title: Ago2 PAR-CLIP analysis of Abelson kinase transformed murine B cell progenitors

summary: Knockout of the ubiquitously expressed microRNA-17~92 cluster in mice produces a lethal developmental defect and blocked B lymphopoiesis. We validated the equally widely expressed Bcl2l11 gene as joint target of miR-17~92 cluster members. Bcl2l11 encodes the pro-apoptotic protein BIM, central to life-death decisions in most mammalian cells. To study the contribution of miR-17~92:Bim interaction to miR-17~92 overall function, we set up a system of conditional mutagenesis of the Bim 3’UTR in mice. Ago2 Photoactivatable-Ribonucleoside Cross-linking and Immunoprecipitation (AGO2 PAR-CLIP) allowed us to assess whether the seed match mutations introduced into the Bim 3’UTR in vivo indeed precluded interaction with the miRNAs of the 17~92 cluster. This analysis was done in Abelson Virus transformed B cell progenitors which we generated from wild type and Bim3’UTRmut/mut E14.5 fetal livers, knowing that these cells express both BIM and miR-17~92, can be expanded to large numbers and incorporate 4-thiouridine sufficiently well. Focusing on 21 nt windows around the 9 putative miR-17~92 seed matches in the Bim 3’UTR and excluding reads lacking T-to-C transitions, we we verified that the introduced mutationsare functional, and we discovered differential seed match coverage in the wild type, with one miR-19 seed match co-dominating with two miR-92 seed matches, while in the mutant 3’UTR miR-17~92 binding was completely abolished. These results demonstrate functionality and efficiency of our genetically engineered mouse model for in vivo conditional seed-match inactivation.  These results demonstrate functionality and efficiency of our genetically engineered mouse model for in vivo conditional seed-match inactivation.

overall_design: Identification of miRNA binding sites by Ago2 PAR-CLIP using 4-Thiouridine treatment in n=2 wild type Abelson transformed B cells  vs. n=2 Bim3’UTRmut/mut Abelson transformed B cells, cultivated in vitro.


title: Next generation sequencing facilitates promoter-level analysis of pancreatic cancer cell lines transcriptomes

status: Public on Nov 13 2019

city: kyoto

first: Ru

last: chen

address: kawahara-cho 53, shogoin, sakyo-ku

country: Japan

institute: kyoto university

type: Expression profiling by high throughput sequencing

summary: Both pancreatic intraepithelial neoplasia (PanIN), a frequent precursor of pancreatic cancer, and intraductal papillary mucinous neoplasm (IPMN), a less common precursor, undergo several phases of molecular conversions and finally develop into highly malignant solid tumors with negative effects on the quality of life. We approached this long-standing issue by examining the following PanIN/IPMN cell lines derived from mouse models of pancreatic cancer: Ptf1a–Cre; KrasG12D; p53f/+ and Ptf1a–Cre; KrasG12D; Brg1f/f PDAs. The mRNA from these cells was subjected to a cap analysis of gene expression (CAGE) to map the transcription starting sites and quantify the expression of promoters across the genome.

overall_design: Two RNA samples extracted from three individual subcutaneous tumors generated by the transplantation of PanIN or IPMN cancer cell lines were used to generate libraries and Illumina Seq, with four RNA samples in total.

last: Chen

first: Aiko

last: Sugiyama

first: Hiroshi

last: Seno


title: Recapitulating and Deciphering Tumor-stroma Microenvironment by Using a “LEGO” like 3D printed microfluidic device

city: Beijing

first: Yang

last: Liu

address: 30 Xueyuan Road, Haidian District

country: China

institute: University of Science and Technology Beijing

summary: The tumor-stroma microenvironment is extremely important on tumor progression, metastasis and angiogenesis. Development of in vitro technology that can quantitatively gain migration and cell-cell interaction data is there high desirable. Conventional methods for study tumor migration and cell-cell interaction are plagued by inaccessible to get quantitative data or complication of microfabrication process which brings into additional efforts rather than study the biological question itself. Herein, we developed a “LEGO”-like 3D printed device combined with a quantitative data gaining process which can be used for investigation into tumor cell migration process dynamically at single cell resolution and tumor-stromal interactions with high flexibility. These interactions showed to alter the genotype and phenotype of tumor cells or fibroblasts. RNA sequence analysis of homocultured and cocultured fibroblasts or HT1080 cells identified several differentially expressed genes. We found that fibroblasts cocultured with HT1080 for 24 h were in an intermediate state relative to the CAF and the normal fibroblast, and promoted tumor cell migration but inhibited tumor cell proliferation. In terms of DEGs from fibroblasts and HT1080 cells, we deciphered this phenomenon in detail.

overall_design: Whole mRNA profiles of HT1080 (Coculture with NHDF vs Homoculture) and NHDF (Coculture with HT1080 vs Homoculture) were generated by deep sequencing, in triplicate, using Illumina HiSeq

first: Liang

last: Zhao

first: Xueji

last: Zhang


title: Vital role and diversity of miRNA control through a single target gene

city: Innsbruck

first: Verena

last: Labi

address: Innrain 80-82

department: Developmental Immunology

country: Austria

institute: Medical University Innsbruck

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

overall_design: Refer to individual Series


title: Defining the impact of exoribonucleases  in the shift between exponential and stationary phases

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

summary: The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

overall_design: RNA-Seq of E. coli K-12 MG1693 wild-type(wt) and four exoribonucleases mutants was done with Illumina Hi-Seq platform.

first: Vânia

last: Pobre

first: Susana

last: Barahona

first: Tatiane

last: Dobrzanski

first: Maria

middle: B

last: Steffens

first: Cecília

middle: M


title: Importance of AMPK in metformin suppression of liver glucose production

city: Baltimore

first: Ling

last: He

state: MD

address: 600 North Wolfe St

department: Department of Pediatrics-Division of Endocrinology

country: USA

institute: The Johns Hopkins University School of Medicine

summary: Metformin is now the most widely prescribed oral anti-diabetic agent worldwide, taken by over 150 million people annually. Although metformin has been used clinically to treat type 2 diabetes for over 60 years. Its mechanism of action remains only partially understood and controversial. In particular, this includes whether AMPK plays a role in metformin  suppression of liver glucose production. To address this issue, we knocked out the AMPK catalytic alpha1 and alpha 2 subunits in the liver of HFD-fed adult homozygous mice. These mice were treated with a physiological relevent metformin dose (50 mg/kg/day) for 3 weeks. Liver samples were collected.

overall_design: 6 weeks old male floxed homozygous AMPK alpha1/2 mice were fed an HFD for 4 weeks, AAV8-TBG-E.V. and AAV8-TBG-Cre (1X10^11GC/mouse) were injected via jugular vein, and mice were treated with metformin (50 mg/kg/day) for 3 weeks, liver samples were collected after 16 h fast. There are 14 samples, 6 samples from control group (WT), another 8 samples from treated group (Cre KO).


title: Stepwise chromatin remodeling by two lincRNAs underlies cell fate in fission yeast

city: Huddinge

first: Olga

last: Khorosjutina

department: Bioscience and nutrition

country: Sweden

institute: Karolinska Institutet

type: Expression profiling by genome tiling array

summary: The cell-fate decision leading to gametogenesis requires the convergence of multiple signals on the promoter of a master regulator. In fission yeast, starvation-induced signaling leads to the transcriptional induction of the ste11 gene, which enodes the central inducer of mating and gametogenesis, know as sporulation. We find that the long intergenic non-coding (linc) RNA rse1 is transcribed divergently upstream of the ste11 gene. rse1 directly recruits a Mug187-Lid2-Set1 complex that mediates SET3C-dependent deacetylation and repression at the ste11 promoter. Upon starvation, the activation of the ste11 promoter is bidirectional, generating a second lincRNA, rce1, overlapping the promoter of rse1. The transcription of rce1 establishes repressive chromatin at the rse1 promoter, therefore relieving the repression on ste11. Thus, the transcription of two lincRNAs governs the switch from vegetative growth to sexual differentiation in fission yeast. Our data reveals that the remodeling of chromatin through ncRNA scaffolding of repressive complexes that is observed in higher eukaryotes is a conserved, likely very ancient mechanism for tight control of cell differeniation.

overall_design: In total 4 samples: duplicate mutant cDNA samples were compared to duplicate wild type cDNA samples

first: Sylvain

last: Fauquenoy

first: Valerie

last: Migeot

first: Olivier

last: Finet

last: Khorosjustina

first: Karl

last: Ekwall

first: Damien

last: Hermand


title: Microarray profiling identifies extracellular circulating miRNAs dysregulated in cystic fibrosis

status: Public on Nov 12 2019

city: Chicago

first: Justin

middle: Eze

last: Ideozu

state: IL

address: 255 E Chicago Avenue

department: Human Molecular Genetics

institute: Lurie Children's Hospital

summary:
Extracellular circulating miRNAs (ECmiRNAs) play a crucial role in cell-to-cell communication and serve as non-invasive biomarkers in a wide range of diseases, but their abundance and functional relevance in cystic fibrosis (CF) remain poorly understood.
Microarray technology was employed to identify aberrantly expressed plasma ECmiRNAs in CF and elucidate the functional relevance of their targets.

overall_design: Total RNA isolated from plasma samples of cystic fibrosis patients (n=5) and healthy controls (n=5) were used for miRNA microarray profiling

middle: E

first: Xi

first: Vittobai

last: Rangaraj

first: Susanna

last: McColley

first: Hara

last: Levy


title: Cell-autonomous FLT3L shedding via ADAM10 mediates conventional dendritic cell development in mouse spleen

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

summary: To characterize the changes that had occurred in splenic pre-cDCs in the absence of ADAM10, we performed RNA sequencing on sorted pre-cDC1 and 2 from the spleens of wild-type and ADAM10ΔDC mice. Unsupervised hierarchical clustering and principal component analysis of all four groups demonstrated that distinct transcriptomic changes had taken place in ADAM10ΔDC pre-cDC2, while minimal changes were observed for pre-cDC1

overall_design: Examination of sorted splenic pre-cDC1 and pre-cDC2 from WT and CD11c-cre Adam10fl/fl mice

first: Svetoslav

last: Chakarov

first: Florent

last: Ginhoux


title: Progenitor-Derived Human Endothelial Cells Evade Alloimmunity by CRISPR/Cas9-Mediated Complete Ablation of MHC Expression

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

summary: Purpose: To compare human progenitor cell-derived endothelial cells ablated of MHC molecules to endothelial cells transduced with control vector after IFN-y treatment

overall_design: Comparison of interferon-gamma treated cord-blood endothelial cells with CRISPR/Cas9 targeting of B2-Microglobulin and CIITA

first: Merola

last: Jonathan

first: Pober

last: Jordan


title: Potent Anti-Myeloma Activity of the TOPK inhibitor OTS514 in Pre-Clinical Models

first: Andrzej

last: Jakubowiak

address: 900 E 57th St

department: Medicine

institute: University of Chicago

summary: Evaluation of gene expression upon treatment with OTS514 in combination with existing thereapeutics in H929 cells

overall_design: H929 cells treated for 24h with DMSO control or OTS514 (15 nM) and/or carfilzomib(CFZ, 5nM) and/or lenalidomide (LEN, 15µM)

first: A

middle: T

last: Stefka

first: D

last: Johnson

middle: J


title: Transcriptomics analysis of circular RNAs differentially expressed in apoptotic HeLa cells

city: Izmir

first: ipek

last: erdogan

address: Gulbahce

country: Turkey

institute: Izmir Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: We have performed a transcriptomics study in which we first triggered apoptosis in HeLa cells through treatment with four different agents, namely cisplatin, doxorubicin, TNF-α and anti-Fas mAb. Total RNAs isolated from control as well as treated cells were treated with RNAse R to eliminate the linear RNAs. The remaining RNAs were then subjected to deep-sequencing to identify differentially expressed circRNAs. Interestingly, some of the dys-regulated circRNAs were found to originate from protein-coding genes well-documented to regulate apoptosis. A number of candidate circRNAs were validated with qPCR with or without RNAse R treatment as well. We then took advantage of bioinformatics tools to investigate the coding potential of differentially expressed RNAs. Additionally, we examined the candidate circRNAs for the putative miRNA-binding sites and their putative target mRNAs. Our analyses point to a potential for circRNA-mediated sponging of miRNAs known to regulate apoptosis. In conclusion, this is the first transcriptomics study that provides a complete circRNA profile of apoptotic cells that might shed light onto the potential role of circRNAs in apoptosis.

overall_design: Total RNA was isolated from cisplatin, doxorubicin, TNF-alpha, anti Fas mAb and DMSO (0.1%)-treated HeLa cells in triplicate, to perform deep-sequencing in order to reveal circRNA profile for apoptosis. DMSO (0.1%)-treated group was used as control and denoted as C1a, C2a and C3a.

first: Bilge

last: Yaylak

first: Ipek

last: Erdogan

first: Bunyamin

last: Akgul


title: Effect of acupuncture treatments on retinal transcriptome after optic nerve injury

first: Linqing

last: Miao

state: Beijing

address: No.5 Zhongguancun South St, Haidian District

department: Advanced Innovation Center

institute: Beijing Institute of Technology

summary:
Purpose: We used RNA sequencing to investigate the effect of acupuncture treatment on retinal transcritome after optic nerve injury
Methods: Retinal mRNA profiles of 5-week-old wild-type (WT), optic nerve crush injury (ONC), ONC injury with acupuncture treatment at acupoint GB20 (ONC-F) and ONC injury with acupuncture treatment at acupoint BL1 (ONC-J) mice were generated by deep sequencing, in triplicate, using Illumina Hiseq platform. The sequence reads that passed quality filters were analyzed with DESeq2 R package to identify differently expressed genes with padj<0.05. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Results: RNA-seq revealed that 436 genes including 31 transcription factors (TFs) were changed after injury, which include many well-known neural degeneration related TFs such as Jun, Ddit3, Atf3 and Atf4. Interestingly, acupuncture treatment at acupoint GB20 (Fengchi) or BL1(Jingming) after ONC injury both resulted in change of retinal gene expression, compared with ONC injury without treatment; furthermore, acupuncture treatment also reversed several gene expression status induced by axon injury.
Conclusions: Our research first reported that acupuncture treatment after injury can regulated retinal transcriptome and reversed the gene expression level induced after injury, which will provide novel therapeutic targets for treatment of retinopathy diseases.

overall_design: Retinal mRNA profiles of 5-week-old  mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.


title: Transcriptome and DNA methylome of mouse Müller glia

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

institute: Zhongshan Ophthlamic Center

type: Methylation profiling by high throughput sequencing

summary: Müller cells are the primary glia of the neural retina and play crucial roles in maintaining the structural and functional homeostasis of the retina. Müller cells also possess certain levels of retinal regeneration capacity, especially in lower vertebrates. In this study, we deep sequenced the transcriptomes and methylomes of mouse Müller cells and early retinal progenitor cells (RPCs), as well as Müller cells from injured retinas and aged retinas, which will help to reveal molecular mechanisms governing Müller cells development, physiological functions and regeneration activities.

overall_design: Total RNAs were extracted and deep sequenced (2 biological replicates each for young Müller cells and aged Müller cells, 3 replicates each for NMDA-treated Müller cells and RPCs). Methylomes of genomic DNAs were deep sequenced using RRBS method (3 biological replicates each for young Müller cells, NMDA-treated Müller cells, aged Müller cells, and RPCs).


title: Age-associated changes in human CD4+ T cells point to mitochondrial dysfunction consequent to impaired autophagy.

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: To gain understanding on the mechanisms that drive immunosenescence in humans, we examined CD4+ T cells obtained from younger (20-39 years-old) and older (70+ years-old) healthy participants of the Baltimore Longitudinal Study on Aging (BLSA). We found that mitochondrial proteins involved in the electron transport chain were overrepresented in cells from older participants, with prevalent dysregulation of oxidative phosphorylation and energy metabolism molecular pathways. Surprisingly, gene transcripts coding for mitochondrial proteins pertaining to oxidative phosphorylation and electron transport chain pathways were underrepresented in older individuals. Paralleling the observed decrease in gene expression, mitochondrial respiration was impaired in CD4+ T cells from older subjects. Though mitochondrial number in both naïve and memory cells visualized with electron microcopy was similar in older versus younger participants, there were a significantly higher number of autophagosomes, many of them containing undegraded mitochondria, in older individuals. The presence of mitochondria inside the accumulated autophagic compartments in CD4+ T cells from older individuals was confirmed by immunofluorescence. These findings suggest that older age is associated with persistence of dysfunctional mitochondria in CD4+ T lymphocytes caused by defective mitochondrial turnover by autophagy, which may trigger chronic inflammation and contribute to the impairment of immune defense in older persons.

overall_design: CD4+ T cells from 8 younger (20-39 years old) and 25 older (70+ years old) healthy participants of the Baltimore Longitudinal Study on Aging (BLSA) were examined by gene expression for microarrays.

first: Arsun

last: Bektas

first: Shepherd

middle: H

last: Schurman

first: Marta

last: Gonzalez-Freire

first: Christopher

middle: A

last: Dunn

first: Amit

middle: K

last: Singh

first: Fernando

last: Macian

first: Ana

last: Cuervo

first: Ranjan

last: Sen

first: Luigi

last: Ferrucci


title: Bifidobacterium kashiwanohense expresses fucosidases necessary for fucosyllactose utilisation as an adaptation to the infant gut environment

city: Cork

first: Kieran

last: James

address: Biosciences Institute, Gaol Cross, Western Road

department: Microbiology

country: Ireland

institute: APC Microbiome Institute, University College Cork

summary: Bifidobacteria dominate the composition of the neonatal gut microbiota in the first number of weeks following birth. A number of species in particular are found with a significantly higher frequency in the microbiome of breastfed infants, owing to their ability to rely on Human Milk Oligosacchraides (HMOs) as their sole carbohydrate substrate; namely B. bifidum, B. longum spp. infantis and B. breve. Bifidobacterium kashiwanohense is a species that has been isolated previously only from the faeces of infants, but extremely infrequently at that. Relatively little is currently known about the species itself, let alone the metabolic pathways that allow it to successfully establish a population in the infant gut. We have isolated a novel strain of B. kashiwanohense from the faeces of a breastfed infant on the basis of its ability to utilise the HMO component fucosyllactose as its sole carbohydrate source. In this study, we read and annotate the full genome sequence of this novel strain, and use the data obtained to direct our further experimental analysis of fucosyllactose metabolism in B. kashiwanohense. Using transcriptomic and growth analysis results, we identify the genes responsible for B. kashiwanohense to utilise fucosyllactose, and employ a combination of cloning, in vitro hydrolysis assays, and further, recombinant transcriptomic and growth assays to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense, as well as revealing insight into fucosyllactose and fucose metabolism in Bifidobacteria as whole.

sample_organism: Bifidobacterium catenulatum subsp. kashiwanohense

overall_design: DNA-microarrays containing oligonucleotide primers representing each of the 1864 annotated genes on the genome of B. breve UCC2003, and DNA-microarrays containing oligonucleotide primers representing each of the 2110 annotated genes on the genome of B. kashiwanohense APCKJ1 were designed by and obtained from Agilent Technologies (Palo Alto, Ca., USA). Methods for cell disruption, RNA isolation, RNA quality control, complementary DNA synthesis and labeling were performed as described previously (Pokusaeva et al., 2009)(van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, 2005). Labeled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050). Following hybridization, microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A). Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5). DNA-microarray data were processed as previously described (Garcia De La Nava et al., 2003). Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long et al., 2001). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.


title: Inactivation of mTORC2 in macrophages is a signature of colorectal cancer that promotes tumorigenesis.

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

institute: Medical University of Vienna

summary:
Gene expression analysis of sorted colon macrophages of Rictor fl/fl LysM+/+ and Rictor fl/fl LysM+/cre mice
Dysregulations of immune and metabolic processes can lead to chronic inflammation, which is one of the driving forces for the development of cancer. Macrophages are regulators of these processes and therefore have a fundamental role for the initiation of cancer. Here we find that deletion of Rictor in myeloid cells increases tumor number and size in the colitis-associated colorectal cancer model and leads to a stronger inflammatory response in the underlying acute DSS-colitis model. OPN is shown to be upregulated in the serum of myeloid-specific Rictor-KO mice during the DSS-colitis and the more severe phenotype, characterized by decreased survival, increased weight loss, shorter colons and enhanced infiltration of immune cells into the colon, can be reverted by the neutralization of OPN in these mice. Microarray analysis reveals a change in inflammatory and metabolic gene signatures of Rictor-KO colon macrophages that is also seen in the Rictor-KO BMDM in vitro. Therefore, our data show that myeloid Rictor controls macrophage polarization and the cellular energy metabolism, thereby suppressing colitis and colitis-associated colorectal cancer.

overall_design: Total RNA of sorted colon macrophages of Rictorfl/fl LysM+/+ and Rictorfl/fl LysM+/cre mice (n=3-4/group) was subjected to microarray analysis on Affymetrix GeneChip® Mouse Gene 2.0 ST arrays. Array data were processed using Affymetrix Expression Console. No technical replicates were performed.

first: Karl

last: Katholnig

first: Martin

last: Hirtl

first: David

last: Schörghofer

first: Monika

last: Linke

first: Nyamdelger

last: Sukhbaatar

first: Stephanie

middle: D

last: Fritsch

first: Birgit

last: Schütz

first: Merima

last: Herac

first: Andreas

last: Spittler

last: Bergthaler

first: Markus

last: Hengstschläger

first: Mario

last: Mikula

first: Mark

last: Magnuson


title: nCounter analysis of mRNAs associated with GBM tissue using a Nanostring custom assay

city: Houston

first: Sreyashi

last: Basu

address: 7455 Fannin Street

institute: MDACC

summary: Gene expression of GBM specimens from untreated and anti-PD-1 treated patients were analyzed using customized 739- gene Nanostring panel

overall_design: 6 untreated and 4 anti-PD1 treated patient samples were analyzed

first: P

last: Sharma


title: Expression data from isoalted adult cardiomyocytes w/o Isopretrenol stimulation.

status: Public on Nov 11 2019

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: Sympathetic activation of β-adrenergic receptors (β-AR) represent a hallmark in the development of heart failure (HF). Genome-wide analysis of CaMKII-mediated H3S28p in response to chronic β-AR stress by chromatin-immunoprecipitation followed by massive genomic sequencing led to the identification of CaMKII-dependent H3S28p target genes.40 % of differentially H3S28p-enriched genomic regions were associated with differential, mostly increased expression of the nearest genes, pointing to CaMKII-dependent H3S28p as an activating histone mark.

overall_design: To investigate whether Iso-induced H3S28p is associated with changes of gene expression, we performed microarray analyses (Affymetrix) to compare mRNA expression in Adult mouse ventricular myocytes (AMVMs) obtained from CaMKII WT and DKO mice after Iso stimulation.

first: Ali

middle: R

last: Saadatmand

first: Johannes

last: Backs


title: Characterization of novel primary miRNA transcription units in human cells using Bru-seq nascent RNA sequencing

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: MicroRNAs (miRNAs) are key contributors to gene regulatory networks. Because miRNAs are processed from RNA polymerase II transcripts, insight into miRNA regulation requires a comprehensive understanding of the regulation of primary miRNA transcripts. We used Bru-seq nascent RNA sequencing and hidden Markov model segmentation to map primary miRNA transcription units (TUs) across 32 human cell lines, allowing us to describe TUs encompassing 1462 miRNAs from miRBase and 465 from MirGeneDB. We identified 54 TUs not previously described for MirGeneDB miRNAs. Many primary transcripts containing miRNA sequences failed to generate mature miRNAs, suggesting that miRNA biosynthesis is under both transcriptional and post-transcriptional control. In addition to constitutive and cell-type specific TU expression regulated by differential promoter usage, miRNA synthesis can be regulated by transcription past polyadenylation sites (transcriptional read through) and promoter divergent transcription (PROMPTs). We identified 203 miRNA TUs with novel promoters, 99 with transcriptional read-throughs and 3 miRNA TUs that resemble PROMPTs in at least one cell line. The miRNA TU annotation data resource described here reveals a greater complexity in miRNA regulation than previously known and provides a framework for identifying cell-type specific differences in miRNA transcription in cancer and following exposure to environmental insults or therapeutics.

overall_design: Nascent RNA Bru-seq used to map primary miRNA transcripts across 32 diverse human cell lines, allowing for systematic assessment of the various transcription units encompassing known miRNAs

first: K

last: Bedi

first: M

last: Paulsen

first: T

last: Wilson


title: Genetic expressions alteration affect on lateral neck node metastasis of thyroid papillary microcarcinoma

city: Seoul

first: Sohee

last: Lee

address: 222 BANPO-DAERO, SEOCHO-GU

department: Surgery

country: South Korea

institute: The Catholic University of Korea

summary: We performed oligonucleotide microarray analysis to assess the genetic expression alteration wich affected on lateral neck node metastasis of thyroid papillary microcarcinoma(PTMC).   We performed microarray analysis in three PTMCs without cervical lymph-node metastases (N0), and five PTMCs with lateral neck-node metastasis (N1b) at initial diagnosis,   using an Illumina HumanHT-12 v4.0 Expression BeadChip.

overall_design: Total 16 samples (3 T1aN0 PTMC and 5 T1aN1b or T3N1b PTMC(papillary thyroid microcarcinoma) and its paired normal thyroid tissue) were used.   We obtained thyroid tissues from eight PTMC patients who underwent thyroidectomy.  We also obtained eight normal thyroid tissue specimens from the thyroid lobes of the same patients for pairwise analysis.   Of eight PTMC, three did not have nodal involvement and extrathyroidal extension (T1aN0). The remaining patients had lateral neck-node metastasis at initial diagnosis (T1aN1b or T3N1b) and   underwent modified radical neck dissection combined with thyroidectomy.   Immediately after thyroidectomy, we obtained the three pairs of 0.2 × 0.2 × 0.2-cm cubes of both cancer and normal thyroid tissue from the surgeon;   the samples were snap-frozen in liquid nitrogen at the operation theater and then stored at ˗80°C.

first: Ja

middle: S

last: Bae

first: Chan-Kwon

last: Jung

first: Woong

middle: Y

last: Chung


title: Discovery of lncRNA biomarkers of prostate cancer

city: Paris

first: Marina

last: Pinskaya

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: In the last decade, new high-throughput sequencing techniques have revealed the complexity of the human transcriptome, allowing the characterization of long non-coding (lnc)RNAs. Since their expression has been reported as very specific to tissue, developmental stage and pathological variations, some lncRNAs have been proposed as biomarkers for diagnosis as well as prognosis of tumors. In this project, we aim to build an exhaustive catalogue of long non-coding RNAs and isolate those which allow detection and risk assessement of prostate cancer. For this purpose we performed a high throughput total stranded  RNA-sequencing of 24 samples (8 normal and 16 tumor tissues).

overall_design: Total RNA was extracted from biopsy specimens, checked for the quality and than converted into cDNA for total stranded RNA-sequencing.

first: Marc

last: Gabriel

first: Antonin

last: Morillon


title: RNA sequencing of Tregs from skin and whole skin from neonatal mice colonized with Staphlyococcus epidermidis versus Staphylococcus aureus

city: San Francisco

first: Tiffany

middle: C

last: Scharschmidt

state: CA

address: 513 Parnassus Ave, 1201B

department: Dermatology

institute: University of California, San Francisco

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

overall_design: Refer to individual Series


title: RNA sequencing of whole skin from neonatal mice colonized with Staphlyococcus epidermidis versus Staphylococcus aureus

overall_design: Mice were colonized every other day from birth with either S. epi or S. aureus. On day 21 of life, skin was harvested for RNA isolation.

last: Crawford Scharschmidt

first: Johnathon

last: Leech


title: Arabiodpsis bsu-q and flg22-responsive genes

city: Stanford

first: Chan Ho

last: Park

address: 260 Panama street

institute: Carnegie institution for science

summary: Comparison of differential gene expression in WT (Col-0) and bsu-q, and flg22-responsive genes in Col-0 and bsu-q.

overall_design: Seedlings of untreated were prepared for identifying genes differentially expressed in WT (Col-0) and bsu-q (3 replicates). Three replicates of flg22-treated seedlings were prepared for identifying flg22-responsive genes in WT (Col-0) and bsu-q. Non-treated and flg22-treated samples were compared to identify flg22-responsive genes (>2FC).

first: Chan

first: Yang

last: Bi

first: Zhi-Yong

last: Wang


title: RUNX1-ETO orchestrates dynamic enhancer promoter communication in t(8;21) Acute Myeloid Leukaemia

city: Birmingham

first: Salam

middle: Adli

last: Assi

address: IBR

department: Institute for Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

type: Genome binding/occupancy profiling by high throughput sequencing


title: Hepatocyte nuclear factor-1β regulates Wnt signaling through genome-wide competition with β-catenin/lymphoid enhancer binding factor

city: Minneapolis

first: Ying

last: Zhang

state: MN

address: 117 Pleasant St S.E.

department: Minnesota Supercomputing Institute

institute: University of Minnesota

summary: Hepatocyte nuclear factor-1β (HNF-1β) is a tissue-specific transcription factor that is essential for normal kidney development and renal tubular function. Mutations of HNF-1β produce cystic kidney disease, a phenotype associated with deregulation of canonical (β-catenin-dependent) Wnt signaling. Here, we show that ablation of HNF-1β in mIMCD3 renal epithelial cells produces hyperresponsiveness to Wnt ligands and increases expression of Wnt target genes, including Axin2, Ccdc80, and Rnf43. Levels of β-catenin and expression of Wnt target genes are also increased in HNF-1β mutant mouse kidneys. Genome-wide ChIP-seq in wild-type and mutant cells showed that ablation of HNF-1β increases by five-fold the number of sites on chromatin that are occupied by β-catenin. Remarkably, 50% of the sites that are occupied by β-catenin in HNF-1β mutant cells colocalize with HNF-1β binding sites in wild-type cells, indicating widespread reciprocal binding. We found that the Wnt target genes Ccdc80 and Rnf43 contain a novel composite DNA element comprising a β-catenin/lymphoid enhancer binding factor (LEF) site overlapping with an HNF-1β half-site. HNF-1β directly competes with the binding of β-catenin/LEF complexes to this element and thereby inhibits β-catenin-dependent transcription. Collectively, these studies reveal a novel mechanism whereby a transcription factor constrains canonical Wnt signaling through direct inhibition of β-catenin/LEF chromatin binding.

overall_design: RNA-seq and β-catenin ChIP-seq of HNF-1β-deficient and WT mIMCD3 cell lines treated with Mock and Wnt3a.

first: Peter

last: Igarashi

first: Siu

last: Chan


title: RUNX1-ETO orchestrates dynamic enhancer promoter communication in t(8;21) Acute Myeloid Leukaemia (ChIP-Seq)

summary: Acute myeloid leukaemia (AML) is caused by mutations in transcriptional and epigenetic regulator genes impairing myeloid differentiation. The t(8;21)(q22;q22) translocation generates the leukemogenic RUNX1-ETO fusion protein which interferes with the hematopoietic master regulator RUNX1. We previously showed that maintenance of t(8;21) AML is dependent on RUNX1-ETO as its depletion causes extensive changes in transcription factor binding and gene expression as well as myeloid differentiation. How changes in gene expression and binding events are connected within a transcriptional network is unclear. To this end, we assigned cis-regulatory elements to each other using promoter-capture chromosomal conformation assays in the presence and absence of RUNX1-ETO. From these data we constructed a RUNX1-ETO dependent dynamic transcriptional network maintaining AML. Integration of these data with gene expression and transcription factor binding data shows that RUNX1-ETO participates in interactions and that differential cis-element interactions are driven by alterations in the binding of RUNX1-ETO regulated transcription factors.

overall_design: CTCF and LDB1 ChIP befor and after RUNX1/ETO knock-down is usded in this study

first: Anetta

last: Ptasinska

first: Constanze

last: Bonifer


title: Single cell RNA Sequencing analysis on CD45 positive cells  isolated form Lewis Lung Carcinoma (LLC) tumors.

city: New Haven

first: Yajaira

last: Suarez

state: Connecticut

address: 10 Amistad Street

department: Comparative Medicine

institute: Yale University School of Medicine

summary: The goal of this study is to compare transcriptome profiling of different populations of CD45 immune cells of isolated from LLC tumors from miR-21 conditionally deleted on LysM expressing cells  (mir-21 flox/flox; lysmCre) mice vs. control (mir-21flox/flox) mice.

overall_design: LLC cells were subqutaneously implated in 8 weeks old control (mir-21flox/flox)  or  miR-21 conditionally deleted on LysM expressing cells  (mir-21 flox/flox; lysmCre) mice. After 14 days tumors were isolated and collagenase diggested then  Cd45 positive cells were FACS sorted  and RNA was straced for subsequent RNA-seq analysis.

first: Y


title: RNA Sequencing analysis on Tumor associated macrophages (TAMs) Isolated form Lewis Lung Carcinoma (LLC) tumors

summary: The goal of this study is to compare transcriptome profiling of miR-21 null TAMs vs. WT macrophages isolated from LLC tumors

overall_design: LLC cells were subcutaneously implanted in 8 weeks old WT or miR-21 null mice. After 14 days tumors were isolated and collagenase digested then macrophages were FACS sorted as (CD45+, CD11b+, MHCII+, F4/80) cells and RNA was extracted for subsequent RNA-seq analysis.


title: Sox11 - a novel activity-regulated gene with dentate gyrus-specific expression

status: Public on Nov 10 2019

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary:
Neuronal activity initiates transcriptional programs that shape long-term changes in plasticity. Although neuron subtypes differ in their plasticity response, most activity-dependent transcription factors are broadly expressed across different neuron subtypes and brain regions. Thus, how regional and neuronal subtype-specific plasticity are established on the transcriptional level remains poorly understood.
Here, we report that the developmental transcription factor Sox11 is induced in mature neurons upon hippocampal circuit activity and that this activity-dependent expression occurs exclusively in the dentate gyrus (DG) of the hippocampus. In addition, we show that Sox11 can modify synaptic plasticity and intrinsic excitability of DG granule cell neurons as well as the expression of plasticity-related genes. We propose that Sox11 is a DG-specific activity-dependent gene and might play a role in fine tuning regional plasticity in the hippocampal circuit.

overall_design: mRNA expression levels in dentate gyrus tissue from 10 mice were compared: In the 5 mice of the treatment group, the gyrus was transduced with Sox11-containing adeno-associated virus (AAV); the other 5, forming the control group, were transduced with AAV containing GFP.

first: D

last: Lie

first: Julia

last: von Wittgenstein

first: Arif

last: Ekici


title: RUNX1-ETO orchestrates dynamic enhancer promoter communication in t(8;21) Acute Myeloid Leukaemia (DNaseI-Seq)

overall_design: DNase I after RUNX1/ETO knock-down is usded in this study


title: Systems biology of S.aureus adaptation under Ser/Thr kinase wild type and mutations of kinase (pknB) or phosphatase (stp)

city: Geneva

first: FRANCOIS

last: Patrice

state: Ge 4

address: Rue Gabrielle-Perret-Gentil, 4

department: Service of Infectious Diseases

country: Switzerland

institute: Genomic Research Laboratory

summary:
Different transcriptome, metabolome, and phosphoproteome studies have already indicated a regulatory role of Ser/Thr phosphorylation in the central metabolism of S. aureus. However, it remains still unknown how this exactly tunes its metabolism. For that reason, Extreme Pathway Analysis was used to understand metabolic flux regulation by Ser/Thr phosphorylation.
YANAsquare software and YANAvergence routine were chosen to calculate pathway activities of WT, ΔpknB, Δstp, and double mutant S. aureus NewmanHG strains.
Gene expression data of S. aureus NewmanHG were collected taking the wild type and mutations of kinase (pknB), phosphatase (stp) or both (pknB/stp) phenotypes. The resulting flux changes were modelled with YANAvergence taking the different gene expression data and an established genome scale model of S. aureus metabolic modes as basis. The fluxes of the different strains were next calculated, taking the gene expression data into account.
A concerted metabolic change of fluxes was observed. In particular the pathways for peptidoglycan, nucleotide, and aromatic amino acid synthesis as well as catabolism involving aspartate transaminase (GOT) changed significantly compared to the wild type. Single mutations of pknB and stp were compared to illustrate their different contribution to the phenotype, e.g. pyrimidine synthesis is dramatically impaired by pknB deletion but much less by loss of stp. In the double knock out strain, there is higher activity of peptidoglycan, purine, and aromatic amino acids synthesis from glucose, but lower activity of pyrimidine synthesis from glucose compared to WT.
The results suggest a probable regulatory role of Ser/Thr phosphorylation in amino acid catabolism and the glycolysis/gluconeogenesis switch to provide the cell with sufficient cell wall components, nucleotides, and aromatic amino acids. Yvck is suggested to serve as regulatory protein linking Ser/Thr phosphorylation to the previous results of S. aureus metabolism. Moreover, Yvck seems in particular to be involved in the switch between glycolysis and gluconeogenesis. However, further studies based on experimental approaches are needed to demonstrate that Ser/Thr phosphorylation and Yvck are necessary for a correct cell growth under gluconeogenic conditions.
The metabolic model allows not only a comprehensive representation of these changes for all involved pathways in the four  strains, it further points out the function of the previously unannotated ycvk operon.. The relevance of these specific metabolic pathway adaptations regarding the pathogenicity of S.aureus and their contributions to the infection process will be analyzed and discussed.

sample_organism: Staphylococcus aureus subsp. aureus str. Newman

overall_design: Expression profiling by microarray covering whole S. aureus genome

first: Liang

last: Chunguang

first: Rios-Miguel

last: Ana

first: Jarick

last: Marcel

first: Priya

last: Neurgaonkar

first: Patrice

last: Francois

first: Jacques

last: Schrenzel

first: Knut

last: Ohlsen

first: Dandekar

last: Thomas


title: miRNA expression in E18.5 murine total lung tissue

city: Innsbruck

first: Verena

last: Labi

address: Innrain 80-82

department: Developmental Immunology

institute: Medical University Innsbruck

summary: Knockout of the ubiquitously expressed microRNA-17~92 cluster in mice produces a lethal developmental lung defect. We validated the equally widely expressed pro-apoptotic Bim gene as joint target of miR-17~92 cluster members. To study the contribution of miR-17~92:Bim interaction to miR-17~92 overall function, we set up a system of conditional mutagenesis of the Bim 3’UTR. Blocking miR-17~92:Bim interaction early in development phenocopied the lethal lung phenotype of miR-17~92 ablation. Thus, despite hundreds of overall predicted targets vital miRNA functions can be mediated by a single target gene.

overall_design: Total RNA was extracted from 5 wild type and 4 Bim3'UTRmut/mut E18.5 total lung tissues. 100 ng of total RNA per sample was used as input for nCounter gene expression analysis (NanoString Technologies).

first: Klaus

last: Rajewsky

first: Filippos

last: Klironomos


title: A significant and global decrease in viral gene expression occurs with deletion of the carboxyl terminal domain of the human cytomegalovirus essential protein pUL34

city: Athens

first: Mark

middle: Daniel

last: Slayton

state: Ohio

address: 7 Depot Street

department: Biomedical Sciences

institute: Ohio University

summary: The human cytomegalovirus UL34 gene encodes sequence-specific DNA-binding proteins and is essential for viral replication.  Functionally, UL34 proteins (pUL34) repress expression of the viral immune evasion genes, US3 and US9.  The amino terminal domain of pUL34 is sufficient for nuclear localization, DNA-binding and transcriptional repression.  A virus lacking the entire carboxyl terminal of pUL34 was replication competent; however, deletion of the carboxyl terminal domain significantly impaired viral replication.  There was a significant decrease in the transcription of viral genes at 4 hours post-infection following infection with the mutant virus which lacks the entire carboxyl terminal end of UL34 (UL34-COOH) relative to wild type virus, and an associated decrease in protein expression levels.  Viral gene expression for the mutant virus was also decreased at 48 hpi but to a much smaller degree.

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: RNA was harvested from human diploid fibroblasts at 4 and 48 hours post-infection with either HCMV AD169 (derived from the BAC pHB5) or from the virus containing a carboxyl terminal truncation of UL34.  Cells were infected at a multiplicity of infection of 1 plaque forming unit/cell.  The infections and RNA extractions were performed in duplicate experiments.  RNA was purified using Direct-zol RNA purification columns (Zymo Research, Irvine, CA, USA) or Qiagen RNA easy kits.  For RNA-seq analysis, strand-specific RNA library construction and sequencing were performed on duplicate biological samples for each virus and time point by Admera Health, South Plainfield, NJ and the team at Admera Health LLC (via Science Exchange).  Over 30 million reads were obtained for each sample.  RNA-seq results were analyzed using CLC Genomics Workbench (Qiagen); reads were aligned against a combined genome comprised of the human and the HCMV AD169 genomes.  TPM (transcripts per kilobase million) were determined for each sample; average TPM and p-values were determined using EDGE analysis.  Genes with fewer than 20 unique reads were discarded as background.

first: Bonita

last: Biegalke


title: Genome-wide transcriptome analysis of organotypic rafts derived from human papillomavirus type 16 infected primary keratinocytes [3D raft]

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

summary: HPV alters the host transcriptional program to establish infection and complete its lifecycle. Infection of keratinocytes has been difficult until our development of extracellular matrix (ECM)  to cell transfer system that allows efficient infection of primary keratinocytes.  Using this model, the transcriptional program of HPV infected keratinocytes grown in raft culture was analyzed by mRNA-seq.

overall_design: mRNA profiles of control and HPV16-infected human foreskin primary keratinocytes grown in 3D raft culture were generated by deep sequencing, in quintuplicate, using Illumina.

first: Martin

last: Sapp


title: Small and compact genome of the Peltaster fructicola suggests a low-energy lifestyle on plant surface [PDA15d and DT15d]

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

institute: Northwest A&F University

summary: RNA sequencing was applied to compare the transcriptome profiles of mycelium on potato dextrose for 15days (PDA15d) and mycelium on apple surface for 15days (DT15d).

overall_design: For each sample type, independent librarie was generated, sequencing was performed on an Illumina NextSeq 500 platform

first: Bo

last: Wang

first: Guangyu

last: Sun


title: Genome-wide transcriptome analysis of human papillomavirus type 16 infected primary keratinocytes


title: Zearalenone-induced aberration in gut microbiome composition and function are associated with degeneration in ovary reserve

status: Public on Nov 09 2019

city: Qingdao

first: Wei

last: Ge

state: Shandong Province

address: Changcheng Road

department: College of life sciences

institute: Qingdao Agricultural University

summary: We applied metagenomic shotgun sequencing to investigate the effects of ZEA exposure on the change of mouse gut microbiota composition and function.

overall_design: In this study, different doses of ZEA solution was intragastrically administrated to the mice according to the body weight (0, 20, 40 μg/kg/ bw/day) for 2 weeks, the mice in control group received the same volume of diluted solution. Two weeks after the final gavage, five mice in each group were randomly selected and the mouse cecum contents were collected into 1.5 ml sterile microcentrifuge tubes separately, then sent to Novogene Co. Ltd. (Beijing, China) at low temperatures quickly after liquid nitrogen flash freezer.

first: Shaojing

last: Tan


title: RNA-sequencing of lidocaine treatment on rat dorsal root ganglion neurons

city: Shanghai

first: Qianqian

last: YIN

address: Chongqing South Road

department: Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

summary: We conducted RNA-sequencing of lidocaine hydrochloride in treating rat dorsal root ganglion neurons to detect lidocaine’s effect of transcriptome profiling changes compared with control.

overall_design: Cultured neurons were treated with 5mM lidocaine or remained untreated for 24 hours before cell harvesting.

last: Yin


title: Butyrate-induced LncRNA lncly6c promotes Ly6Chigh to Ly6Clow/neg macrophages through lncly6c /C/EBP/Nr4A-1 axis

city: Tianjin

first: Ming

last: Wei

address: 94 Weijin road

department: Department of Immunology, Nankai University School of Medicine

institute: Nankai University

summary: Gut macrophages play a critical role in maintaining the homeostasis of gut immunes.   The inflammatory macrophages generally are differentiated into resident macrophages to realize their function in gut tissues. But it is unclear how these inflammatory macrophages to differentiate resident macrophages. We here found that lycLy6c, a novel ultraconserved lncRNA, may promote the differentiation of gut inflammatory macrophage into gut resident macrophages. We demonstrate gut microbiota metabolites butyrate may upregulate the expression of lncly6c. Lncly6c not only binds with transcription factor C/EBPβ but also binds with multiple components of enzyme complexes, which promote the accumulation of H3K4me3 markers on the promoter region of NrA4-1. As a result, lncly6c causes the upregulation of Nr4A-1 to promote inflammatory macrophage to differentiate the resident macrophages. These results not only offer an evidence for gut microbiota to maintaining the gut homeostasis but also suggest a potential target for the therapy for colitis-associated diseases.

overall_design: 10 × Genomics scRNA-seq was performed To further understand the effects of lncly6c on the differentiation of macrophages.

first: Yunhuan

last: Gao

first: Houbao

last: qi

first: Jianmei

first: Yazheng

last: Yang

first: Xinqi

last: Liu

first: Yuan

last: Zhang

first: Rongcun


title: β-cell adaptation in mice expressing exclusively lamin C counteracts glucose intolerance associated with aging, obesity and diabetes

city: Montpellier

first: Marion

last: de Toledo

address: 1919 route de Mende

department: IGMM

institute: CNRS UMR5535

overall_design: Refer to individual Series


title: Whole Transcriptome Characterization of Human Multipotent Adult Stem Cells (MASCs)

status: Public on Nov 08 2019

city: Valhalla

first: Paul

middle: Allen

last: Lucas

state: NY

address: Macy 008, New York Medical College

department: Orthopaedic Surgery

institute: New York Medical School

summary: We report the gene expression profile of a unique population of human multipotent adult stem cells using RNA-Seq

overall_design: Human multipotent adult stem cells isolated from human foreskin were cultured and the gene expression profile was analyzed at passage 20 using RNA-Seq

first: Jessica

last: Puzzuoli

first: Weihua

last: Huang


title: β-cell adaptation in mice expressing exclusively lamin C counteracts glucose intolerance associated with aging, obesity and diabetes (LamineA-C_RRBS)

summary: Lamin A, lamin C and progerin, produced by alternative RNA processing of LMNA gene, are intermediate filaments involved in nuclear and chromatin architecture. We investigate the ability of LMNALCS/LCS mice to adapt insulin level to physiological and physiopathologic conditions. The metabolic status of young vs old mice shows that old LMNALCS/LCS mice are obese but glucose tolerant due to an increased β cell mass and insulin secretion. By combining RNAseq and RRBS analysis, we observed a transcriptional disregulation of genes related to translation and mitochondria, confirmed by functionnal analysis, suggesting that LMNALCS/LCS mice set up a transcriptional program to adapt β cell mass and function to insulin demand. To investigate this point, we challenged young mice by inducing T1DM and T2DM. In these contexts, we show that LMNALCS/LCS mice are able to normalize their fasting glycemia by both increasing insulin secretion and  regenerating β cells.

overall_design: islets of Langherans isolated from wt and lmna LCS mice are analysed as 2 replicates. Each replicate is  made a pool of islets from 3 different mice

first: Carine

last: Chavey

first: Jamal

last: Tazi

first: Marine

last: Pratlong

first: Célia

last: Barrachina


title: Habenular Tcf7l2 links nicotine addiction to diabetes.

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

summary: Translational profiling of cholinergic neurons in the MHb allow identification of genes that are responsive to metabolic changes. Here we use bac TRAP to access translating mRNAs. We confirm a role for the transcription factor Tcf7l2 in the MHb in both glucose homeostasis and nicotine intake.

overall_design: Total RNA from various brain regions was sequenced and Tcf7l2 gene expression compared between regions. Polysome-bound mRNAs from MHb TRAP IPs were compared to determine sucrose-regulated genes.

middle: L

last: Ables

first: Ines

last: Ibanez-Tallon


title: Serum tRNA-derived fragment (tRF-Pro-AGG-018) as a novel diagnostic biomarker for discriminating papillary thyroid carcinoma from nodular goiter

city: Beijing

first: Jiajia

last: Tang

address: No 1 Shuai- fuyuan, Wangfujing

institute: Peking Union Medical College Hospital

summary: Context: Papillary thyroid cancer (PTC) is the most common thyroid cancer with dramatically increasing worldwide. Accurate diagnosis is crucial to avoid unnecessary overtreatment for low-risk patients, but the currently available markers are still insufficient. tRNA-derived fragments (tRFs) are emerging as a new class of small non-coding RNAs due to their potential roles as novel biomarkers and therapeutic targets in cancer. However, their involvement in papillary thyroid carcinoma (PTC) is still unclear. Objectives: This study was performed to identify differentially expressed tRFs in PTC and investigate the role of serum tRFs to discriminate PTC from nodular goiters (NGs).Methods and Materials: tRF expression profiles were measured in pooled sera from patients with PTCs (n=6), NGs (n=6) and healthy subjects (n=6) using high-throughput sequencing (cohort1). One selected tRF candidate was validated in the same individual samples (cohort1) by qRT-PCR. The confirmed tRF was further validated in a larger second cohort including patients with PTCs (n=30), NGs (n=20) and healthy individuals (n=18).Results: Our sequencing results showed that circulating tRFs were differentially expressed in patients with PTC compared with those with NG and healthy people. After the validation in individual samples, tRF-Pro-AGG-018 was confirmed as differentially elevated in serum samples of patients with PTC. These results were further confirmed in a larger second cohort. Moreover, tRF-Pro-AGG-018 exhibited good diagnostic performance with a sensitivity of 0.7222 and a specificity of 0.8846 for PTC and it was associated with several targeted genes of PTC. Conclusions: Our study identified that the serum tRFs were differentially expressed in PTC compared with NG and healthy individuals. Notably, circulating tRF-Pro-AGG-018 was found to have a significant elevation in patients with PTC and exhibited good diagnostic performance with relatively high sensitivity and specificity for PTC. Our findings suggest tRFs might serve as novel circulating biomarkers in predicting patients with PTC, which may prevent unnecessary thyroid surgeries for low-risk and benefit from optimal

first: Qiiong

first: Xuehua

last: Xi

first: Luying

first: Ruina

last: Zhao

first: Xingjian

last: Lai

first: Bo

first: Yuxin

last: Jiang


title: β-cell adaptation in mice expressing exclusively lamin C counteracts glucose intolerance associated with aging, obesity and diabetes (LamineA-C_RNASeq)

first: Marion

overall_design: islets of Langherans isolated from wt and lmna LCS mice are analysed as 3 replicates. Each replicate is made of a pool of islets from 3 different mice


title: Integrated analysis of circRNA-miRNA-mRNA ceRNA network responses to heat stress in rainbow trout (Oncorhynchus mykiss) liver

city: lanzhou

first: jinqiang

last: quan

address: No. 1 Yingmen Village, Anning District

department: College of Animal Science & Technology

institute: Gansu Agricultural University

summary: With the intensification of global warming, rainbow trout is suffering from varying degrees thermal stimulation, heat stress may cause pathological signs or diseases by reducing the immune roles and then lead to mass mortality, so high temperatures severely restrict the development of its aquaculture. Understanding the molecular regulation mechanism of rainbow trout under heat stress is used to take measures to relieve symptoms. We performed multiple transcriptomic analysis of liver tissues from rainbow trout under heat stress (24 °C) and control conditions (18 °C) to identify circRNAs, miRNAs and mRNAs. Changes of non-specific immune parameters revealed that strong stress response of rainbow trout is caused in 24 °C. A total of 324 DEcircRNAs, 105 DEmiRNAs, and 1885 DEmRNAs were identified from six libraries, and ceRNA regulatory network is constructed. 301 circRNA–miRNA and 51 miRNA–mRNA negative correlation pairs were screened from ceRNA regulatory network, and predicted three regulatory correlation pairs that novel_circ_003889 - novel-m0674-3p - hsp90ab1, novel_circ_002325 - miR-18-y - HSPA13 and novel_circ_002446 - novel-m0556-3p - hsp70. Some genes involved in metabolic process, biological regulation or response to stimulus are highly induced at high temperatures. Several important pathways involved in heat stress were characterized, such as Protein processing in endoplasmic reticulum (ER), Estrogen signaling pathway, HIF-1 signaling pathway, etc. These results extend our understanding of the molecular mechanisms of heat stress response and expected to provide a novel insight into develop strategies for relieve heat stress.

overall_design: liver tissues of rainbow trout under heat stress (24℃, HS, n=3) and control (18℃, CG, n=3) conditions to identify induced miRNAs

first: Zhe

last: Liu

first: Jinqiang

last: Quan


title: Effect of SHP2 inhibition on hepatic stellate cell transcriptome.

city: Rochester

first: Aditya

last: Bhagwate

address: 200 1st Street SW

institute: Mayo Clinic

summary:
Hepatic stellate cell autophagy inhibits extracellular vesicle release to attenuate liver fibrosis.
Primary human hepatic stellate cells were treated with PDGF or PDGF + SHP2 inhibitor. RNA was purified and submitted for sequencing to Mayo Clinic Genomics Core. After applying the filters FDR>0.05, Log2(FC)>1 and RPKM>15, we ended up with nearly 300 genes differentially regulated between the two conditions. Ingenuity Pathway Analysis revealed that Ostheoarthritis was the first pathway to be differentially regulated. From this pathway, REDD1 (DDIT4 transcript), an mTOR inhibitor, was further explored, especially in the context of extracellular vesicle release.

overall_design: Primary human hepatic stellate cells were treated with PDGF or PDGF + SHP099 for 48 hours.

first: Enis

last: Kostallari


title: Myeloid-derived suppressor cells facilitie invasion and metastasis of papillary thyroid cancer cells by repressing miR-486-3p

city: Guangzhou

first: Li

last: Chen

address: No. 58, Zhongshan 2nd Road

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

summary:
Background：In present study, we aimed to evaluate the level as well as function of circulating MDSCs in papillary thyroid cancer (PTC), and also explore the underlying mechanism of MDSCs during tumor progression.
Methods：microRNA arrays and RNA-seq analysis were conducted to screened out differentially expressed miRNAs and mRNAs between TPC-1 cells cocultured with PMN-MDSCs and untreated TPC-1 cell line.
Results：19 miRNAs were differentially expressed, of which 10 were downregulated and 9 were upregulated in MDSC-conditioned cancer cells. GO analysis of miRNA predicted target genes showed that inflammatory related response were enriched. Besides, these genes were mainly related to NF-kappa B, PI3K-AKT and TNF signaling pathways which are associated with immune response as well as cancer development by KEGG pathway analysis. For validation, qRT-PCR was used to assess the differentially expressed miRNA and the trends in the expression was consistent between microRNA-seq and qRT-PCR.
Conclusion：Collectively, our work explore the mechanism by which PMN-MDSCs paly a critical role in PTC

overall_design: 6 samples of TPC-1 cells cocultured with PMN-MDSCs and 4 samples of TPC-1 untreated cells were subjected to mirna and mrna profiles


title: Low-dose decitabine priming endows CAR T cells with enhanced and persistent anti-tumor potential by epigenetic reprogramming

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

summary: Chimeric antigen receptor T (CAR T) cells targeting CD19 have achieved breakthroughs in the treatment of haematological malignancies, but many clinical studies have also shown that a proportion of patients relapse after remission.In this study, we designed CART treatment by DNMTi?dCART) inhibitor and found that dCAR T cells retained relatively potent antitumour activity compared with CAR T cell upon target antigen recognition. It may be associated with memory and anti-exhausion. Our transcriptional analysis underscores the potential of  dCAR T cells.

overall_design: In order to assess the different phenotypic and functional patterns of CARs between dCAR T and CAR T, we compared the genome-wide transcriptional profiles of dCAR and CAR T cell before and after cocultured with Raji cells for 24 h.

first: Han

last: Weidong


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [Proximal Colon]

city: Santa Cruz

first: Todd

last: Lowe

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

summary: The goal of this study was to determine the state of the tRNA transcriptome in Proximal Colon tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Proximal Colons.  These experiments were performed in triplicate (biological) and subjected to NGS.

first: Jonathan

middle: M

last: Howard

first: Andrew

last: Holmes

first: Patricia

middle: P

last: Chan

first: Aidan

last: Manning


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [brain]

summary: The goal of this study was to determine the state of the tRNA transcriptome in Brain tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male brains.  These experiments were performed in triplicate (biological) and subjected to NGS.


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [heart]

summary: The goal of this study was to determine the state of the tRNA transcriptome in Heart tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Hearts.  These experiments were performed in triplicate (biological) and subjected to NGS.


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [kidney]

summary: The goal of this study was to determine the state of the tRNA transcriptome in Kidney tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Kidneys.  These experiments were performed in triplicate (biological) and subjected to NGS.


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [liver]

summary: The goal of this study was to determine the state of the tRNA transcriptome in Liver tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Livers.  These experiments were performed in triplicate (biological) and subjected to NGS.


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [Thymus]

summary: The goal of this study was to determine the state of the tRNA transcriptome in Thymus tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Thymus.  These experiments were performed in triplicate (biological) and subjected to NGS.


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq) [Distal Colon]

summary: The goal of this study was to determine the state of the tRNA transcriptome in Distal Colon tissue of Mus Musculus (Mouse).  This includes expression data of mature tRNAs and tRNA fragments (tRFs), as well as associated modification  states of these RNAs assessed using mismatching percentages from sequencing data.

overall_design: Included are ARM-seq and DM-tRNA-seq libraries derived from isolated total small RNA from C57BL/6J male Distal Colons.  These experiments were performed in triplicate (biological) and subjected to NGS.


title: AlkB-facilitated RNA methylation sequencing (ARM-seq) and Demethylase-thermostable group II intron RT tRNA sequencing (DM-tRNA-seq)

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


title: Life-long epigenetic programming of cortical architecture by maternal 'Western' diet during pregnancy [RRBS]

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: The evolution of human diets led to preferences towards polyunsaturated fatty acid (PUFA) content with ‘Western’ diets enriched in ω-6 PUFAs. Mounting evidence points to ω-6 PUFA excess limiting metabolic and cognitive processes that define longevity in humans. When chosen during pregnancy, ω-6 PUFA-enriched ‘Western’ diets can reprogram maternal bodily metabolism with maternal nutrient supply precipitating the body-wide imprinting of molecular and cellular adaptations at the level of long-range intercellular signaling networks in the unborn fetus. Even though unfavorable neurological outcomes are amongst the most common complications of intrauterine ω6 PUFA excess, cellular underpinnings of life-long modifications to brain architecture remain unknown. Here, we show that nutritional ω-6 PUFA-derived endocannabinoids desensitize CB1 cannabinoid receptors, thus inducing epigenetic repression of transcriptional regulatory networks controlling neuronal differentiation. We found that cortical neurons lose their positional identity and axonal selectivity when mouse  fetuses are exposed to excess ω-6 PUFAs in utero. Conversion of ω-6 PUFAs into endocannabinoids disrupted the temporal precision of signaling at neuronal CB1 cannabinoid receptors, chiefly deregulating Stat3-dependent transcriptional cascades otherwise required to execute neuronal differentiation programs. Global proteomics identified the immunoglobulin family of cell adhesion molecules (IgCAMs) as direct substrates, with DNA methylation and chromatin accessibility profiling uncovering epigenetic reprogramming at >1,400 sites in neurons after prolonged cannabinoid exposure. We found anxiety and depression-like behavioral traits to manifest in adult offspring, which is consistent with genetic models of reduced IgCAM expression, to suggest causality for cortical wiring defects. Overall, our data uncover a regulatory mechanism whose disruption by maternal food choices could limit an offspring’s brain function for life.

overall_design:
DNA methylation analysis from embryonic brain, 4 control samples  and 3 treated samples
CeMM - Center for Molecular Medicine

first: Valentina

last: Cinquina

first: Daniela

last: Calvigioni

first: Matthias

last: Farlik

first: Florian

last: Halbritter

first: Victoria

last: Gernedl

first: Sally

last: Shirran

first: Matthew

last: Fuszard

first: Catherine

last: Botting

first: Patrick

last: Poullet

first: Fabiana

last: Piscitelli

first: Zoltán

last: Máté

first: Gábor

last: Szabó

first: Yuchio

last: Yanagawa

first: Siegfried

last: Kasper

first: Vincenzo

last: Di Marzo

first: Ken

last: Mackie

first: Chris

last: McBain

first: Erik

last: Keimpema

first: Tibor

last: Harkany


title: Life-long epigenetic programming of cortical architecture by maternal 'Western' diet during pregnancy [ATAC-seq]

first: Christoph

last: Bock

overall_design:
ATAC-seq analysis from cortical neurons untreated or treated with agonist or antagonist of CB1R (6 samples/condition)
CeMM - Center for Molecular Medicine

first: Valentina

last: Cinquina

first: Daniela

last: Calvigioni

first: Matthias

last: Farlik


title: Transcriptome-SIP of hydrocarbon degrader adaption under dual electron acceptor availability in aquifer sediments

city: Bayreuth

first: Tillmann

last: Lueders

state: Bayern

address: Dr.-Hans-Frisch-Straße 1-3

department: Lehrstuhl Ökologische Mikrobiologie (ÖMIK)

institute: Universitaet Bayreuth

summary: We demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with 13C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of 13C-labelling. The expression of distinct oxygenase-based catabolic pathways for toluene degradation was clearly apparent in 13C-labelled mRNA. We discuss how these direct insights into the gene expression and adaptation mechanisms within complex degrader communities can guide more integrated approaches in monitoring and restoration of contaminated sites.

overall_design: We set up a microcosm experiment using hydrocarbon-contaminated sediment incubated under 4 redox conditions: aerobic, microoxic, microoxic with nitrate, and anoxic with nitrate. Microcosms were provided with 13C-labeled toluene as substrate, and extracted RNA was separated into heavy (labeled) and light (unlabeled) fractions, which were sequenced to determine the identity of toluene-degraders in the 4 experimental conditions.

first: Lauren

last: Bradford


title: Leukocytes

city: Baltimore

first: Donald

middle: Welton

last: MacGlashan

address: 5501 Hopkins Bayview Circle

department: Allergy and Clinical Immunology

institute: Johns Hopkins University

overall_design: Refer to individual Series


title: Basophils, CD34+-derived expression profiles (in vitro)

summary:
CD34+ cells were isolated from leukopheresis preparations by Miltenyi positive selection kits for CD34 cells and cultured in stemPro medium+ supplement
2 culture conditions were compared, G1 = IL-3 at 5 ng/ml for the 17 days of culture or G3 = IL-3 at 5 ng/ml + SCF (stem cell factor) at 4 ng/ml + Flt3L at 8 ng/ml

overall_design: CD34+ progenitor cells were cultured by two methods


title: A systematic analysis of nuclear heat-shock protein 90 identifies a metazoan-specific regulatory module

city: Freiburg

first: Barbara

last: Hummel

address: Stübeweg 51

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: Molecular chaperones such as heat-shock proteins (HSPs) help in protein folding and complex assembly processes. Their role in cytosol has been very well elucidated. Chaperones are also present in the nucleus, a compartment where proteins enter after being fully folded in the cytosol, raising an important question about chaperones function in this compartment. We have performed a systematic analysis of nuclear heat- shock protein 90 to identify regulatory functions of this chaperone in the nucleus. Combining physical and genetic interactomes with a cancer co-expression screen allowed us to define 'core functional interactors' of nuclear HSP90 consisting of five proteins. Using transcriptional studies we identified Host Cell Factor C1 (HCFC1) as a metazoan-specific transcriptional regulator that depends on HSP90 for its stability in the nucleus. We found that HSP90 is required for optimal activity of HCFC1 in transcription. Thus our study provides the first global insight into the function of nuclear HSP90.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-Seq and RNA-Seq

first: Aneliya

last: Antonova

first: Ritwick

last: Sawarkar


title: ATACseq of human basophils, B cells and CD34-derived basophils

summary: human basophils and B cells (that were purified to >98% homogeneity) and CD34-derived basophils were processed for ATACseq

overall_design: 100,000 to 200,000 resting cells were lysed and treated with the transposition reaction mix (Nextera)(all further preparation used Nextera reagents and tags), fragmented DNA amplified by PCR and fragments run on electrophoresis to isolate 200-1000 bp fragments. Sequencing was performed by the Illumina Nextseq sequencing using high-output 75-cycle reagent kit for 75 bp reads. 100-400 million reads


title: Human leukocyte expression profiles (in vitro)

summary:
CD34+ progenitor cells were cultured for 0 or 21 days in StemPro medium + supplement + IL-3 at 5 ng/ml
Basophils, eosinophils and plasmacytoid dendritic cells were purified to near homogeneity and lysed for miRNA and mRNA. Basophils were purified by negative selection (StemSep Abs, miltenyi columns), eosinophils by StemSep Abs and pDC by positive selection after removing monocytes. The method starting with a 2-step Percoll gradient that put eosinophils in the pellet, basophils in the middle layer and pDC in the upper layer.

overall_design: Cells were isolated from purified to high homegeneity (99%) and lysed for RNA.


title: Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs [sRNA-seq]

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

summary: RNA interference (RNAi) is a conserved, RNA-mediated, regulatory mechanism in eukaryotes. In plants, it plays an important role in growth, development and resistance against viral infections. As a counter-defence, plant viruses, e.g. geminiviruses, encode RNAi suppressors, such as AC2, AC4 and AV2. To obtain Nicotiana tabacum virus resistant plants against Tomato leaf curl New Delhi virus (ToLCNDV), we employ the biogenesis pathway of a class of endogenous siRNAs, the trans-acting siRNAs (ta-siRNAs), by engineering artificial ta-siRNAs (ata-siRNAs) targeting the AC2 (TRiV-AC2) and AC4 (TRiV-AC4) RNAi suppressors using miRNA390 dual target sites. The mode of action of ta-siRNAs comprises of the cleavage of the target (similar to the miRNA targeting). Using degradome approaches, the abundance of the resulting 3' fragment of the cleaved transcript can be quantified and the precise localization of the cleavage on the target mRNA can be identified. We sequenced degradome libraries of Nicotiana tabacum plants infected with ToLCNDV which were treated with the ata-siRNA-AC2 construct; mock-treated plants were used as controls. Following quality checks, the abundance distributions of the degradation fragments were normalized. The transcripts with different cleavage patterns was the AC2, supporting the conclusion that an efficient cleavage of the target occurred, without significant off-target effects.

overall_design: 2 biological replicates of small RNA libraries, infiltrated with TRiV-AC2, were analysed.

first: Irina

last: Mohorianu

first: Tamas

last: Dalmay

first: Sunil

last: Mukherjee

first: Indranil

last: Dasgupta


title: Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs


title: Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [WGBS]

city: UNSW Sydney

first: Yizhou

last: Huang

state: NSW

address: High Street

country: Australia

institute: University of New South Wales

summary:
Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types.
This submission represents the WGBS component of the study.

overall_design: Examination of binding profiles of GR, CTCF, H3K9ace, H3K27ace, H3K4me3 and H3K27me3 in combination with RNAseq, ATACseq and whole genome bisulfite sequencing data before and after Dex treatment in ALL xenograft cells.

first: Duohui

last: Jing

first: Richard

last: Lock

first: Dominik

last: Beck


title: Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [ATAC-seq]

summary:
Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types.
This submission represents the ATACseq component of the study.


title: Next-generation sequencing reveals a novel role of lysine-specific demethylase 1 in adhesion of rhabdomyosarcoma cells [RNA-seq]

status: Public on Nov 07 2019

city: Frankfurt am Main

first: Simone

last: Fulda

state: Hessen

address: Komturstraße 3A

department: Institute for experimental cancer research in pediatrics

institute: Goethe University Frankfurt

summary: Lysine-specific demethylase 1 (LSD1) has been shown to be overexpressed in rhabdomyosarcoma (RMS) tumor samples. This study aims at elucidating changes in the RNA expression profile by RNA Sequencing in control and LSD1 knockdown conditions using transient silencing with siRNA. In addition, ChIP Sequencing was employed to investigate changes in the histone methylation pattern of H3K4me2 as a target of LSD1 in control and LSD1 knockdown conditions.

overall_design: Examination of changes in RNA expression profile between wildtype and knockdown conditions. Experiment was performed in three biological replicates.

first: Tinka

last: Haydn

first: Dominica

last: Willmann

first: Eric

last: Metzger


title: Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [ChIP-seq]

summary:
Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types.
This submission represents the ChIPseq component of the study.


title: Next-generation sequencing reveals a novel role of lysine-specific demethylase 1 in adhesion of rhabdomyosarcoma cells


title: Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia


title: Next-generation sequencing reveals a novel role of lysine-specific demethylase 1 in adhesion of rhabdomyosarcoma cells [ChIP-seq]

overall_design: Examination of a histone methylation profile in wildtype and knockdown conditions. Two biological replicates were used and data of both biological replicates was pooled for final analysis.


title: Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [RNA-seq]

summary:
Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including inflammation, autoimmunity, and lymphoid malignancies. While a large component of these effects can be attributed to glucocorticoid-induced apoptosis of normal and malignant lymphocyte, the molecular basis for the lymphocyte-specific apoptosis remains unclear. Moreover, the mechanisms of glucocorticoid resistance in lymphoid malignancy are poorly defined, and remain a significant barrier to cure. To address these issues, we first performed a global analysis of chromatin accessibility in lymphoid and non-lymphoid cells to map lymphocyte-specific open chromatin domains (LSOs). We then integrated these domains with glucocorticoid receptor (GR) binding-induced RNA transcription and chromatin modulation in an in vivo patient-derived xenograft (PDX) model of acute lymphoblastic leukemia (ALL). This led to the identification of LSOs associated with glucocorticoid resistance in ALL. One such LSO was at the pro-apoptotic BIM gene locus, where a chromatin architectural protein CTCF binding was found only in lymphocytes but not in other cell types. The GR cooperated with CTCF to mediate interactions between the BIM promoter and the LSO to direct DNA looping, thus triggering BIM transcription. Importantly, this LSO was heavily DNA methylated in glucocorticoid resistant PDXs and non-lymphoid cells. This study demonstrates for the first time that lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in ALL and proposes a model for the lack of glucocorticoid sensitivity in non-lymphoid cell types.
This submission represents the RNAseq component of the study.


title: Nicotiana tabacum degradome analysis using high definition adapters proves an efficient targeting method against the Tomato leaf curl New Delhi virus using artificial ta-siRNAs [PARE]

overall_design: Degradome libraries comprising of 2 biological replicates of control samples and 2 biological replicates of treatment samples.


title: Fork Pausing Complex Engages Topoisomerases at the Replisome

city: Geneva

first: Maksym

last: Shyian

state: Geneva

address: 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland

department: Molecular Biology

institute: University of Geneva

summary: Replication forks temporarily or terminally pause at hundreds of hard-to-replicate regions around the genome.  A conserved pair of budding yeast replisome components Tof1-Csm3 (fission yeast Swi1-Swi3 and human TIMELESS-TIPIN) acts as a ‘molecular brake’ and promotes fork slowdown at proteinaceous replication fork barriers (RFBs), while the accessory helicase Rrm3 assists the replisome in removing protein obstacles.  Here we show that Tof1-Csm3 complex promotes fork pausing independently of Rrm3 helicase by recruiting topoisomerase I (Top1) to the replisome.  Topoisomerase II (Top2) partially compensates for the pausing decrease in cells when Top1 is lost from the replisome.  The C-terminus of Tof1 is specifically required for Top1 recruitment to the replisome and fork pausing but not for DNA replication checkpoint (DRC) activation.  We propose that forks pause at proteinaceous RFBs through a ‘sTOP’ mechanism (‘slowing down with TOPoisomerases I-II’), which we show also contributes to protecting cells from topoisomerase-blocking agents.

overall_design: Genome-wide distribution of Top1 was measured by ChIP-seq at the time of early origin firing in budding yeast synchronized in S phase. Genome-wide replisome components (Cdc45, Mcm4, Pol2) distribution was measured by ChIP-seq in asynchronous budding yeast cultures.

first: Benjamin

last: Albert

first: Andreja

last: Zupan

first: Vitalii

last: Ivanitsa

first: Gabriel

last: Charbonnet

first: Daniel

last: Dilg

first: David

last: Shore


title: The transcriptomic differences between Th1, Tr1, and Tneg cells in controlled human malaria infection

city: Herston

first: Susanna

last: Ng

state: QLD

address: 300 Herston Road

department: Immunology

institute: QIMR Berghofer Medical Research Institute

summary: This study was designed to determine the differences in gene transcripts between CD4+ T helper (Th)1, Tr1, and Tneg cells during controlled human malaria infection.

overall_design: Bulk RNA-sequencing was performed on CD4+ T helper (Th)1 (IFNγ+ IL-10-), Tr1 (IFNγ+ IL-10+), and Tneg (IFNγ- IL-10-) cells sorted from the peripheral blood mononuclear cells (PBMCs) of n = 6 participants in a controlled human malaria infection trial at day 14 p.i. Cells were stimulated with phorbol 12-myristate 13-acetate (PMA) and ionomycin prior to sorting by cytokine capture flow cytometry.

first: Christian

last: Engwerda

first: Chelsea

last: Edwards


title: CHCHD2 gene KO effect in iPSC drived motor neurons

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

summary: We investigate the transcriptional changes caused by the knock-out of neuropathy linked gene CHCHD2.

overall_design:
Two independent controls (independent differentiations) of the same control are used to compare alternations caused by the loss of CHCHD2 in the same background. All cell lines are derived from the same control iPSC. Each sample has 4 replicates.

Please note that the control raw data from GSE133763 study is being re-analyzed as indicated in the corresponding sample description field.

first: Sandra

last: Harjuhaahto

first: Markus

last: Sainio

first: Henna

last: Tyynismaa


title: CHCHD10 gene KO effect in iPSC drived motor neurons

summary: We investigate the transcriptional changes caused by the knock-out of neuropathy linked gene CHCHD10.

overall_design: Two independent controls (independent differentiations) of the same control are used to compare alternations caused by the loss of CHCHD10 in the same background. All cell lines are derived from the same control iPSC. Each sample has 4 replicates.


title: Transcriptome profiling of differentiating mESCs upon treatment with Crataegus extract WS®1442 and its subfraction MeOH eluate

city: Kiel

first: Dennis

last: Schade

address: Gutenbergstr. 76

department: Pharmaceutical and Medicinal Chemistry

institute: Christian-Albrechts-University Kiel

summary: In order to get mechanistic insights into the cardiomyogenic and differentiation-promoting activity of Crataegus spp. Extract WS®1442 and the identified bioactive subfractions (MeOH eluate), we have employed whole genome microarray expression profiling after 6 hours and 24 hours of treatment. We found that stress-associated genes are affected as well as specific signaling pathways such as TGFbeta, FGF, BDNF and retinoic acid.

overall_design: Cardiac differentiation assays in murine embryonic stem cells (mESCs, CGR8-Myh6-GFP) were performed on 384-well plates and cells treated on day 4 with vehicle control (DMSO, n = 2), WS®1442 (0.25 mg/mL, n = 3) or MeOH eluate (0.1 mg/mL, n = 3) for either 6 hours or 24 hours before cells were collected for RNA extraction (= total of 16 samples). RNA extraction and microarray analysis on ArrayXS Mouse chips was done by OakLabs (Hennigsdorf, Germany).

first: Halver

last: Jonas

first: Schade

last: Dennis


title: Transcriptomic changes of mouse monocytes and macrophages after ischemic stroke

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

summary: Blood monocytes/macrophages infiltrate the brain after ischemic stroke and critically influence brain injury and regeneration. We investigated stroke-induced transcriptomic changes of monocytes/macrophages by RNA sequencing profiling, using a mouse model of permanent focal cerebral ischemia. Compared to non-ischemic conditions, brain ischemia induced only moderate genomic changes in blood monocytes, but triggered robust genomic reprogramming in monocytes/macrophages invading the brain. Surprisingly, functional enrichment analysis of the transcriptome of brain macrophages revealed significant overrepresentation of biological processes linked to neurovascular remodeling, such as angiogenesis and axonal regeneration, as early as 5 days after stroke, suggesting a previously underappreciated role for macrophages in initiating post-stroke brain repair. Upstream Regulator analysis predicted peroxisome proliferator-activated receptor gamma (PPARγ) as a master regulator driving the transcriptional reprogramming in post-stroke brain macrophages. Importantly, myeloid cell-specific PPARγ knockout (mKO) mice demonstrated lower post-stroke angiogenesis and neurogenesis than wild-type mice, which correlated significantly with the exacerbation of post-stroke neurological deficits in mKO mice. Collectively, our findings reveal a novel repair-enhancing transcriptome in brain macrophages during post-stroke neurovascular remodeling. As a master switch controlling genomic reprogramming, PPARγ is a rational therapeutic target for promoting and maintaining beneficial macrophage functions, facilitating neurorestoration, and improving long-term functional recovery after ischemic stroke.

overall_design: C57BL/6J mice (9 weeks old, male) were subjected to focal cerebral ischemia induced by permanent occlusion of the left distal middle cerebral artery and left common carotid artery. The CD11b+CD45high cell population was collected by fluorescence-activated cell sorting from the blood after sham operation, and from the blood and brain after ischemic stroke. There were 3 groups: sham blood, stroke blood, and stroke brain. In each group there were 3 biological replicates. For blood samples, each replicate was from one mouse. For brain samples, each replicate was pooled from 5 mouse brains. The sorted cells were subjected to mRNA sequencing.

first: Jun

last: Chen