciences

country: Sweden

institute: Stockholm University

summary: We designed a new specific mRNA microarray targeting a subset of genes (956) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways, specifically nitrogen fixation and how they possibly differed between the closely related strains based on environment and host association. In this study we focused on the RintRC01 and RintHH01. To better understand how the gene expression of nitrogen fixation genes relates to nitrogen fixation rates both gene expression and rate measurements were done in parallell.

platform_organism:
Calothrix rhizosoleniae
Richelia intracellularis

overall_design: In total 7 samples from 2 stations were collected during daytime, and in 2 depth profiles (2-36 m). The microarray was designed with one probe for each target gene, which some had cross-hybridization with a cultured and closely related strain. Therefore, the final number of probes included in the study decreased to 750. An updated Agilent microarray design, without cross-hybridization, has been applied elsewhere (ID: Agilent-085960). The microarray was printed with a total of 15 probe replicates.

first: Rachel

middle: A

last: Foster

first: David

last: Brodin


title: DNA Adenine Methyltransferase Identification (DamID) Coupled to Next Generation Sequencing For Profiling Lamina Associated Domains

status: Public on Nov 01 2019

city: Baltimore

first: Karen

last: Reddy

state: MD

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

country: USA

institute: Johns Hopkins University

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: To compare the interaction of various proteins (in particular Lap2b and Lamin A) at the nuclear periphery with the Lamina Associated Domains (LADs)
Results:  Using an optimized data analysis workflow (LADetector, available at https://github.com/thereddylab/LADetector), We found near identical sequences within the genome-wide maps indicating that LAP2β and Lamin A, and hence LaminB1, are in close proximity to all LADs, suggesting that these proteins are not involved in discriminating subsets of LADs.

overall_design: LAD profiles, of MEFs, corresponding to various proteins at the nuclear periphery (LMNA, Lap2b) were generated following the DamID protocol (L.Guelen et al, Nature 2008), library randomization and sequencing preparation using Illumina Paired End Sequencing Kit and sequenced on the Illumina HiSeq 2000.

middle: L

first: Xianrong

last: Wong


title: Targeted microarray analysis of three symbiotic cyanobacterial diazotroph strains in the South China Sea

summary: We designed a new specific mRNA microarray targeting a subset of genes (748) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways and how they possibly differed between the closely related strains based on environment and host association. To better understand how the different environments might affect gene expressions, the samples were taken in depth profiles, at night and day, during a cruise in the South China Sea.

overall_design: In total 21 samples from 9 stations were collected, where 9 was from the surface (<  5m). Moreover, 12 of the samples were collected during the night. The microarray was designed with one thoroughly cross-hybridization tested probe for each target gene, and printed with a total of 18 probe replicates.


title: Expression data from mouse macrophages after being cultured on different surfaces

city: Shenzhen

first: ANG

last: GAO

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

country: China

institute: Shenzhen Institutes of Advanced Technology,Chinese Academy of Sciences

summary:
The adverse macrophage-mediated immune response elicited by the bioinert surface of polyetheretherketone (PEEK) is responsible for the formation of fibrous encapsulation and inferior osseointegration for PEEK implants in the dental and orthopedic fields. A nanoporous thin film constructed by layer-by-layer technique was deposited on PEEK surface, and it can effectively suppress the acute inflammatory response of macrophages. However, the underlying molecular mechanism why macrophages respond differently on the modified surface is unknown.
We used microarrays to elucidate the underlying molecular mechanisms why macrophages respond differently on the modified surface of PEEK.

overall_design: The murine-derived macrophage cell line RAW264.7 was used as the model cells. Cells were seeded on pristine PEEK surface (Control) and modified PEEK surface (Sample) in triplicate and cultured for 3 days. Then the RNA of these cells were extracted and hybridized on Affymetrix microarrays.

first: Yueyang

last: Xie

first: Yanwei

last: Bian


title: Proliferation-correlated expression

city: Beijing

first: Zhisheng

last: Jiang

state: Beijing

address: No.5 Yiheyuan Road

department: Center for Quantitative Biology, Peking-Tsinghua Center for Life Sciences

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: To determine how gene expression varies between fast and slow proliferating cells we developed a CFSE-based method to sort cells by intrapopulation heterogeneity in proliferation rate. We sorted cells by proliferation rate, as well as by the mitochondria dye TMRE, and performed mRNA-seq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Sort high and low CFSE subpopulations

first: Lucas

middle: B

last: Carey

first: Bernhard

last: Payer

first: Andreas

middle: F

last: Meyerhans

first: Javier

last: Vesga

first: Serena

last: Generoso

first: Marta

last: Graset


title: Gene expression data from LRRK2-WT and LRRK2-G2019S astrocytes

city: Suwon

first: jeehoon

last: lee

state: Gyoungido

address: San5, Woncheondong

department: Pharmacology

country: South Korea

institute: Ajou university, School of Medicine

summary:
LRRK2-G2019S (LRRK2-GS), a pathogenic mutation in the PD-associated gene LRRK2, promote ER stress-induced cell death by reducing transcriptional activity of X-box-binding protein 1 (XBP1), a key transcription factor of the UPR.
We used microarrays to detail the programme of gene expression and identified distinct classes of up-regulated or down-regulated genes during ER stress.

overall_design: LRRK2-WT and -GS astrocytes were treated with tunicamycin, and then RNA were extrated and hybridized on Affymetrix GeneChip® Mouse 2.0 ST Arrays.

first: Jeehoon

last: Lee

first: Ilo

last: jou


title: DNA methylation in airway epithelial cells isloated by pronase and bronchial brush from individuals with and without asthma

city: nottingham

first: Rachel

last: Clifford

address: Biodiscovery Institute 3

country: United Kingdom

institute: University of Nottingham

type: Methylation profiling by genome tiling array

summary: The airway epithelium forms the interface between the inhaled environment and the lung. The airway epithelium is dysfunctional in asthma and epigenetic mechanisms are considered a contributory factor. We hypothesised that the DNA methylation profiles of cultured primary airway epithelial cells (AECs) would differ between cells isolated from individuals with asthma (n=17) versus those without asthma (n=16). AECs were isolated from patients by two different isolation techniques; pronase digestion (9 non-asthmatic, 8 asthmatic) and bronchial brushings (7 non-asthmatic and 9 asthmatic). DNA methylation was assessed using an Illumina Infinium HumanMethylation450 BeadChip array. DNA methylation of AECs clustered by isolation technique and linear regression identified 111 CpG sites differentially methylated between isolation techniques in healthy individuals. As a consequence, the effect of asthmatic status on DNA methylation was assessed within AEC samples isolated using the same technique.  In pronase isolated AECs, 15 DNA regions were differentially methylated between asthmatics and non-asthmatics. In bronchial brush isolated AECs, 849 differentially methylated DNA regions were identified with no overlap to pronase regions. In conclusion, regardless of cell isolation technique, differential DNA methylation was associated with asthmatic status in AECs, providing further evidence for aberrant DNA methylation as a signature of epithelial dysfunction in asthma.

overall_design: asthma vs no asthma using two different isolation techniques


title: Active and repressed chromatin domains exhibit distinct nucleosome segregation during DNA replication

city: new york

first: Danny

last: Reinberg

state: new york

address: 522 first avenue

department: Biochemistry

institute: NYU school of Medicine

summary: Chromatin domains and their associated structures must be faithfully inherited through cellular division to maintain cellular identity. Yet, accessing the localized strategies preserving chromatin domain inheritance, specifically the transfer of parental, pre-existing nucleosomes with their associated post-translational modifications (PTMs) during DNA replication is challenging in living cells. We devised an inducible, proximity-dependent labeling system to irreversibly mark replication-dependent H3.1 and H3.2 histone-containing nucleosomes at single desired loci in mouse embryonic stem cells such that their fate after DNA replication could be followed. Strikingly, repressed chromatin domains are preserved through the local re-deposition of parental nucleosomes. In contrast, nucleosomes decorating active chromatin domains do not exhibit such preservation. Notably, altering cell fate leads to an adjustment in the positional inheritance of parental nucleosomes that reflects the corresponding changes in chromatin structure. These findings point to important mechanisms that contribute to parental nucleosome segregation to preserve cellular identity.

overall_design: A method that permanently labels histones at chosen loci revealed that nucleosomes from repressed (but not active) chromatin domains are re-deposited locally after DNA replication.

first: Thelma

middle: M

last: Escobar

first: Ozgur

last: Oksuz

first: Ricardo

last: Saldaña-Meyer

first: Nicolas

last: Descostes

first: Roberto

last: Bonasio


title: Transcriptional profiling of a laboratory and clinical Mycobacterium tuberculosis strain in the presence of the drug Delamanid

city: Paris

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: In this study, the transcriptional response of two Mycobacterium tuberculosis strains to a pressure of the recently approved delamanid is investigated. RNA sequencing revealed that the response to this bicyclic nitroimidazole shows many similarities with the anti-tuberculous drug from the same class pretomanid. Although delamanid is found to inhibit cell wall synthesis, the expression of genes involved in this process were only mildly affected. In contrast, a clear parallel was found with components that affect aerobic respiration. This demonstrates that respiratory poisoning plays a fundamental role in the bactericidal effect of delamanid. Remarkably, the most highly induced genes comprise poorly characterized genes for which functional characterization might hint to the target molecule(s) of delamanid and its exact mode of action.

overall_design: To investigate the transcriptional response of MTB to exposure of delamanid, triplicates of a laboratory (H37Rv) and a DLM susceptible clinical (ITM-04-1195) MTB strain were spiked with a bactericidal concentration of delamanid or its solvent DMSO, and sampled after 6h and  24h of incubation. Total RNA was extracted, RNA sequencing and differential expression analyses were performed.

first: An

last: Van den Bossche

first: Hugo

last: Varet

first: Odile

last: Sismeiro

first: Jean-Yves

last: Coppee

first: Vanessa

last: Mathys

first: Pieter-Jan

last: Ceyssens


title: Gene expression in Human Bronchial Epithelial Cells under Differing Oxygen Regimes

city: Oklahoma City

first: david

middle: c

last: hutchings

state: OK

address: 6500 S MacArthur Blvd

department: CAMI

institute: FAA

summary:
Bronchial epithelial cells line the small airways bronchii and small airways of the lungs, acting to trap and remove contaminants deposited in the lung through the process of inhalation.  These cells are sensitive decreased oxygen concentrations, and are invoved in local signaling in hypoxic conditions, such as when airways are occluded.
We grew cultured human bronchial epithelial cells for three passes, and treated the fourth pass under three different oxygen concentrations (21%, 15%, 2%).  RNA from each of three replicates of each treatment was extracted, processed, and hybridized onto Affymetrix Human Transcriptome Array 2.0 microarrays to examine alterations in gene expression under these oxygen regimes.  This data was collected to complement ATAC-seq data from cells aliquotted from each replicate.

overall_design: Primary Human Bronchial epithelial cells from the same individual were grown under standard conditions (5% CO2, 37C, 100% humidity) for three passes, and trasnferred during the fourth pass to 6-well plates for treatment.  Treatment proceeded in a controlled-oxygen environmental chamber at 2%, 15%, or 21% oxygen. Three biological replicates were obtained per treatment, each of which were prepared and analyzed separately.

first: Scott

middle: J

last: Nicholson

first: David

middle: C

last: Hutchings


title: Identification of Differentially Expressed Circular RNAs between the RNA of Drug Resistant HCT-116 Colorectal Cancer cells and its Extracellular Vesicle- Derivative

city: KUALA LUMPUR

first: NADIAH

last: ABU

state: KUALA LUMPUR

address: UKM Medical Molecular Biology, UMBI, UKM MEDICAL CENTER

country: Malaysia

institute: UKM MEDICAL MOLECULAR BIOLOGY INSTITUTE (UMBI)

summary: Drug resistant HCT116 cells were developed and the circular RNA profiles were compared between the cellular RNA and exosomal RNA

overall_design: Two condition experiment; exosomal RNA(exoR) vs cellular RNA(cellR); three biological replicates, independently grown and harvested

first: nadiah

last: abu


title: RNA-seq data of proximal and distal granulosa cells in chicken F1 and F5 ovarian follicles

city: chengdu

first: qiang

middle: guo

last: zhu

state: sichuan

address: yihuanlu nanyiduan 24hao

institute: sichuan university

summary: Transcriptomics of proximal granulosa cells vs distal granulosa cells from F5 and F1 in chicken ovary

overall_design: Totally four different granulosa cells in chicken ovary : two types of granulosa cell subpopulations (proximal and distal to the germinal disc), two types of follicles in different developing stages (F5 and F1)

first: G

last: Zhu

first: J

last: Li


title: Comparison of the activated lymphocyte into which shPTPN3 was introduced and the activated lymphocyte into which a control vector was introduced

city: Fukuoka

first: Akiko

last: Fujimura

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Cancer Therapy and Research

country: Japan

institute: Graduate School of Medical Sciences Kyushu University

summary: Immunotherapy using activated lymphocytes has recently been developed, but there is not yet the biomarker which can predict curative effect. In our recent study, we found that random migration is significantly increased in activated lymphocyte. Furthermore, it is suggested that random migration may affect cytotoxicity. Therefore we considered that migration of lymphocyte may become the effect prediction biomarker of Immunotherapy. And then we analyzed the gene which fluctuated by lymphocyte activation to search the molecules which regulate migration of lymphocyte.As the result, we found out that expression of PTPN3 fluctuates before and after activation of the lymphocyte.Next, we compared the gene expression of the activated lymphocyte into which shPTPN3 was introduced and of the activated lymphocyte into which a control vector was introduced to search the action mechanism of PTPN3.

overall_design: We prepared human peripheral blood mononuclear cells (PBMCs) and cultured PBMCs in RPMI medium supplemented with 200 U/ml interleukin(IL)-2 in culture plates coated with 2.5 ug/ml monoclonal antibody to CD3 for five days to activate lymphocytes. The non-attached fraction was collected and divided 2 groups.And then shPTPN3 was transfected into 1 group by using lentivirus and control vector was transfected into the other equally. We compared the gene expression of two groups to search the action mechanism of PTPN3.

first: Hideya

last: Onishi

first: Takashi

last: Morisaki

last: Nakagawa


title: Investigating Gene expression profiles of whole blood and peripheral blood mononuclear cells using multiple methods

city: Silver Spring

first: Aarti

last: Gautam

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

summary: Gene expression profiling using blood samples is a valuable tool for biomarker discovery in clinical studies. Different whole blood RNA collection and processing methods are highly variable and might confound comparisons of results across studies. The main aim of the study was to compare how blood storage, extraction methodologies, and the blood component itself may influence gene expression profiling where samples were collected in triplicate from five healthy donors. Whole blood was collected in RNAGard™, PAXgene™ as well as  collection tubes with anticoagulant such as  dipotassium ethylenediaminetetraacetic acid (K2EDTA) and acid citrate dextrose solution A (ACD-A). Peripheral blood mononuclear cells (PBMCs) were separated using sodium citrate cell preparation tubes (CPT), FICOLL™, immunomagnetic and Leukolock™ methods. The Leukolock™, K2EDTA and ACD-A blood tubes were shipped overnight using cold conditions and rest of the methods were immediately frozen with or without pre-processing.  The RNA was isolated from whole blood and peripheral blood mononuclear cells (PBMCs) with a total of 10 different experimental conditions employing several widely utilized RNA isolation methods. The RNA quality as assessed by RNA integrity Number (RIN) showed that all PBMC procedures had the highest RIN values when processed and stabilized in TRIzol before RNA extraction. Initial data analysis showed that human blood stored at 4°C overnight performed equally well when compared to frozen stabilized blood. Comparisons within and across donor/method replicates showed signal to noise patterns which were not captured by RIN value alone. Our results provide some new insights into RNA isolation from blood samples, how the RNA isolation quality and apparent gene expression is influenced by the choice of storage, handling, and methodologies, and how careful consideration is necessary to avoid bias resulting from downstream processing. Better characterization of the effects of collection method idiosyncrasies will facilitate further research into understanding the effect of gene expression on variability in human sample types.

overall_design:
The objective of this study was to investigate how blood storage, extraction methodologies, and the blood component itself may influence what genes appear to be expressed in downstream applications. Blood was collected in triplicate from 5 donors into five different collection tubes. Few of the tubes were frozen post collection, while others were stored at 4°C overnight. The RNA was isolated from whole blood and peripheral blood mononuclear cells (PBMCs) employing several widely utilized RNA isolation methods. After extraction, the RNA was quantified using a spectrophotometer and RNA quality was assessed by the RNA Integrity Number (RIN) value.  The RNA was then profiled using Agilent Human Gene Expression microarrays to investigate the different expression levels for the experimental conditions. The RNA quality was assessed by RIN value and we found out that all PBMC procedures had the highest RIN values when processed and stabilized in TRIzol before RNA extraction. Initial data analysis showed that human blood stored at 4°C overnight performed equally well when compared to frozen stabilized blood. Comparisons of blood collection methods within and across donor replicates showed signal to noise patterns which were not captured by RIN value alone. Our results provide some new insights into RNA isolation from blood samples, how the RNA isolation quality and apparent gene expression is influenced by the choice of storage, handling, and methodologies, and how careful consideration is necessary to avoid bias resulting from downstream processing. Better characterization of the effects of collection method idiosyncrasies will facilitate further research into understanding the effect of gene expression on variability in human sample types.
[Collection protocol] Blood was collected and preserved in five tubes, namely, PAXgene™ RNA tubes, RNAgard® Blood Tubes, BD Vacutainer™ tubes with ACD-A and K2EDTA and CPT (LeukoLOCK) tubes from five healthy volunteers. In parallel, PBMCs were isolated from EDTA, CPT and ACD-A tubes following the manufacturer’s instructions.

first: Rasha

last: Hammamieh

first: Marti

last: Jett


title: Gene expression profile of monocyte-derived macrophages following induction by recombinant and natural IFNα

city: London

first: Kelly

last: Marno

address: 4 Newark Street

department: Centre for Immunology and Infectious Disease

institute: Blizard Institute, Barts and the London SMD, Queen Mary University of London

summary:
Type I interferon is naturally produced in response to pathogens to generate an anti-viral state within the cell. There are 13 naturally occurring genetic isoforms of IFN alpha (IFNα) in humans that result in 12 IFNα subtypes (IFNα1 and α13 are identical but are coded by different genes). They all bind the same ubiquitously expressed receptor, interferon alpha receptor (IFNAR), but have been shown to differ in their biological and anti-viral activities (reviewed in Gibbert et al, Br J Pharmacol 2013). We investigated the ability of natural and recombinant IFNα to regulate mRNA expression.
Here we present a dataset comprising whole genome microarray data from primary human monocyte-derived macrophages following treatment with different preparations of IFNα. These data are suitable for determination of IFN-stimulated genes, and additionally allow differential analysis of gene induction in response to natural versus recombinant IFNα. For example, this comparison may be useful in identifying cellular anti-viral effector proteins involved in viral restriction, thus potentially providing novel therapeutic approaches without the historical negative outcomes of IFNα therapy.

overall_design: Total RNA obtained from MDMs treated with two preparations of IFNα: recombinant and natural as well as untreated; 3 replicate experiments per primary cell type.

first: Cleo

last: Bishop

first: Graham

middle: R

last: Foster

first: Áine

last: McKnight


title: Effect of 2-ITX on mRNA expression in the liver of male Wistar rats

city: Wageningen

first: Peter

last: Hendriksen

address: Akkermaalsbos 2

department: RIKILT

country: Netherlands

institute: Wageningen University & Research

summary: 2-Isopropylthioxanthone (2-ITX), a photoinitiator used in ink for printing of food packaging materials, has been detected in products like milk and fruit beverages. Previous in vitro research demonstrated 2-ITX to 1) exert agonistic effects on the aryl hydrocarbon receptor (AhR), 2) exert antagonistic effects on both the androgen (AR) and estrogen receptor (ER), and 3) to increase aromatase activity. To validate these findings in vivo, male rats were treated by gavage with 50, 150 or 500 mg 2-ITX/kg b.w. per day from postnatal day 23 to 53. For comparison, other groups were treated with 50 ng TCDD/kg b.w./day (AhR agonist), 30 mg bicalutamide/kg b.w./day (Casodex, AR antagonist) or 50 mg flutamide/kg b.w./day (AhR agonist and AR antagonist).   2-ITX, from the lowest dose onwards, decreased the weight of the ventral prostate, and from the middle dose onwards the weight of the seminal vesicles and coagulating gland. The highest dose of 2-ITX reduced the number of spermatozoa in the cauda of the epididymis. Similar effects, but more severe, were induced by flutamide and bicalutamide. Epididymal weight, caput sperm count and preputial separation were negatively affected by Casodex and flutamide but not by 2-ITX. The two highest doses of 2-ITX as well as TCDD increased liver weight. Whole genome mRNA expression profiling of the liver revealed similarity between the effects of 2-ITX and flutamide. In addition, many genes induced by TCDD were also induced by 2-ITX and flutamide. These results demonstrate 2-ITX to express AhR agonistic and AR antagonistic activities, both in vitro and in vivo.

overall_design: Male Wistar rats (PND23, mean body weight (b.w.) 46 g, n = 45 in total) were housed in cages (3 per cage) in a room with controlled temperature (±22°C)  relative humidity (±55%) and a 12:12 h light:dark cycle (lights on at 7:00 AM). The rats were fed a phytoestrogen-free diet (Research Diet Services, Wijk bij Duurstede, the Netherlands). Feed and drinking water were provided ad libitum. The body weight of the animals was measured daily.   The rats were dosed by oral gavage for 31 subsequent days (PND 23-53) between 9 and 11 AM with either corn oil alone (0.5 ml per 100 g b.w.) for the vehicle control group, or three different doses of 2-ITX (50, 150 or 500 mg/kg b.w./day, further referred to as 2-ITX-50, 2-ITX-150 and 2-ITX-500), or 50 ng/kg b.w./day TCDD (strong AhR agonist), or 50 mg/kg b.w./day flutamide (AR antagonist and AhR agonist) or 30 mg/kg b.w./day Casodex (AR antagonist). Six rats were assigned to each of the six treatment groups; nine rats were assigned to the control group.


title: NK cells derived exosomes carry miR-207 and alleviate depression-like symptoms in mice

status: Public on Oct 30 2019

city: Nanjing

first: Dongping

state: Jiangsu

address: Zhilan Road 18

department: Department of State Key Laboratory of Natural Medicines

institute: China Pharmaceutical University

summary: MicroRNAs (miRNAs) are 20–24 nt RNAs that can be packaged into exosomes and play important regulatory roles. Here we show that miRNA-containing exosomes from NK cells could alleviate symptoms of chronic mild stress in mice. In vivo experiment, these exosomes decreased the levels of pro-inflammatory cytokines such as IL-1β, IL-6 and TNF-α in the medium of astrocytes. By microarray analysis of exosome miRNA profiles, miR-207 was found to be an overexpressed miRNA in exosomes derived from unstressed mice. Experiments confirmed that miR-207 directly targets TLR4 interactor with leucine-rich repeats (Tril) and inhibits NF-κB signaling downsream of TLRs in astrocytes. When overexpressed in astrocytes, miR-207 decreased the release of pro-inflammatory cytokines and by inclusion of miR-207 inhibitor in astrocytes, higher release of pro-inflammatory cytokines and higher expression of Tril was found in vitro experiments. When NK cells were transfected with miR-207 inhibitor, miR-207 levels in NK cells derived exosomes were also declined. These exosomes with low miR-207 levels showed a decreased antidepressant activity in the vivo experiment. Collectively, our findings revealed that exosomal miR-207 alleviated the depression symptoms of stress mice by targeting Tril to inhibit NF-κB signaling downstream of TLRs in astrocytes.

overall_design: 106 NK cells extracted from unstressed mice and stress mice respectively, cultured them with RPMI-1640 containing 10% exosome-free FBS for 48h. Exosomes were obtained from culture supernatants which collected from NK cells of unstressed mice (n=3) and stress mice (n=3), and exosomal miRNA microarray assays were carried out.

first: Ying

last: Wang

first: Hanmei

last: Xu

first: Jialiang

last: Hu


title: Nuclear Ccr4-Not mediates the degradation of telomeric and transposon transcripts at chromatin in the Drosophila germline

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

type: Non-coding RNA profiling by high throughput sequencing

summary: Ccr4-Not is a highly conserved complex involved in cotranscriptional RNA surveillance pathways in yeast. In Drosophila, Ccr4-Not is linked to the translational repression of miRNA targets and the posttranscriptional control of maternal mRNAs during oogenesis and embryonic development. Here, we describe a new role for the Ccr4-Not complex in nuclear RNA metabolism in the Drosophila germline. Ccr4 depletion results in the accumulation of transposable and telomeric repeat transcripts in the fraction of chromatin-associated RNA; however, it does not affect small RNA levels or the heterochromatin state of the target loci. Nuclear targets of Ccr4 mainly comprise active full-length transposable elements (TEs) and telomeric and subtelomeric repeats. Moreover, Ccr4-Not foci localize at telomeres in a Piwi-dependent manner, suggesting a functional relationship between these pathways. Indeed, we detected interactions between the components of the Ccr4-Not complex and piRNA machinery, which indicates that these pathways cooperate in the nucleus to recognize and degrade TE transcripts at transcription sites. These data reveal a new layer of transposon control in the germline, which is critical for the maintenance of genome integrity.

overall_design: The fractions of small RNAs (19-29 nt) from ovaries of 12 transgenic lines of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

first: Alla

last: Kalmykova


title: Serum tRNA-derived fragments (tRFs) as potential candidates for diagnosis of non-triple-negative breast cancer

first: yue

last: huang

state: 江苏省

address: 300 Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: Breast cancer is one of the most common cancers in the world and non-triple-negative breast cancer (non-TNBC) accounts for 80-90% of all invasive breast cancers. Early detection of breast cancer is considered as key to successful treatment. Conventionally，breast imaging and needle core biopsy are used for detection and monitoring of disease progression. However, small volume changes may be ignored on imaging and traditional biopsy is spatially and temporally limited, leading to a significant lag time in detecting cancer progression. This thus prompted renewed focus on early and accurate diagnosis. In this article, we committed to investigate whether there exists accurate molecule in peripheral blood which can help diagnose breast cancer. tRNA-derived fragments (tRFs) have been reported to be involved in many pathological processes, but whether it can serve as biomarkers for the diagnosis of breast cancer remains unclear. Using high-throughput sequencing technology, we identified 4021 differentially expressed tRFs in normal breast epithelial cell lines and non-triple-negative breast cancer cell lines and 8 tRFs were selected to construct a signature to predict the non-TNBC. Further, qRT-PCR was conducted to verify its expression and to analyze the correlation between dysregulated tRFs and breast cancer. The results indicated that tDR-7816, tDR-5334, tDR-4733 might be promising biomarkers. Through further bioinformatics analysis, we predicted that tDR-7816 influences xenobiotic metabolic process that support the oncogenesis of breast cancer. Taken together, our results provide a rationale for using circulating tDR-7816 expression as a novel potential biomarker to diagnose early non-TNBC patients.

overall_design: Examination of differentially expressed tRFs in non-triple-negative breast cancer cell lines and normal cell lines.

first: Yue

last: Huang

first: Han

last: Ge

first: Yangyang

last: Cui

first: Mingjie

last: Zheng


title: Spatial organization of endometrial gene expression at the onset of embryo attachment in pigs

status: Public on Oct 29 2019

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: the aim of this present study was to characterize the complex transcriptome changes in different endometrial cell types during the preimplantation period for improving our understanding of localization of endometrial gene expression regulation in context of recognition of pregnancy. To do this analysis in a transcriptome-wide manner, RNA-seq was performed for samples derived from luminal epithelium (LE), glandular epithelium (GE), blood vessel (BV), and stroma (S) isolated by the use of LCM

overall_design: Four types of endometrial cells, luminal epithelial (LE), glandular epithelial (GE), blood vessel (BV), and stromal cells (S) were isolated by laser capture microdissection from endometria of Day 14 pregnant and cyclic control gilts (each group n=4), respectively, and then subjected to RNA-sequencing (RNA-Seq). The obtained datasets were compared to a RNA-Seq dataset from complete endometrial tissue samples collected in the same experiment.

first: Shuqin

last: Zeng

first: Jochen

last: Bick

first: Susanne

middle: E

last: Ulbrich


title: Deficiency of mitoribosomal S10 protein affects translation and splicing in Arabidopsis mitochondria

city: Wroclaw

first: Artur

last: Tomal

address: Fryderyka Joliot-Curie 14a

department: Faculty of Biotechnology

country: Poland

institute: University of Wroclaw

summary: The ribosome is not only a protein-making machine, but also a regulatory element in protein synthesis. This view is supported by our earlier data showing that Arabidopsis mitoribosomes altered due to the silencing of the nuclear RPS10 gene encoding mitochondrial ribosomal protein S10 differentially translate mitochondrial transcripts compared with the wild-type. Here, we used ribosome profiling to determine the contribution of transcriptional and translational control in the regulation of protein synthesis in rps10 mitochondria compared with the wild-type ones. Oxidative phosphorylation system proteins are preferentially synthesized in wild-type mitochondria but this feature is lost in the mutant. The rps10 mitoribosomes show slightly reduced translation efficiency of most respiration-related proteins and at the same time markedly more efficiently synthesize ribosomal proteins and MatR and TatC proteins. The mitoribosomes deficient in S10 protein protect shorter transcript fragments which exhibit a weaker 3-nucleotide periodicity compared with the wild-type. The decrease in the triplet periodicity is particularly drastic for genes containing introns. Notably, splicing is considerably less effective in the mutant, indicating an unexpected link between the deficiency of S10 and mitochondrial splicing. Thus, a shortage of the mitoribosomal S10 protein has wide-ranging consequences on mitochondrial gene expression.

overall_design: Mitochondrial ribosome footprints from youngest leaves of 9-10 week-old wildtype or P2 and P3 phenotypes of heterozygous rps10 mutant

first: Malgorzata

last: Kwasniak-Owczarek

first: Urszula

last: Kazmierczak

first: Pawel

last: Mackiewicz

first: Hanna

last: Janska


title: RNA-seq to measure mRNA expression in normal lung tissues, KRasG12D; p53-null(KP)-driven and Eml4-Alk(EA)-driven lung adenocarcinomas

status: Public on Oct 27 2019

city: Princeton

first: Yuri

last: Pritykin

state: NJ

address: 245 Carl Icahn Lab, Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

summary: The identification of miRNA targets by Ago2-CLIP methods has provided major insights into the biology of this important class of non-coding RNAs. However, these methods are technically challenging and not easily translated to an in vivo setting. To overcome these limitations and to facilitate the investigation of miRNA functions in mice, we have developed a method (HEAP) to map miRNA-mRNA binding sites. This method uses a novel mouse strain harboring a conditional Halo-Ago2 allele expressed from the Ago2 locus. By using a resin conjugated to the HaloTag ligand, Ago2-miRNA-mRNA complexes can be efficiently purified from cells and tissues expressing Halo-Ago2. We demonstrate the reproducibility and sensitivity of this method in embryonic stem cells, in embryos, in adult tissues and in autochthonous mouse models of cancers. These tools and datasets are valuable resources to the scientific community and will facilitate the characterization of miRNA functions under physiological and pathological conditions.

overall_design: Gene expression measured in three biological replicates of normal lung tissues, four replicates of KP and four replicates EA lung adenocarcinomas

first: Xiaoyi

last: Li

first: Christina

last: Leslie

first: Andrea

last: Ventura


title: Disruption of cardiac Med1 inhibits RNA polymerase-II promoter occupancy and induces chromatin remodeling

city: Iowa City

first: Long-Sheng

last: Song

state: IA

address: 285 Newton Rd

department: Internal Medicine

institute: University of Iowa

summary: The Mediator co-activator complex directs gene specific expression by binding distal enhancer-bound transcription factors through its Med1 subunit while bridging to RNA Polymerase-II (Pol-II) at gene promoters. In addition, Mediator scaffolds epigenetic modifying enzymes that determine local DNA accessibility. We previously found that deletion of Med1 in cardiomyocytes deregulates more than 5000 genes and promotes acute heart failure and hypothesize Med1 deficiency disrupts enhancer-promoter coupling. Using ChIP-seq, we find Pol-II pausing index is increased in Med1 knockout versus floxed control hearts primarily from decreased Pol-II occupancy at the majority of transcriptional start sites. Med1-dependent gene expression correlates strongly with histone H3 K27 acetylation while H3 K27 tri-methylated levels are increased and inversely correlate with absolute expression levels. Furthermore, Med1 deletion leads to dynamic changes in acetyl-K27 associated super-enhancer regions and their enriched transcription factor binding motifs that are consistent with altered gene expression. Our findings suggest that Med1 is important in establishing enhancer-promoter coupling in the heart by facilitating the recruitment of Pol-II to gene promoters, determining chromatin accessibility within genes and enhancer regions and altering transcription factor binding motifs that are likely important in directing gene-specific expression.

overall_design: ChIP-sequencing data of RNA Pol-II, acetylated H3K27, and tri-metylated H3K27 from hearts of Med1 floxed and cardiac knockout mice.

first: Duane

middle: D

last: Hall

first: Kathryn

last: Spitler

first: Chad

last: Grueter


title: Identification of a novel arthritis-associated osteoclast precursor macrophage regulated by FoxM1.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Macrophages comprise a variety of subsets with diverse biological activity, contributing to tissue homeostasis and a broad spectrum of pathogenesis. In response to environmental cues, they follow distinct developmental pathways such as differentiation into osteoclasts. In rheumatoid arthritis (RA), deep infiltration of the inflamed synovium eventually leads to irreversible destruction of the joints caused by pathological osteoclasts formed on periosteal surface. Although bone marrow macrophages have been extensively examined in the field, the precise entity of osteoclast precursors (OP) in pannus has yet to be identified, so as the trajectory of them. Here we show that OPs in pannus are exclusively derived from bone marrow through circulation, not from locally resident origins, and identify CX3CR1hiLy6CintF4/80+I-A/I-E+ macrophages, which we term ‘arthritis-associated osteoclastogenic macrophages (AtoM)’, as a population of OPs in inflamed synovium, comprising a distinct subset from conventional OPs in bone marrow represented by CX3CR1+Ly6ChiF4/80+I-A/I-E- fraction. Transcriptional profiling showed that AtoM differentially expresses genes related to osteoclastogenesis and mitochondrial biosynthesis, and is regulated by a characteristic transcription factor, FoxM1.

overall_design:
(i)  We performed an unbiased global transcriptomic comparison of R1 cells in the blood, R2’ and R3’ cells in the inflamed synovium in triplicates by RNA-sequencing analysis.
(ii)  CX3CR1hiLy6Cint subset in situ cells were sorted and targeted single-cell RNA-seq analysis was conducted (8682 single cells).

first: Tetsuo

last: Hasegawa

first: Junichi

last: Kikuta


title: Comparison of apical leaf halves of Arabidopsis thaliana PP2A-B´-mutants and wild type plants

city: Turku

first: Guido

last: Durian

address: Tykistokatu 6A

department: Biochemistry, Molecular Plant Biology

country: Finland

institute: University of Turku

summary: The objective of this RNAseq-experiment has been to compare apical leaf halves of different mutants with that of wild type plants.

overall_design: mRNA profiles of 5 pools each of apical and basal leaf halves of seven-week-old Arabidopsis thaliana wild type (Col-0) plants and mutant pp2a-b’γ, double mutants pp2a-b’γ sid2 and pp2a-b’γζ and complementation line pp2a-b´γ P35S:PP2A-B’γ were generated by sequencing using Illumina HiSeq 3000.


title: RNA pol II ChIP-seq LR14 and HFF human fibroblasts

city: Illkirch

first: Farrah

last: El-Saafin

address: 1 rue Laurent Fries

department: Development and Stem Cells

institute: IGBMC

summary: The aim of the experiment is to determine if RNA pol II occupancy and abundance is altered human fibroblasts from a patient that has a mutation in the gene Taf8, which plays an important role in RNA pol II mediated transcription.

overall_design: I performed ChIP with an antibody against RNA pol II, and have submitted the precipitated DNA from patient and control samples (L-IP and H-IP, respectively). In order to aid with normalisation, I spiked the fibroblast chromatin with 1/10 drosophila chromatin. Input for the HFF sample will also be submitted.


title: Transcriptional basis of mouse and human dendritic cell heterogeneity revealed by single-cell profiling

status: Public on Oct 25 2019

city: New York

first: Herman

last: Gudjonson

state: NY

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

summary: Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to serve as a principal antigen-presenting cell type capable of initiating T cell responses.  Classical dendritic cells have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells and direct their differentiation into effectors. Whilst the transcriptional features of the cDC1 subset have been well characterized, the heterogeneity of cDC2 and the development and function of distinct cell types comprising this subset remain poorly understood. Unbiased single-cell RNA sequencing analysis of DCs, combined with genetic reporter expression and fate-mapping revealed two principal cDC2 lineages, their developmental pathways and transcriptional regulators, including the expression of T-bet and RORt, two key transcription factors known to define functional adaptive and innate lymphocyte subsets. The cDC2 lineages were characterized by distinct metabolic and functional programs with phenotypic conservation observed across tissues. Extending the findings in mice to humans revealed conserved characteristics of DC heterogeneity and the presence of the newly defined DC subsets in human autoimmune disease and cancer.

overall_design: Single-cell RNA sequencing was performed on mouse and human splenic dendritic cells. Two samples of mouse dendritic cells were FACS purified based on Tbx21Cre-RFP reporter expression. Single-cell RNA sequencing was also performed on CD45-positive cells in melanoma tumors from two patients.

first: Chrysothemis

last: Brown

first: Deeksha

last: Deep

first: Vincent-Phillippe

last: Lavallee

first: Alejandra

last: Mendoza

first: Rachel

last: Fromme

first: Linas

last: Mazutis

first: Charlotte

last: Ariyan

first: Dana

last: Pe'er

first: Alexander

middle: Y

last: Rudensky


title: Halo-enhanced Ago2 pulldown (HEAP) to identify miRNA targets in vivo

first: Yuri

last: Pritykin

overall_design: HEAP libraries were produced in E13.5 embryos, normal lungs, cortices, two models of lung adenocarcinomas and gliomas

first: Xiaoyi

last: Li

first: Christina

last: Leslie

first: Andrea

last: Ventura


title: Effect of ILF3 on translation during homeostasis and the antiviral response

city: Aarhus C

first: Samir

last: Watson

state: Midtjylland

address: Universitetsbyen 83

department: Institute of Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

summary:
Upon detection of viral infections, cells activate the expression of type I interferons (IFNs) and pro-inflammatory cytokines to control viral dissemination. As part of their antiviral response, cells also trigger the translational shutoff response which prevents translation of viral mRNAs and cellular mRNAs in a non-selective manner. Intriguingly, mRNAs encoding for antiviral factors bypass this translational shutoff, suggesting the presence of additional regulatory mechanisms enabling expression of the self-defence genes. Here, we identified the dsRNA binding protein ILF3 as an essential host factor required for efficient translation of the central antiviral cytokine, IFNB1, and a subset of interferon-stimulated genes. By combining polysome profiling and next-generation sequencing, ILF3 was also found to be necessary to establish the dsRNA-induced transcriptional and translational programs. We propose a central role for the host factor ILF3 in enhancing expression of the antiviral defence mRNAs in cellular conditions where cap-dependent translation is compromised.
In this dataset we use polysome profiling in combination with RNA-seq to investigate the effect of ILF3 on the translation of mRNAs in HeLa cells in homeostasis and the antiviral response.

overall_design: To study the effect of ILF3 on translation, HeLa cells were first depleted of ILF3 by transfection with either a pool of siRNAs that target all splice isoforms of ILF3 (siILF3) or a pool of non-targeting control (Mock) siRNAs for 72h. Following the depletion, the antiviral response was activated by transfection with poly(I:C) for 4 hours. 30min prior to harvest, the cells were treated with 50ng/mL Cycloheximide to inhibit protein synthesis. Cytoplasmic lysates of identical numbers of cells were then subject to separation by velocity sedimentation through 10-60% sucrose gradients. This separated the subpolysomal fractions (which include free mRNA complexed to RNPs and the 40S, 60S and 80S ribosomal subunits) with the polysomal fractions (>2 polysomes) which were collected in a fraction collector. RNA was extracted from the subpolysomal and polysomal pools by precipitation with ethanol followed by Trizol LS RNA purification. The purified RNA was then enriched for poly(A) tailed mRNAs and subject to Illumina based RNA sequencing.

first: Nicolas

last: Bellora

first: Sara

last: Macias


title: Efficient in vivo mapping of miRNA targets by Halo-enhanced Ago2 pulldown

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

overall_design: Refer to individual Series


title: ILF3 contributes to the establishment of the antiviral type I interferon program


title: Effect of ILF3 depletion in HeLa cells on RNA steady state levels

summary: Upon detection of viral infections, cells activate the expression of type I interferons (IFNs) and pro-inflammatory cytokines to control viral dissemination. As part of their antiviral response, cells also trigger the translational shutoff response which prevents translation of viral mRNAs and cellular mRNAs in a non-selective manner. Intriguingly, mRNAs encoding for antiviral factors bypass this translational shutoff, suggesting the presence of additional regulatory mechanisms enabling expression of the self-defence genes. Here, we identified the dsRNA binding protein ILF3 as an essential host factor required for efficient translation of the central antiviral cytokine, IFNB1, and a subset of interferon-stimulated genes. By combining polysome profiling and next-generation sequencing, ILF3 was also found to be necessary to establish the dsRNA-induced transcriptional and translational programs. We propose a central role for the host factor ILF3 in enhancing expression of the antiviral defence mRNAs in cellular conditions where cap-dependent translation is compromised.

overall_design: HeLa cells were depleted of ILF3 using a pool of siRNAs that target ILF3 (siILF3) and a pool of non targeting siRNAs as a control (Mock) for 72 hours. the cells were then transfected with or without poly(I:C) for 4 hours and harvested using Trizol. For each experimental condition we used 3 biological replicates. The RNA was the sequenced using the Illumina Platform


title: Papillomavirus-Colonized Murine Skin Confers Cancer Resistance

city: Boston

first: Jonathan

middle: Leigh

last: Messerschmidt

state: MA

address: 149 13th Street

department: Center for Cancer Immunology, Cutaneous Biology Research Center, Center for Cancer Research

institute: Massachusetts General Hospital

summary: Herein we hypothesize that there are distinct gene expression changes that occur following MmuPV1 skin colonization that activates antiviral immune mechanisms capable of suppressing tumor growth.

overall_design: Total RNA sequencing of skin, tumors and warts from colonized and nieve mice.

first: Shadmehr

last: Demehri


title: RNA-seq and ATAC-seq to study dendritic cell heterogeneity

summary: The cDC2 subset is heterogeneous. We found the expression of T-bet delineates two distinct cDC2 subsets. Transcriptional profiling and analysis of chromatin accessibility in newly defined DC subsets identifies phenotypic specialisation and transcriptional regulators.

overall_design: ATAC-seq in cDC1s, T-bet+ cDC2 and T-bet- cDC2s (duplicates). RNA-seq in cDC1s, T-bet+ cDC2 and T-bet- cDC2s (triplicates or duplicates).

first: Chrysothemis

last: Brown


title: PIASy overexpression effects on gene expression in mouse 2-cell embryos

status: Public on Oct 23 2019

city: Kinokawa

first: Chika

last: Higuchi

state: Wakayama

address: 930 Nishimitani

department: Faculty of Biology-Oriented Science and Technology

institute: Kindai University

summary: During the maternal-to-zygotic transition (MZT), maternal mRNAs and proteins are degraded, and zygotic genes are activated. We have previously shown that the ubiquitin-proteasome system (UPS) after fertilization plays a role in onset of zygotic transcription. However, the maternal proteins, which are degraded by UPS and can contribute to the zygotic transcription, have not been identified. Here, we identified PIASy (Protein inhibitor of activated STAT y), which is an E3 SUMO ligase, as the maternal proteins that were degraded via UPS after fertilization and by examining the overexpression of PIASy. We observed developmental arrest at the mouse 2-cell stage. Therefore, we examined the effect of PIASy overexpression on zygotic gene expression by using the RNA-sequencing analysis.

overall_design: Total RNA-seq was performed using (1) PIASy-WT, (2) PIASy-C335F (SUMO ligase mutant) overexpressed mouse 2-cell embryos, and (3) non-injected mouse 2-cell embryos, in duplicates.

first: Kei

last: Miyamoto

first: Kazuya

last: Matsumoto


title: ‘Sertoli cell-only’ phenotype and single-cell RNA-seq define PRAMEF12 as a germline-specific factor for male stem cell maintenance and differentiation [scRNA-seq]

status: Public on Oct 22 2019

city: Bethesda

first: Cameron

last: Palmer

state: MD

address: 50 South Drive

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

summary: Spermatogonial stem cells (SSCs) have the dual capacity to self-renew and differentiate into progenitor spermatogonia that develop into mature spermatozoa. Here, we document that preferentially expressed antigen of melanoma family member 12 (PRAMEF12) is a key regulator of germline stem cell maintenance and differentiation. In male mice, genetic ablation of Pramef12 arrests spermatogenesis and results in sterility which can be rescued by transgenic expression of Pramef12. Pramef12 deficiency globally decreases expression of spermatogenic-related genes and single-cell transcriptional analysis of male germline cells identifies four spermatogonial states. In the absence of Pramef12 expression, there are fewer spermatogonial stem cells which exhibit lower expression of SSC maintenance-related genes and are defective in their ability to differentiate. The disruption of the first wave of spermatogenesis in junenile mice results in agametic seminiferous tubules. These observations mimic a ‘Sertoli cell-only’ phenotype in humans and may have translational implications for reproductive medicine.

overall_design: Single-cell RNA-seq was performed using P7 testicular cells from control and knockout mice to identify different subpopulations. Re-clustering of germ cells was performed to determine the germ cell distribution changes in knockout mice.

first: Zhengpin

last: Wang

first: Xiaojiang

last: Xu

first: Jian-Liang

first: Jurrien

last: Dean


title: The Transcriptome Of Cmml Monocytes Is Highly Inflammatory And Reflects Leukemia-Specific And Age-Related Alterations

status: Public on Oct 24 2019

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

summary: Chronic myelomonocytic leukemia (CMML) is an aggressive myeloid neoplasm of older individuals characterized by persistent monocytosis. Somatic mutations in CMML are heterogeneous and only partially explain the variability in clinical outcomes. Recent data suggest that cardiovascular morbidity is increased in CMML and contributes to reduced survival. Clonal hematopoiesis of indeterminate potential (CHIP), the presence of mutated blood cells in hematologically normal individuals, is a precursor of age-related myeloid neoplasms and associated with increased cardiovascular risk. To isolate CMML-specific alterations from those related to aging, we performed RNA sequencing and DNA methylation profiling on purified monocytes from CMML patients and from age-matched (old) and young healthy controls. We found that the transcriptional signature of CMML monocytes is highly pro-inflammatory, with upregulation of multiple inflammatory pathways, including tumor necrosis factor, IL-6 and IL-17 signaling, while age per se does not significantly contribute to this pattern. We observed no consistent correlations between aberrant gene expression and CpG island methylation, suggesting that pro-inflammatory signaling in CMML monocytes is governed by multiple and complex regulatory mechanisms. We propose that pro-inflammatory monocytes may contribute to cardiovascular morbidity in CMML patients, and promote progression by selection of mutated cell clones. Our data raise questions whether asymptomatic CMML patients may benefit from monocyte-depleting or anti-inflammatory therapies.

overall_design: CD14+ monocytes RNAseq from CMML, age-matched and young controls

first: Michael

last: Deininger

first: Thomas

last: O'Hare

first: Anca

last: Franzini


title: ‘Sertoli cell-only’ phenotype and single-cell RNA-seq define PRAMEF12 as a germline-specific factor for male stem cell maintenance and differentiation [RNA-Seq]

overall_design: RNA-seq was performed using post natal day 2 (P2) or P7  testes between control and knockout mice in order to identify the differentially expressed genes.

last: Li


title: Aberrant expression of RSK1 characterizes high-grade gliomas with immune infiltration

status: Public on Oct 26 2019

city: Ottawa

first: Martin

last: Roffe

state: ON

address: 401 Smyth Rd

country: Canada

institute: CHEO Research Institute

summary: The p90 ribosomal S6 kinase (RSK) family, a downstream target of Ras/extracellular signal-regulated kinase (ERK) signaling, can mediate cross-talk with the mammalian target of rapamycin complex 1 (mTORC1) pathway. As RSK connects two oncogenic pathways in gliomas, we investigated the protein levels of the RSK isoforms RSK1-4 in non-tumoral brain (NB) and grade I-IV gliomas. RSK4 expression was not detected in any brain tissues, whereas RSK3 expression was very low, with GBMs demonstrating the lowest RSK3 protein levels. When compared to NB or low-grade gliomas (LGG), a group of glioblastomas (RSK1hi) that excluded long-survivor cases expressed higher levels of RSK1. No difference was observed in RSK2 median-expression levels among NB and gliomas; however, high levels of RSK2 in glioblastomas (GBM) were associated with worse survival. RSK1hi and, to a lesser extent, RSK2hi GBMs, showed higher levels of phosphorylated RSK, which indicates RSK activation. Transcriptome analysis indicated that most RSK1hi GBMs belonged to the mesenchymal subtype, and RSK1 expression strongly correlated with gene expression signature of immune infiltrates, in particular of activated-natural killer cells and M2 macrophages. In an independent cohort, we confirmed that RSK1hi GBMs exclude long-survivors, and RSK1 expression was associated with high protein levels of the mesenchymal subtype marker LAPTM5, as well as with high expression of CD68, which indicated the presence of infiltrating immune cells. An RSK1 signature was obtained based on differentially expressed mRNAs and validated in public glioma datasets. Enrichment of RSK1 signature followed glioma progression, recapitulating RSK1 protein expression, and was associated with worse survival not only in GBM but also in LGG. In conclusion, both RSK1 and RSK2 associate with glioma malignity, but displaying isoform-specific peculiarities. The progression-dependent expression and association with immune infiltration, suggests RSK1 as a potential progression marker and therapeutic target for gliomas.

overall_design: mRNA from the 30 glioblastoma (GBM) samples from the A.C.Camargo Cancer Center (ACCCC) cohort was extracted from formalin-fixed, paraffin-embedded (FFPE) slices using the ReliaPrep™ FFPE Total RNA Miniprep System (Promega) and processed using the SensationPlus™ FFPE Amplification and 3' IVT Labeling Kit (Thermo), followed by GeneChip Human Transcriptome Array 2.0 (Thermo) according to the manufacturer’s instructions. RSK1 protein levels were determined in slices of the 30 samples.


title: ‘Sertoli cell-only’ phenotype and single-cell RNA-seq define PRAMEF12 as a germline-specific factor for male stem cell maintenance and differentiation

status: Public on Oct 21 2019


title: A mouse mutation that dysregulates neighboring Galnt17 and Auts2 genes is associated with phenotypes related to the human AUTS2 syndrome

status: Public on Oct 18 2019

city: Urbana

first: Lisa

last: Stubbs

state: ILLINOIS

address: 2402 IGB, 1206 W. Gregory Drive, MC-195

department: Cell and Developmental Biology, Institute for Genomic Biology

institute: University of Illinois

summary: AUTS2 was originally discovered as the gene disrupted by a translocation in human twins with Autism spectrum disorder (ASD), intellectual disability, and epilepsy. Since that initial finding, AUTS2-linked mutations and variants have been associated with a very broad array of neuropsychiatric disorders, suggesting that AUTS2 is required for fundamental steps of neurodevelopment. However, genotype-phenotype correlations in this region are complicated, because most mutations could also involve neighboring genes.  Of particular interest in this regard is the nearest downstream neighbor of AUTS2, GALNT17, encoding a brain-expressed N-acetylgalactosaminyltransferase of unknown brain function.  Here we describe a mouse (Mus musculus) mutation, T(5G2;8A1)GSO (abbreviated 16Gso), a reciprocal translocation that breaks between Auts2 and Galnt17 and dysregulates both genes. Despite this complex regulatory effect, 16Gso homozygotes model certain human AUTS2-linked phenotypes very well. In addition to abnormalities in growth, craniofacial structure, learning and memory, and behavior, 16Gso homozygotes display distinct pathologies of the cerebellum and hippocampus that are similar to those associated with ASD and other types of neurological disease associated with this genomic region.  Analyzing the mutant cerebellar and hippocampal transcriptomes, we identified disturbances in pathways related to neurite and synapse maturation, neurotransmitter signaling, and cellular stress, suggesting possible cellular mechanisms for 16Gso phenotypes. These pathways, coupled with the translocation’s selective effects on Auts2 isoforms and coordinated dysregulation of Galnt17, suggest novel hypotheses regarding the etiology of the human “AUTS2 syndrome” and the wide array of neurodevelopmental disorders linked to variance in this genomic region.

overall_design: We collected cerebellum (CB) and hippocampus (HC) from 16Gso homozyotes and wild type (WT) animals at postnatal day 14 (P14) and P35.  RNA from three animals of each genotype and age was used to generate Illumina RNA-seq libraries.  We compared mutant and WT gene expression at each age in each tissue to identify differentially expressed genes.


title: Obesity-linked suppression of MBOAT7 promotes liver injury

status: Public on Oct 17 2019

city: Cleveland

first: J.

middle: Mark

state: OH

address: 99089 Carnegie Ave

department: Cardiovascular and Metabolic Sciences

institute: Cleveland Clinic Foundaton


title: VE-Cadherin-Mediated Epigenetic Regulation of Endothelial Gene Expression

status: Public on Oct 19 2019

city: Uppsala

first: Elisabetta

last: Dejana

address: Dag Hammarskjolds väg 20

department: Immunology, Genetics and Pathology

institute: Uppsala University

summary:
Rationale: The mechanistic foundation of vascular maturation is still largely unknown. Several human pathologies are characterized by deregulated angiogenesis and unstable blood vessels. Solid tumours, for instance, get their nourishment from newly formed structurally abnormal vessels which present wide and irregular inter-endothelial junctions. Expression and clustering of the main endothelial-specific adherens junction protein, vascular endothelial (VE)-cadherin (VEC), upregulate genes with key roles in endothelial differentiation and stability.
Objective: We aim at understanding the molecular mechanisms through which VEC triggers the expression of a set of genes involved in endothelial differentiation and vascular stabilization.
Methods and Results: We compared a VEC-null cell line with the same line reconstituted with VEC wild type cDNA. VEC expression and clustering upregulated endothelial-specific genes with key roles in vascular stabilization including claudin-5, Vascular Endothelial-Protein Tyrosine Phosphatase (VE-PTP) and von Willebrand factor (vWf). Mechanistically VEC exerts this effect by inhibiting Polycomb protein activity on the specific gene promoters. This is achieved by preventing nuclear translocation of FoxO1 and β-catenin, which contribute to Polycomb repressive complex-2 (PRC2) binding to promoter regions of claudin-5, VE-PTP and vWf. VE-cadherin/β-catenin complex also sequesters a core subunit of PRC2 (Ezh2) at the cell membrane, preventing its nuclear translocation. Inhibition of Ezh2/VE-cadherin association increases Ezh2 recruitment to claudin-5, VE-PTP and vWf promoters, causing gene downregulation. RNAseq comparison of VEC-null and VEC-positive cells suggested a more general role of VE-cadherin in activating endothelial genes and triggering a vascular stability-related gene expression program. In pathological angiogenesis of human ovarian carcinomas, reduced VEC expression paralleled decreased levels of Claudin-5 and VE-PTP. Conclusions: These data extend the knowledge of Polycomb-mediated regulation of gene expression to endothelial cell differentiation and vessel maturation. The identified mechanism opens novel therapeutic opportunities to modulate endothelial gene expression and induce vascular normalization through pharmacological inhibition of the Polycomb-mediated repression system. Keywords: Polycomb, endothelial cells, VE-cadherin, vessel maturation, vascular biology, vascular permeability, cell signalling, epigenetics, gene regulation. Downloaded from http://circres.ahajour
Conclusions: These data extend the knowledge of Polycomb-mediated regulation of gene expression to endothelial cell differentiation and vessel maturation. The identified mechanism opens novel therapeutic opportunities to modulate endothelial gene expression and induce vascular normalization through pharmacological inhibition of the Polycomb-mediated repression system

overall_design: mRNA expression profiles are generated in triplicate from VEC-null cell line and VEC-positive cell line ( VEC-positive cell line were generated by  indroducing wild type form of VEC into VEC-null cells)

first: Marco

last: Morini

first: Costanza

last: Giampietro

first: Monica

last: Corada

first: Federica

last: Pisati

first: Elisa

last: Lavarone

first: Sara

middle: I

last: Cunha

first: Lei

last: Conze

first: Nicola

last: O’Reilly

first: Dhira

last: Joshi

first: Svend

last: Kjaer

first: Roger

last: George

first: Emma

last: Nye

first: Anqi

last: Ma

first: Jian

last: Jin

first: Richard

last: Mitter

first: Michela

last: Lupia

first: Ugo

last: Cavallaro

first: Diego

last: Pasini

first: Dinis

middle: P

last: Calado

first: Andrea

last: Taddei


title: MBOAT7's role in the progression of Non-alcoholic Fatty Liver Disease (NAFLD) and Non-Alcoholic Steatohepatitis (NASH)

first: J.

last: Brown

summary: Recent studies have identified a genetic variant rs641738 near two genes encoding membrane bound O-acyltransferase domain-containing 7 (MBOAT7) and transmembrane channel-like 4 (TMC4) that associate with increased risk of non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), alcohol-related cirrhosis, and liver fibrosis in those infected with viral hepatitis1-7. Based on hepatic expression quantitative trait loci analysis it has been suggested that MBOAT7 loss of function promotes liver disease progression1-7, but this has never been formally tested. Here we show that Mboat7 loss, but not Tmc4, in mice is sufficient to promote the progression of NAFLD in the setting of high fat diet. Mboat7 loss of function is associated with accumulation of its substrate lysophosphatidylinositol (LPI) lipids, and direct administration of LPI promotes hepatic inflammatory and fibrotic transcriptional changes in an Mboat7-dependent manner. These studies reveal a novel role for MBOAT7-driven acylation of LPI lipids in suppressing the progression of N

overall_design:
RNAseq of liver homogenates from high fat diet fed: MBOAT7 ASO knockdown vs MBOAT7 Control ASO mice

Please note that the processed data file contains raw count data for both GSE138945 and GSE138946 samples.

first: Mark


title: Osteoprotegrin induced expression in human pulmonary artery smooth muscle cells

city: Sheffield

first: Allan

last: Lawrie

address: University of Sheffield

department: Infection Immunity and Cardiovascular Disease

institute: University of Sheffield

summary: To profile gene expression in a disease relevant cell type human PASMCs were stimulated with 50ng/ul OPG (Peprotech) or 0.2% FCS (control).

overall_design: Gene expression was measured 6hs post stimulation with either 50ng/ul of Osteoprotegrin (OPG) or 0.2% FCS.

first: Nadine

last: Arnold

first: Josephine

middle: A

last: Pickworth

first: Laura

last: West

first: Sarah

last: Dawson

first: Joana

last: Carvalho

first: Helen

last: Casbolt

first: Adam

middle: T

last: Braithwaite

first: James

last: Iremonger

first: Lewis

last: Renshall

first: Volker

last: Germaschewski

first: Matthew

last: McCourt

first: Philip

last: Bland-Ward

first: Hagar

last: Kowash

first: Abdul

middle: G

last: Hameed

first: Alexander

last: Rothman

first: Maria

last: Frid

first: A

last: Thompson

first: Holly

last: Evans

last: Southwood

first: Nicholas

middle: W

last: Morell

first: David

last: Crossman

first: Moira

middle: K

last: Whyte

first: Kurt

last: Stenmark

first: Christoher

last: Newman

last: Kiely

first: Sheila

last: Francis


title: LPI's role in the progression of Non-alcoholic Fatty Liver Disease (NAFLD) and Non-Alcoholic Steatohepatitis (NASH)

first: J.

last: Brown

summary:
Recent studies have identified a genetic variant rs641738 near two genes encoding membrane bound O-acyltransferase domain-containing 7 (MBOAT7) and transmembrane channel-like 4 (TMC4) that associate with increased risk of non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), alcohol-related cirrhosis, and liver fibrosis in those infected with viral hepatitis1-7. Based on hepatic expression quantitative trait loci analysis it has been suggested that MBOAT7 loss of function promotes liver disease progression1-7, but this has never been formally tested. Here we show that Mboat7 loss, but not Tmc4, in mice is sufficient to promote the progression of NAFLD in the setting of high fat diet. Mboat7 loss of function is associated with accumulation of its substrate lysophosphatidylinositol (LPI) lipids, and direct administration of LPI promotes hepatic inflammatory and fibrotic transcriptional changes in an Mboat7-dependent manner. These studies reveal a novel role for MBOAT7-driven acylation of LPI lipids in suppressing the progression of N
To assess the role of MBOAT7 loss of function in NAFLD and NASH. We injected the substrate of MBOAT7, lysophosphatidylinostiol 18:0, or Saline in the portal vein of mice. The livers were then snap frozen and a standard RNA isolation was run to assess transcriptome changes after the addition of LPI's for six hours.

overall_design:
RNAseq of Liver homogenate +/- 18:0 Lysophosphatidylinositol

Please note that the processed data file contains raw count data for both GSE138945 and GSE138946 samples.

first: Mark

middle: J


title: A meta-analysis of two high-risk prospective studies reveals autism-specific transcriptional changes to chromatin, autoimmune, and environmental response genes in umbilical cord blood

city: Davis

first: Charles

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects more than 1% of children in the USA. ASD risk is thought to arise from both genetic and environmental factors, with the perinatal period as a critical window. Understanding early transcriptional changes in ASD would assist in clarifying disease pathogenesis and identifying biomarkers. However, little is known about umbilical cord blood gene expression profiles in babies later diagnosed with ASD compared to non-typically developing and non-ASD (Non-TD) or typically developing (TD) children. Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in RNA from cord blood samples from both the Markers of Autism Risk in Babies-Learning Early Signs (MARBLES) and the Early Autism Risk Longitudinal Investigation (EARLI) high-risk pregnancy cohorts that enroll younger siblings of a child previously diagnosed with ASD. Younger siblings were diagnosed based on assessments at 36 months, and 59 ASD, 92 Non-TD, and 120 TD subjects were included. Using both differential expression analysis and weighted gene correlation network analysis, gene expression between ASD and TD, and between Non-TD and TD, was compared within each study and via meta-analysis. While cord blood gene expression differences comparing either ASD or Non-TD to TD did not reach genome- wide significance, 172 genes were nominally differentially expressed between ASD and TD cord blood (log2(fold change) > 0.1, p < 0.01). These genes were significantly enriched for functions in xenobiotic metabolism, chromatin regulation, and systemic lupus erythematosus (FDR q < 0.05). In contrast, 66 genes were nominally differentially expressed between Non-TD and TD, including 8 genes that were also differentially expressed in ASD. Gene coexpression modules were significantly correlated with demographic factors and cell type proportions. ASD-associated gene expression differences identified in this study are subtle, as cord blood is not the main affected tissue, it is composed of many cell types, and ASD is a heterogeneous disorder. This is the first study to identify gene expression differences in cord blood specific to ASD through a meta- analysis across two prospective pregnancy cohorts. The enriched gene pathways support involvement of environmental, immune, and epigenetic mechanisms in ASD etiology.

overall_design:
Genome-wide transcript levels were measured by Affymetrix Human Gene 2.0 array in umbilical cord blood samples from both the Early Autism Risk Longitudinal Investigation (EARLI) and the Markers of Autism Risk in Babies--Learning Early Signs (MARBLES) studies, which are high-risk pregnancy cohorts of mothers with a child previously diagnosed with ASD. An algorithm-based child diagnosis was based on 36 month assessments, categorized as either ASD, typical development (TD), or not ASD but non-typical (Non-TD). RNA from a total of 59 ASD, 92 Non-TD, and 120 TD subjects were included and differences were analyzed by comparing ASD versus TD subjects, with Non-TD versus TD as a specificity control.
Note: only files from those who consented to share data were uploaded.

first: Bo

last: Park

first: Janine

middle: M

last: LaSalle

first: Rebecca

last: Schmidt

first: M

last: Fallin


title: TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites [RIP-seq]

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

summary: Identification of RNA targets of RNA-binding proteins (RBPs) is essential for complete understanding of their biological functions. However, it is still a challenge to identify the biologically relevant targets of RBPs through in vitro strategies of RIP-seq, HITS-CLIP, or GoldCLIP due to the potentially high background and complicated manipulation. In malaria parasites, RIP-seq and gene disruption are the few tools available currently for identification of RBP targets. Here, we have adopted the TRIBE (Targets of RNA binding proteins identified by editing) system to in vivo identify the RNA targets of PfDis3, a key exoribonuclease subunit of RNA exosome in Plasmodium falciparum. We generated a transgenic parasite line of Pfdis3-ADARcd, which catalyzes an adenosine (A)-to-inosine (I) conversion at the potential interacting sites of PfDis3-targeting RNAs. Most of PfDis3 target genes contain one edit site. The majority of the edit sites detected by PfDis3-TRIBE locate in exons and spread across the entire coding regions. The nucleotides adjacent to the edit sites contain ~ 75% of A+T. PfDis3-TRIBE target genes are biases toward higher RIP enrichment, suggesting that PfDis3-TRIBE preferentially detects stronger PfDis3 RIP targets. Collectively, PfDis3-TRIBE is a favorable tool to identify in vivo target genes of RBP with high efficiency and reproducibility. Additionally, the PfDis3-targeting genes are involved in stage-related biological processes during the blood-stage development. PfDis3 appears to shape the dynamic transcriptional transcriptome of malaria parasites through post-transcriptional degradation of a variety of unwanted transcripts from both strands in the asexual blood stage

overall_design: RIP-seq data of Pfdis3 targets throughout the IDC

first: Cizhong

last: Jiang

first: Qingfeng

last: Zhang

first: Meng

last: Liu

first: Binbin

last: Lu


title: TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites


title: MITF regulates SCD and fatty acid saturation to control melanoma phenotypic state.

status: Public on Oct 16 2019

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

institute: Ludwig Institute for Cancer Research


title: TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites [TRIBE]

summary: Identification of RNA targets of RNA-binding proteins (RBPs) is essential for complete understanding of their biological functions. However, it is still a challenge to identify the biologically relevant targets of RBPs through in vitro strategies of RIP-seq, HITS-CLIP, or GoldCLIP due to the potentially high background and complicated manipulation. In malaria parasites, RIP-seq and gene disruption are the few tools available currently for identification of RBP targets. Here, we have adopted the TRIBE (Targets of RNA binding proteins identified by editing) system to in vivo identify the RNA targets of PfDis3, a key exoribonuclease subunit of RNA exosome in Plasmodium falciparum. We generated a transgenic parasite line of Pfdis3-ADARcd, which catalyzes an adenosine (A)-to-inosine (I) conversion at the potential interacting sites of PfDis3-targeting RNAs. Most of PfDis3 target genes contain one edit site. The majority of the edit sites detected by PfDis3-TRIBE locate in exons and spread across the entire coding regions. The nucleotides adjacent to the edit sites contain ~ 75% of A+T. PfDis3-TRIBE target genes are biases toward higher RIP enrichment, suggesting that PfDis3-TRIBE preferentially detects stronger PfDis3 RIP targets. Collectively, PfDis3-TRIBE is a favorable tool to identify in vivo target genes of RBP with high efficiency and reproducibility. Additionally, the PfDis3-targeting genes are involved in stage-related biological processes during the blood-stage development. PfDis3 appears to shape the dynamic transcriptional transcriptome of malaria parasites through post-transcriptional degradation of a variety of unwanted transcripts from both strands in the asexual blood stage.

overall_design: TRIBE result of Pfdis3 targets throughout the IDC

last: LU


title: Lineage-restricted regulation of SCD and fatty acid saturation by MITF controls  melanoma phenotypic plasticity

summary: Phenotypic and metabolic heterogeneity within tumors is a major barrier to effective cancer therapy. Yet how metabolism is implicated in specific phenotypes, and whether lineage-restricted mechanisms control key metabolic vulnerabilities remains poorly understood. In melanoma, down-regulation of the lineage addiction oncogene Microphthalmia-associated Transcription Factor (MITF) is a hallmark of the proliferative-to-invasive phenotype switch, though how MITF promotes proliferation and suppresses invasion is poorly defined. Here we show that MITF is a lineage restricted activator of the key lipogenic enzyme stearoyl-CoA desaturase (SCD), and that SCD is required for MITFHigh melanoma cell proliferation. By contrast MITFLow cells are insensitive to SCD inhibition. Significantly, the MITF-SCD axis suppresses metastasis, inflammatory signalling, and an ATF4-mediated feedback-loop that maintains dedifferentiation. Our results reveal that MITF is a lineagespecific regulator of metabolic reprogramming, whereby fatty acid composition is a driver of melanoma phenotype-switching, and highlight that cell phenotype dictates response to drugs targeting lipid metabolism.

overall_design: 501mel and IGR37 melanoma cell lines were treated with the indicated siRNA or SCD inhibitors for 48h prior to RNA extraction and sequencing

first: Yurena

last: Vivas-Garcia

first: Colin

last: Goding


title: Comprehensive transcriptional atlas of intestinal immune cells reveals that neuropeptide α-CGRP orchestrates ILC2 responses

city: Cambridge

first: Aviv

last: Regev

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

summary: We combine single-cell RNA sequencing (scRNA-seq) with physiological and genetic perturbations to dissect the cellular circuit of type 2 intestinal inflammation. To uncover key responding cellular components, we profiled individual immune cells in the lamina propria (LP) and Peyer’s patches (PPs), regions of the small intestine enriched for immune cells, in homeostasis and in an intestinal type 2 inflammatory model. We obtained 36,797 and 21,270 high-quality cells passing initial filtering from PP and LP regions, respectively.

overall_design: To understand the small intestine in homeostasis, untreated cells from wild-type mice were collected; while to investigate the impacts of type 2 inflammation on intestinal immune cells, cells from mice after induction of an inflammatory reaction to ovalbumin were used. Cells were profiled using both 3'-droplet-based single-cell RNA sequencing, obtained 30,723 cells from wild-type mice and 27,344 cells from treated mice. To study the functions of the alpha-calcitonin gene-related peptide (α-CGRP) in ILC2s, flow sort-purified intestinal KLRG1+ ILC2s were stimulated in vitro with IL-25 and/or α-CGRP for 3 hours.

first: Heping

last: Xu

first: Jiarui

last: Ding

first: Caroline

last: Porter

first: Ariel

last: Lefkovith

first: Ramnik

last: Xavier


title: Transcriptomics profiling of some commonly used cell lines at the base-line culture condition

summary: In vivo, melanoma cells transition though distinct phenotypic states in response to a changing microenvironment, and most notably can switch between invasive and proliferative phenotypes characterized by high and low levels of MITF activity (Hoek and Goding, 2010; Hoek et al., 2008). Since melanoma cell lines isolated from human tumors tend also to fall into either proliferative or invasive, slow-growing phenotypes (Hoek et al., 2006), it seems likely that established lines reflect specific phenotypic states within tumors, including those detected using single cell RNA-seq, that are then fixed and maintained under nutrient–rich culture conditions where the microenvironmental stresses encountered in vivo are absent. Indeed, it has been shown that melanoma cell lines presenting distinct phenotypic states exhibit very different responses to microenvironmental cues such as hypoxia (Louphrasitthiphol et al., 2019). The aim of this study is to characterise some of the commonly use cell lines and assign each with a phenotypic state base on its transcriptomics.

overall_design: Indicated cell line were grown in RPMI without any treatment prior to RNA extraction and sequencing


title: Small RNA sequencing of LA-N-2 and LAN-5 cells exposed to ciliary neurotrophic factor for 30/60 min and 2/4 days

status: Public on Oct 15 2019

city: Frankfurt

first: Sebastian

last: Lobentanzer

address: Max-von-Laue-Str. 9

department: Pharmacology

country: Germany

institute: Johann-Wolfgang-von-Goethe University

summary: To examine the impact of gp130-mediated, pro-cholinergic neurokine intervention on the small RNA systems in female and male human neuronal cells, we exposed cultured LA-N-2 cells (female) to 100 ng/ml ciliary neurotrophic factor (CNTF), and LAN-5 cells (male) to 10 ng/ml CNTF. RNA sequencing of time points at 30/60 minutes and 2/4 days of CNTF exposure shows a significant response and an “immediate early”/”long term” dichotomy in differentially expressed miRNAs.

overall_design: Small RNA profiles were generated by Illumina sequencing (NextSeq) of 4 biological replicates each and analysed with miRExpress2.


title: Transcriptional redirection of activated SKN-1/NRF2 abates the negative metabolic outcomes of a perceived pathogen infection

city: Los Angeles

first: Sean

last: Curran

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

summary: Optimal health requires perpetual transcriptional fidelity of gene expression.  SKN-1/NRF2 is a cytoprotective transcription factor in C. elegans that regulates the expression of cellular defenses during stress, including: nutrient deprivation, redox imbalance, and xenobiotic and pathogen exposure. Constitutive activation of SKN-1 results in pleiotropic outcomes, including shortened lifespan and protective redistribution of somatic fat to the germline.  We measured lipid distribution between the soma and germ tissues after manipulation of SKN-1 activity.  Modulating the epigenetic landscape refines SKN-1 activity away from innate immunity targets and alleviates negative metabolic outcomes.  Similarly, paraquat exposure redirects SKN-1 activity toward oxidative stress responses and away from pathogen response genes, which restores lipid distribution across tissues.  Lastly, activating p38 MAPK signaling is sufficient to drive SKN-1-dependent loss of somatic fat.  These data reveal a coordination of organismal metabolic homeostasis with pathogen responses and identifies mechanisms for counteracting the pleiotropic consequences of aberrant transcriptional activity.

overall_design: Our study aim to look at transcriptional signatures that changes in Day 3 adults, when loss of fat phenotype occurs in constitutively active SKN-1 worms compared to wild type. We are also interested in transcriptional changes when that loss of fat phenotype is suppressed by paraquat exposure or chromatin restriction.

first: James

last: Nhan


title: 5' scRNAseq of splenic CD3+ cells from immunodeficient mice injected with progenitor T-cells generated from naïve, non-expanded or SR1-expanded human cord blood-derived CD34+ cells

city: Toronto

first: Jastaranpreet

last: Singh

state: Ontario

address: 2075 Bayview Avenue

institute: University of Toronto

summary: We report the gene expression profile of single cell peripheral CD3+ cells from immunodeficient mice injected with human progenitor T-cells (proT-cells). ProT-cell subsets were  generated in vitro using human umbilical cord blood-derived CD34+ cells that were either non-expanded (naive), or expanded in vitro with the hydrocarbon receptor antagonist, StemRegenin-1 (SR1).

overall_design: Splenic CD3+ T-cells were FACS sorted from immunodeficient mice injected with naive progenitor T-cells (generated from non-expanded CD34+ cells) or SR1 progenitor T-cells (generated from StemRegenin-1-expanded CD34+ cells).

first: Edward

middle: L

last: Chen

first: Yan

last: Xing

first: Heather

last: Stefanski

first: Bruce

last: Blazar

first: Juan

middle: C

last: Zúñiga-Pflücker


title: 3' V(D)J scRNASeq of splenic CD3+ cells from immunodeficient mice injected with progenitor T-cells generated from naïve, non-expanded or SR1-expanded human cord blood-derived CD34+ cells

overall_design: CD3+ T-cells were FACS sorted from immunodeficient mice injected with naive progenitor T-cells (generated from non-expanded CD34+ cells) or SR1 progenitor T-cells (generated from StemRegenin-1-expanded CD34+ cells).

middle: R


title: TRIBE uncovers the role of Dis3 in shaping the dynamic transcriptome in malaria parasites [RNA-seq]

first: meng

last: liu

overall_design: RNA-seq data of Pfdis3 KD throughout the IDC. We constructed PfDis3-DD clone line(PfDis3-DD) and used drug GlcN to induce the ribonuclease to degrade the mRNA of PfDis3  thus knock down PfDis3

first: Cizhong

last: Jiang

first: Qingfeng

last: Zhang

first: Meng

last: Liu

first: Binbin

last: Lu


title: ABCB5 is activated by MITF and b-catenin and is associated with melanoma differentiation

first: Pakavarin

last: Louphrasitthiphol

summary: Defining markers of different phenotypic states in melanoma is important for understanding disease progression, determining the response to therapy, and defining the molecular mechanisms underpinning phenotype-switching driven by the changing intratumor microenvironment. The ABCB5 transporter is implicated in drug-resistance and has been identified as a marker of melanoma-initiating cells. Indeed, ongoing studies are using ABCB5 to define stem cell populations. However, we show here that the ABCB5 is a direct target for the Microphthalmia-associated transcription factor MITF and its expression can be induced by b-catenin, a key activator and co-factor for MITF. Consequently, ABCB5 mRNA expression is primarily associated with melanoma cells exhibiting differentiation markers. The results suggest first that ABCB5 is unlikely to represent a marker of dedifferentiated melanoma stem cells, and second that ABCB5 may contribute to the non-genetic drug-resistance associated with highly differentiated melanoma cells. To reconcile the apparently conflicting observations in the field we propose a model in which ABCB5 may mark a slow-cycling differentiated population of melanoma cells.

overall_design: Doxycycline inducible CTNNB1 cell line was generated using piggyBAC transposable system into IGR37 melanoma cell line. Positively integrated cells were selected using 1mg/ml G418. In order the assess the effect of ectopic Beta-catenin on transciptomics, the nuclear localisation signal derived from SV40 Large T-antigen was introduced to the N-terminus of CTNNB1 to confer constant nuclear localisation upon induction with doxycycline.

first: Colin

last: Goding


title: scRNASeq of splenic CD3+ cells from immunodeficient mice injected with progenitor T-cells generated from naïve, non-expanded or SR1-expanded human cord blood-derived CD34+ cells

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

overall_design: Refer to individual Series


title: Fatty Liver Due to Increased de novo Lipogenesis: Alterations in the Hepatic Peroxisomal Proteome

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: In non-alcoholic fatty liver disease (NAFLD) caused by ectopic lipid accumulation, lipotoxicity is a crucial molecular risk factor. Mechanisms to eliminate lipid overflow can prevent the liver from functional complications. This may involve increased secretion of lipids or metabolic adaptation to ß-oxidation in lipid-degrading organelles such as mitochondria and peroxisomes. In addition to dietary factors, increased plasma fatty acid levels may be due to increased triglyceride synthesis, lipolysis, as well as de novo lipid synthesis (DNL) in the liver. In the present study, we investigated the impact of fatty liver caused by elevated DNL, in a transgenic mouse model with liver-specific overexpression of human sterol regulatory element-binding protein-1c (alb-SREBP-1c), on hepatic gene expression, on plasma lipids and especially on the proteome of peroxisomes by omics analyses, and we interpreted the results with knowledge-based analyses. In summary, the increased hepatic DNL is accompanied by marginal gene expression changes but massive changes in peroxisomal proteome. Furthermore, plasma phosphatidylcholine (PC) as well as lysoPC species were altered. Based on these observations, it can be speculated that the plasticity of organelles and their functionality may be directly affected by lipid overflow.

overall_design:
C57Bl6 (C57Bl6) and C57Bl6-TgN alb-HA-hSREBP-1c-NT (alb-SREBP-1c)[Knebel et al. PLoS One. 2012;7(2):e31812. doi: 10.1371/journal.pone.0031812] mice were bred and maintained under standard conditions to until alb-SREBP-1c mice develop fatty liver and adipositas phenotype (24 weeks of age).

https://www.frontiersin.org/articles/10.3389/fcell.2019.00248/abstract

first: Jorg

last: Kotzka

first: Dirk

last: Müller-Wieland


title: Aberrant intragenic DNA methylation in a neurogenic region in autism spectrum disorders

city: New York

first: Michael

last: Corley

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

institute: Weill Cornell Medicine

summary: Genome-wide DNA methylation profiling of postmortem brain tissue in the subventricular zone of the lateral ventricles from individuals with autism and without.

overall_design: Bisulphite converted DNA from the 34 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Alika

last: Maunakea


title: Wide versus cell type restricted deletion of four tumor suppressor genes determines the type of high grade neuroendocrine lung cancer

city: Madrid

first: Corina

last: Lorz

state: Madrid

address: Avda. Complutense 40

country: Spain

institute: Ciemat (Centro de Investigaciones Energeticas Mediambientales y Tecnologicas)

summary:
Here we describe novel murine models of High Grade Neuroendocrine Lung Carcinomas driven by the loss of four tumor suppressors: deletion of Rb, PTEN, and p53, in a Rbl1 null background, in a wide variety of lung epithelial cells produces Large Cell Neuroendocrine Carcinoma whereas inactivation of these genes exclusively in basal cells leads to the development of Small Cell Lung Carcinoma, showing that Keratin K5 expressing cells contribute to the development/act as cell of origin of Small Cell Lung Carcinoma differentially influencing the lung cancer type developed.
Conditional ablation of Rb1, Trp53 and Pten in pulmonary cells was achieved by intratracheal administration of purified Ad5-CMVcre or  Ad5-K5cre (Du Page et al, 2009) to Rb1F/F;Trp53F/F;PtenF/F;Rbl1−/− 8–10 week old mice. Mice were sacrificed 3 to 5 months after the Ad5-cre infection and tumors processed for whole transcriptome analysis. As control animals, RbF/F;p53F/F;PtenF/F;Rbl1−/− littermates were used.

overall_design: Gene expression was studied in control mouse lung (Rbl1-/-) and in lung tumours from Rb1F/F;Trp53F/F;PtenF/F;Rbl1−/− mice treated by intratracheal administration of Ad5-CMVcre or Ad5-K5cre to ablate Rb1, Trp53 and Pten in pulmonary cells.

first: Sara

last: Lázaro

first: Miriam

last: Pérez-Crespo

first: Jesús

last: Paramio

first: Mirentxu

last: Santos


title: Small RNA sequencing of LA-N-2 cells exposed to ciliary neurotrophic factor for 30/60 min and 2/4 days

first: Sebastian

last: Lobentanzer

summary: To examine the impact of gp130-mediated, pro-cholinergic neurokine intervention on the small RNA systems in human neuronal cells, we exposed cultured LA-N-2 cells to 100 ng/ml ciliary neurotrophic factor (CNTF). RNA sequencing of time points at 30/60 minutes and 2/4 days of CNTF exposure shows a significant response and an “immediate early”/”long term” dichotomy in differentially expressed miRNAs.

overall_design: Small RNA profiles were generated by Illumina sequencing (NextSeq) of biological triplicates and analysed with BWA, bowtie2, and miRExpress2.


title: Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

status: Public on Oct 14 2019

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

sample_organism:
Drosophila melanogaster
Drosophila virilis
Drosophila busckii


title: Full-length transcriptome reconstruction reveals large diversity of RNA isoforms and open reading frames in rat hippocampus

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

summary: We developed a hybrid-sequencing workflow, combining next-generation and third-generation sequencing, to reconstruct full-length transcriptomes. Integrating with polysome profiling and ribosome footprinting data, we predicted isoform–specific translational status and reconstructed ORFeome. Moreover, we identified isoforms with specific subcellular localization pattern in neurons.

overall_design: At least two replicates were performed on the adult rat hippocampus.

first: Jingyi

last: Hou

first: Claudia

last: Quedenau

first: Wei

last: Chen


title: Developmental competence and antigen switch frequency can be uncoupled in Trypanosoma brucei

status: Public on Oct 10 2019

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution