title: DNA Methylation Reprograms Metabolic Gene Expression in End-Stage Human Heart Failure

status: Public on Jul 25 2019

first: Mark

middle: Emile

last: Pepin

address: 870 Quarry Road

department: Cardiovascular Medicine

summary: Heart Failure (HF) is a complex clinical disease and leading cause of hospitalization in the United States. Although precision-based treatment options are ultimately preferred, understanding the common underlying features of HF is also needed to develop universal therapies that address its pathogenesis. Among the etiology-independent molecular changes known to occur in HF is a global shift in the heart’s metabolic substrate preference. Transcriptional reprogramming of the heart has been shown to mediate this metabolic switch towards glycolytic metabolism; however, the molecular machinery that reactivate dormant genes remain largely unknown. In the current study, we hypothesized that the cardiac epigenome regulates metabolism via alterations in DNA methylation.

overall_design: We used paired whole-genome bisulfite sequencing and next-generation RNA sequencing of left ventricle tissue from 6 patients with end-stage heart failure and 3 non-failing donor hearts. Distribution of genome-wide methylation changes was localized to both the promoter-associated and gene body-associated CpG sites in HF relative to non-failing hearts. Gene set enrichment of genes coupled with promoter hyper-methylation identified suppression of oxidative metabolic pathways, whereas hypo-methylated promoters identified genes associated with anaerobic glycolysis. Furthermore, we found the Nuclear Respiratory Factor 1 (NRF1) binding site as a candidate DNA methylation-sensitive regulator of cardiac fatty acid oxidation. The current study therefore underscores the importance of DNA methylation as a molecular feature describes the failing hearts fetal-like metabolic preference.

middle: E

first: Stavros

last: Drakos

first: Adam

last: Wende

first: Omar

last: Wever-Pinzon


title: Trunk events present minimal intra- and inter-tumoral heterogeneity in hepatocellular carcinoma [gene expression]

status: Public on Jul 05 2019

city: Barcelona

first: Sara

last: Torrecilla

state: Catalonia

address: Rossello Street, 149

country: Spain

institute: IDIBAPS

summary: Introduction: According to the clonal model of tumor evolution, trunk alterations arise at early stages and are ubiquitous. Through the characterization of early stages of hepatocarcinogenesis, we aimed to identify trunk alterations in HCC and study their intra- and inter-tumor distribution in more advanced lesions.    Methods: 151 samples representing the multi-step process of hepatocarcinogenesis were analyzed by targeted-sequencing and SNP array. Genes altered in early lesions [31 dysplastic nodules (DNs) and 38 small HCCs (sHCC)] were defined as trunk. The distribution of candidate trunk genes was explored in: a) different regions of large tumors [43 regions of 21 tumors, (2-3 regions/tumor)]; and b) different nodules of the same patient [39 multinodular tumors from 17 patients]. Multinodular lesions were classified as intrahepatic metastases (IMs) or synchronous tumors based on chromosomal aberrations.     Results: TERT promoter mutations (10.5%) and broad copy-number aberrations in chromosomes 1 and 8 (3-7%) were identified as trunk gatekeepers in DNs and were maintained in sHCCs. Trunk drivers identified in sHCCs included TP53 (23%) and CTNNB1 (11%) mutations, and focal amplifications or deletions in known drivers (6%). Overall, TERT, TP53 and CTNNB1 mutations were the most frequent trunk events in early stages. 89% of mutations in these genes were shared between different regions of large tumors. In multinodular HCCs, 35% of patients harbored IMs. 85% of mutations in TERT, TP53 and/or CTNNB1 were retained in primary and metastatic tumors.    Conclusions: Trunk events in early stages (TERT, TP53, CTNNB1 mutations) were ubiquitous across different regions of the same tumor and between primary and metastatic nodules in >85% of cases. This concept supports the knowledge that single biopsies would suffice to capture trunk mutations in HCC.

overall_design: 36 paraffin-embedded tumors from 16 patients presenting multinodular cases (2-3 nodules/patient) were collected and RNA was extracted. Matched non-tumor cirrrhotic tissue was also collected for all cases. Whole-genome trasncriptome analysis was done using HumanHT-12 WG-DASL V4.0 R2 expression beadchip (Illumina) according to manufacturer’s protocols. Raw data were normalized using cubic spline algorithm implemented in the Illumina Normalizer module of the GenePattern analysis toolkit (www.broadinstitute.org/genepattern) as previously described (Sia D et al, Gastroenterology, 2013).

first: Josep

middle: M

last: Llovet

first: Daniela

last: Sia


title: Transcriptomic analysis of class I odorant receptor enhancer deletion [LD]

status: Public on Jul 04 2019

city: Evanston

first: Thomas

last: Bozza

state: IL

address: 2205 Tech Drive, Hoga 2-160

department: Neurobiology

country: USA

institute: Northwestern University

type: Expression profiling by high throughput sequencing

summary: We used RNAseq based transcriptome analysis to compare gene expression changes in the olfactory mucosa resulting from CRISPR-based deletion of a putative enhancer in the class I odorant receptor gene cluster.

overall_design: 6 control and 6 enhancer deletion animals. Age matched. Large Deletion = 408,217 bp (chr7: 102,509,797-102,918,014)


title: Transcriptomic analysis of class I odorant receptor enhancer deletion [eC]

overall_design: 3 control and 3 enhancer deletion animals. Age matched. Delection eC = 1,005 bp (chr7:102,916,999-102,918,004)


title: Transcriptomic analysis of class I odorant receptor enhancer deletion

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

overall_design: Refer to individual Series


title: Transcriptomic analysis of class I odorant receptor enhancer deletion [eA]

overall_design: 6 control and 6 enhancer deletion animals. Age matched. Deletion eA = 912 bp (chr7:102,509,701-102,510,612)


title: Aging affects expression and variability of genes in the human liver

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

summary:
Identification of genes altered by aging in the human liver
We identified genes that were differentially expressed in males only, females only, or in all individuals between the young and old using microarray.

overall_design: We compared gene expression profiles in liver samples from young (21-45 years) and old (69+ years) men and women to determine changes in the expression of xenobiotic metabolism enzymes and transporters.

first: Janice

middle: S

last: Lee

first: J

middle: C


title: Effect of 5-HT and fluoxetine on Turicibacter sanguinis gene expression in vitro

city: Los Angeles

last: Fung

state: CA

address: 610 Charles E Young Dr. East

institute: University of California, Los Angeles

summary: The overall goal of this study is the test the effect of 5-HT and fluoxetine on Turicibacter sanguinis gene expression in vitro

overall_design: Triplicates were performed on each condition (vehicle, 5-HT, fluoxetine, 5-HT plus fluoxetine)

first: Elaine

last: Hsiao


title: Genome-wide measurement of H3K4me3 and H3K36me3 levels following depletion of RNAPII from the nucleus via an anchor-away system.

city: Oxford

first: Jane

last: Mellor

address: South Parks Rd

department: Biochemistry

country: United Kingdom

institute: University of Oxford

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Despite the well-reported association between H3K4me3 and transcription, depletion of RNAPII from the nucleus has little effect on H3K4me3, while having a much larger effect on H3K36me3

overall_design: Measuring genome-wide levels of H3K4me3 and H3K36me3 in 20 minute intervals following removal of RNAPII from the nucleus via an anchor-away system.

first: Philipp

last: Lorenz


title: Genome-wide levels of H3K4me3 following deletion of COMPASS subunit SPP1

summary: We report a drastic genome-wide reduction of H3K4me3 levels following deletion of SPP1.

overall_design: Comparison of genome-wide levels of H3K4me3 in strains with or without SPP1, determined by ChIP-seq, comparable due to S. Pombe DNA spike-in controls

first: Françoise

last: Howe


title: Florigen Accelerates Secondary Cell Wall Biogenesis to Harmonize   Vascular Maturation with flowering and reproductive phase Development

city: Haifa

first: Eliezer

last: Lifschitz

address: Technion City

department: Faculty of Biology

country: Israel

institute: Technion

summary: The protein hormone florigen is a universal systemic inducer of flowering and a generic growth terminator across meristems. To understand the developmental rational for its pleiotropic functions and to uncover the deep cellular systems mobilized by florigen beyond flowering we explored the radial expansion of tomato stems. RNAseq, genetic analysis and histological validations show that endogenous, mobile, or induced florigen accelerate secondary cell wall biogenesis (SCWB), and hence vascular maturation, in coordination with but independently of flowering. Conversely, a systemic FT-like florigen antagonist from Ginkgo biloba, arrests SCWB. Downstream of florigen, RNAseq identified MADS/FUL and MIF genes, that similarly impact SCWB independent from flowering. Florigen we show is remarkably stable and distributed to all organs regardless of pre-existing endogenous levels. By accelerating SCWB, florigen triggers a global redistribution of resources, signals and mechanical loads, thereby harmonizing vascular maturation with the reproductive development it had originally set into motion.

overall_design: The florigen hormone, vegetative functions, growth and end cellular targets.

first: Akiva

last: Shalit-Kaneh

first: Tamar

last: Eviatar–Ribak

first: Guy

last: Horev

first: Naomi

last: Suss

first: Roni

last: Aloni

first: Yuval

last: Eshed


title: Gene expression profiling of human neural crest cells and smooth muscle cells treated with DMSO or Nutlin3a

city: Stanford

first: Margot

middle: Elizabeth

last: Bowen

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford University

summary: Activation of the p53 transcription factor triggers apoptosis only in certain cell types. Human neural crest cells (hNCCs), which can be generated from human embryonic stem cells, undergo apoptosis when treated with the p53 activating drug Nutlin3a. In contrast, when hNCCs are differentiated towards the smooth muscle cell lineage (early-hSMCS), they no longer undergo apoptosis in response to Nutlin3a treatment. Here, we sought to determine whether the transcriptional response to p53 activation differs between cells that are susceptible to p53-driven apoptosis and cells that are resistant to p53-driven apoptosis. To this end, we performed RNA-seq to assess the transcriptional response to Nutlin3a treatment in hNCCs and early-hSMCs.

overall_design: RNA-seq was performed on hNCCs and early-hSMCs treated with DMSO (vehicle control) or Nutlin3a for 8 hours. n=3 per cell type and treatment.

first: Laura

middle: D

last: Attardi


title: Effect of miR17-92 and miR-106b-25 loss in primary calvarial cells

city: Boston

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street

institute: Massachusetts General Hospital

summary: Gene expression profiling of  primary calvarial cells with miR-17-92:miR-106b-25 conditional deletion

overall_design: 10-day-old primary calvarial cells of floxed miR-17-92(fl/fl):miR-106b-25(-/-) mice were isolated with collagenase digestion, cultured in alpha-MEM containing 10% fetal bovine serum, and  infected with adenoviruses  expressing Cre or YFP.  3 days after adenovirus infection, RNA was extracted with Trizol, purified with Zymo spin columns, and subjected to RNA-seq

first: Anastasia

last: Kozlova


title: H3K4me3 is neither instructive for, nor informed by, transcription


title: Transcriptomic analysis of class I odorant receptor enhancer deletion [eB]

first: Thomas

last: Bozza

overall_design: 6 control and 6 enhancer deletion animals. Age matched. Deletion eB = 1,155 bp (chr7:102,847,692-102,848,846)


title: RNA-seq analysis of Tr1 cells from islet transplanted monkeys with and without ADL infusion

status: Public on Jul 03 2019

city: Minneapolis

first: Sabarinathan

last: Ramachandran

state: MN

address: 515 Delaware St. SE

department: Surgery

institute: University of mionnesota

summary:
We report our results of RNA-seq analysis on flow sorted Tr1 cells
Immune tolerance to allografts has been pursued as an important goal in transplantation for decades. Administration of apoptotic donor splenocytes effectively induced antigen-specific tolerance to allografts in murine studies. Here we show that two peritransplant infusions of apoptotic donor leukocytes under short-term immunotherapy with antagonistic anti-CD40 antibody 2C10R4, rapamycin, soluble tumor necrosis factor receptor, and anti-interleukin 6 receptor antibody induce long-term (≥1 year) tolerance to islet allografts in 5 of 5 nonsensitized, MHC class I-disparate, and 1 MHC class II DRB allele- matched rhesus macaques. Tolerance in our preclinical model is associated with a regulatory network, involving antigen-specific Tr1 cells exhibiting a distinct transcriptome and indirect specificity for matched MHC class II and mismatched class I peptides. Apoptotic donor leukocyte infusions warrant continued investigation as a cellular, nonchimeric, and translatable method for inducing antigen- specific tolerance in transplantation.

overall_design: RNA was isolated from FACS-sorted cells. Libraries were created using standard Illumina reagents and analyzed using a HiSeq2500.

first: Amar

last: Singh

first: Juan

last: Abrahante

first: Bernhard

last: Herring


title: RNA sequencing of WT and Srp72+/- LT-HSCs from aged mice

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

summary: To investigat the role of Srp72 in hematopoiesis and the development of myelodysplasia and bone marrow aplasia, we generated a transgenic mouse strain with a Srp72 KO strand. Heterozygous loss of SRP72 in mice is not associated with major changes in steady-state hematopoiesis, although we did observe mild reductions in peripheral blood and BM cellularity. Moreover, we also detected minor changes within the stem/progenitor compartment as well as in their propensity to generate a balanced lineage output. We did not observe the development of any haematological disorder, thus the Srp72+/- mouse model only partially recapitulates the more severe aplasia and myelodysplasia observed in families with inherited SRP72 lesions. We thereafter extracted RNA from LT-HSCs of old mice to observe transcriptional changes in those mice. Interestingly, gene expression analysis demonstrated that genes encoding secreted factors, including cytokines and cell-surface receptors, were transcriptionally down-regulated in Srp72+/- animals. This can potentially provide mechanistic insights into why SRP72 lesions are associated with the development of severe aplasia and myelodysplasia in humans.

overall_design: RNA sequencing of LT-HSCs from 4 WT and 3 Srp72+/- aged mice

first: Teresa

last: D'Altri

first: Anne

last: Wenzel

middle: T


title: Genome-wide nascent transcription patterns following deletion of COMPASS subunit SPP1

first: Jane

last: Mellor

summary: Despite the well-reported association between H3K4me3 and transcription, ablation of H3K4me3 by deletion of SPP1 has little effect on nascent transcription.

overall_design: Comparison of genome-wide patterns of nascent transcription in strains with or without SPP1, determined by Nacent Elongating Transcript sequencing (NET-seq).

first: Harry

last: Fischl


title: Tox reinforces the phenotype and longevity of dysfunctional T cell populations during chronic viral infection [WT vs KO +/- Tim3]

city: Freising

first: Dietmar

last: Zehn

address: Weihenstephaner Berg 3

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

summary: Chronic CD8 T-cell stimulation in persisting infections or tumors can induce a stable gene expression program, known as T-cell dysfunction or exhaustion, that limits the cell’s effector functions and anti-viral and anti-tumor immunity. Thus far, the underlaying molecular mechanisms that induce and stabilize this phenotype are vaguely understood. We report here that establishing this program requires the thymocyte selection-associated high mobility group-box protein (Tox). Genetic disruption of Tox augments effector function, decreases the expression of PD-1, and significantly enhances immunopathology. These changes are linked to a failure in fixing the dysfunctional phenotype in the critical Tcf1+ progenitor population and to impaired epigenetic programing. Surprisingly, the gains in effector function co-incide with declining numbers of Tcf1+ cells and result ultimately in reduced total numbers of pathogen-specific T-cells. Thus, we establish Tox as a critical factor for the development of T-cell dysfunction and establish a clear link between CD8 T-cell intrinsic suppression of effector function and protection against immune-pathology.

overall_design: 2*10^3 wt or Tox∆ P14 T-cells were transferred into C57BL6 host, infected with 5x10^6 PFU LCMV-c13 and collected on day 8. Tim3+ and Tim3- P14 T-cells were isolated and FACS-sorted, then lysed for the following RNA extraction using the Agencourt RNAdvance Cell v2 kit (A47942, Beckman Coulter). Samples with RIN>8 were used for cDNA synthesis and library preparation. 1 ng of total RNA was used for cDNA synthesis and PCR using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634891, Takara/Clontech). 150 pg of the amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). The fragmented libraries were amplified and the samples purified with (0.6x) Agencourt AMPure XP beads. The quality of the library was checked with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). Library quantification was performed with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems). The sequencing of the samples was performed with the Illumina HiSeq 2500 system at rapid run, 100 base pairs single-end read, dual-indexed sequencing resulting in 20 million reads per sample.

first: Francesca

last: Alfei

first: Kristiyan

last: Kanev

first: Ming

last: Wu

first: Patrick

last: Roelli


title: Tox reinforces the phenotype and longevity of dysfunctional T cell populations during chronic viral infection [ToxKO vs WT Day 20]

overall_design: 2*10^3 wt or Tox∆ P14 T-cells were transferred into C57BL6 host, infected with 5x10^6 PFU LCMV-c13 and collected on day 20. P14 T-cells were isolated and FACS-sorted, then lysed for the following RNA extraction using the Agencourt RNAdvance Cell v2 kit (A47942, Beckman Coulter). Samples with RIN>8 were used for cDNA synthesis and library preparation. 1 ng of total RNA was used for cDNA synthesis and PCR using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634891, Takara/Clontech). 150 pg of the amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). The fragmented libraries were amplified and the samples purified with (0.6x) Agencourt AMPure XP beads. The quality of the library was checked with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). Library quantification was performed with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems). The sequencing of the samples was performed with the Illumina HiSeq 2500 system at rapid run, 100 base pairs single-end read, dual-indexed sequencing resulting in 20 million reads per sample. 5 replicates per genotype, each from different donor mice.


title: Genome-wide measurement of RNA levels following depletion of RNAPII from the nucleus, in wildtype and SPP1 deletion strains.

summary: Ablation of H3K4me3 by deletion of SPP1 has no strong or consistent effect on the rate of mRNA degradation following depeletion of RNAPII from the nucleus.

overall_design: Comparison of the rate of mRNA transcript degradation in strains with or without SPP1 following RNAPII depletion from the nucleus via an anchor-away system, determined by RNA-seq.

first: Françoise

last: Howe


title: Regulation of intestinal gene expression by Turicibacter sanguinis colonization in mice

last: Fung

summary: The objective of this study is to determine whether monocolonization of germ-free mice with Turicibacter sangiunis results in changes in intestinal gene expression

overall_design: 7 week old germ-free (GF) C57BL/6 mice were monocolonized with Turicibacter sanguinis MOL361 for 2 weeks. Control groups include age- and sex-matched GF and specific pathogen free (SPF) C57BL/6 mice. N = 5 per group.

first: Elaine

last: Hsiao


title: SS-31 Reverses Mitochondrial Fragmentation in Fibroblasts from Patients with DCMA, a Mitochondrial Cardiomyopathy

city: Calgary

first: Steven

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

summary: We used patient dermal fibroblasts to characterize the mitochondrial abnormalities associated with the dilated cardiomyopathy with ataxia syndrome (DCMA) and to study the effect of the mitochondrially-targeted peptide SS-31 as a potential novel therapeutic.

overall_design: Dermal fibroblasts from four pediatric patients with DCMA were used to establish parameters of mitochondrial dysfunction. Mitochondrial structure, reactive oxygen species (ROS) production, cardiolipin composition and gene expression were evaluated. Total RNA was extracted from DCMA fibroblasts (n=4) and control fibroblasts (n=4) using the RNA extraction Mini kit (Invitrogen) according to the manufacturer’s protocol. The sequencing library was prepared using 2 μg of RNA and the TruSeq Stranded mRNA library preparation kit (Illumina) on NextSeq500 platform. RNA-Seq identifies changes in gene expression related to DCMA. Comparison between DCMA and control fibroblasts identified 288 transcripts that were significantly differentially-expressed . However, there were five transcripts that were highly significantly different. Implicated genes of particular note included DNAJC19 and those involved in oxidative stress (GSTM1) and mitochondrial biogenesis (GATD3A).

first: Pranav

last: Machiraju

first: Xuemei

last: Wang

first: Joshua

last: Huang

first: Tian

last: Zhao

first: Fatima

last: Iqbal

first: Melissa

last: King

first: Dimple

last: Prasher

first: Arijit

last: Lodha

first: Amir

last: Ravandi

first: Bob

last: Argiropoulos

first: David

last: Sinasae

first: Aneal

last: Khan

first: Timothy

last: Shutt


title: Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [Bisulfite-Seq]

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

type: Methylation profiling by high throughput sequencing

overall_design: C57BL/6 mice engrafted with wt or Tox∆Ex5 2x10^3 P14 T-cells were infected with 2x10^6 PFU of LCMV clone-13. On day 8 post infection, splenic wt and Tox∆Ex5 P14 T-cells were sorted into Tim-3+ and Tim-3- T-cells and whole-genome DNA methylation analysis was performed as previously described (Ghoneim, et al. Cell 2017, PMID: 28648661).  On day 8 and day 13 post infection, ATAC-seq was performed on splenic wt and Tox∆Ex5 P14 T-cells.

first: Francesca

last: Alfei

first: Hazem

last: Ghoneim

first: Yiping

last: Fan

first: Benjamin

last: Youngblood

first: Dietmar

last: Zehn


title: Tox reinforces the phenotype and longevity of dysfunctional T cell populations during chronic viral infection [KO vs WT Day 8]

overall_design: 2*10^3 wt or Tox∆Ex5 P14 T-cells were transferred into C57BL6 host, infected with 5x10^6 PFU LCMV-c13 and collected on day 8. P14 T-cells were isolated and FACS-sorted, then lysed for the following RNA extraction using the Agencourt RNAdvance Cell v2 kit (A47942, Beckman Coulter). Samples with RIN>8 were used for cDNA synthesis and library preparation. 1 ng of total RNA was used for cDNA synthesis and PCR using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (634891, Takara/Clontech). 150 pg of the amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). The fragmented libraries were amplified and the samples purified with (0.6x) Agencourt AMPure XP beads. The quality of the library was checked with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). Library quantification was performed with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems). The sequencing of the samples was performed with the Illumina HiSeq 2500 system at rapid run, 100 base pairs single-end read, dual-indexed sequencing resulting in 20 million reads per sample.  5 replicates per genotype, each from different donor mice.

first: Kristiyan

last: Kanev

first: Ming

last: Wu

first: Patrick

last: Roelli


title: Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection

overall_design: Refer to individual Series


title: RNA-seq reveals genes regulated by type I interferon during Rickettsia infection in WT and Irf-deficient bone marrow-derived macrophages

city: Berkeley

first: Thomas

middle: Patrick

last: Burke

address: 301 LSA

department: Molecular and Cell Biology

institute: University of California, Berkeley

summary: We report transcript abundance in murine bone marrow-derived macrophages (BMDMs) upon Rickettsia parkeri infection and treatment with type I interferon (IFN-I). Infections and IFN-I treatment were performed in parallel between WT BMDMs and BMDMs lacking genes encoding interferon-responsive factor (IRF) transcription factors, including IRF1, IRF5, and double mutant cells lacking both IRF3 and IRF7. Control cells were uninfected and not treated with IFN-I. The abundance of transcripts between these cells can be compared in order to identify genes specifically regulated by each IRF upon IFN-I treatment.

overall_design: Examination of a total of 6 BMDM populations.

middle: P

first: Matthew

last: Welch


title: Sex-specific programming effects of parental obesity in pre-implantation embryonic development_Microarray data on blastocyst transcriptomes

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

summary:
Obesity is a global rising problem with epidemiological dimension. Obese parents can have programming effects on their offspring leading to obesity and associated diseases in later life. This constitutes a vicious circle. Epidemiological data and studies in rodents demonstrated differential programming effects in male and female offspring, but the timing of their developmental origin is not known. This study investigated if sex-specific programming effects of parental obesity can already be detected in the pre-implantation period. Diet induced obese male or female mice were mated with normal-weight partners and blastocysts were recovered. Gene expression profiling revealed sex-specific responses of the blastocyst transcriptome to maternal and paternal obesity. The changes in the transcriptome of male blastocysts were more pronounced than those of female blastocysts, with a stronger impact of paternal than of maternal obesity. The sperm of obese mice revealed an increased abundance of several miRNAs compared to lean mice. Our study indicates that sex-specific programming effects of parental obesity already start in the pre‑implantation period and reveals specific alterations of the sperm miRNA profile as mechanistic link to programming effects of paternal obesity.
We used microarrays to analyze the transcriptomes of sex-sorted blastocysts of mice, with one parent (either mother or father) being obese at the time of conception and compared it to the transcriptome of blasocysts of peri-conceptionally lean parents.

overall_design: NMRI mice (RjHan:NMRI) were purchased from Janvier (Le Genest St Isle, France). For a period of nine weeks, cohorts of three-week-old mice were fed a modified D12492 high-fat, high-calorie diet (HFD) (E15741-34; ssniff, Soest, Germany), or received a control diet to D12492 (CD) (ssniff). At the age of 12 weeks mice were mated and at day 3.5 post coitum, blastocysts were isolated. The sex of the blastocysts was determined and the transcriptome of a pool of three sex-matched blastocysts was analyzed using microassrays. In total, we performed 24 microarrays. Of each parental pair (obese mother/lean father, lean mother/obese father, lean mother/lean father as controls), we investigated the the transcriptome of four male and four female blastocyst pools, respectively.

first: Kathrin

last: Hedegger

first: Julia

last: Philippou-Massier

first: Stefan

last: Krebs

first: Helmut

last: Blum

last: Kunzelmann

first: Klaus

last: Förstemann

first: Martina

last: Gimpfl

first: Adelbert

middle: A

last: Roscher

first: Regina

last: Ensenauer

first: Eckhard

last: Wolf

first: Maik

last: Dahlhoff


title: RNA Sequencing Facilitates Quantitative Analysis of Adenovirus-treated Eed Floxed Mouse Mesenchymal Stem Cells Gene Expression

first: Tatsuya

last: Kobayashi

summary:
Purpose: RNA sequencing has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare Cre-treated versus YFP-treated mouse mesenchymal stem cells regarding gene expression.
Mesenchymal miRNA profiles of 10-day-old Eed floxed calvaria infected with YFP and Adenovirus-CRE cells were generated by deep sequencing, in triplicate, using BGISEQ-500.  The sequence reads that passed quality filters were mapped using HISAT and Bowtie2. Isoform expression levels were analyzed using RSEM.

overall_design: Calvarial mRNA profiles of 10-day old YFP and Cre treated mice with floxed Eed genes were generated by deep sequencing, in triplicate, using BGISEQ-500.

first: Anastasia

last: Kozlova


title: PRDM15 promotes lymphomagenesis by transcriptionally rewiring B cells metabolism

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: RNAseq of samples to identify changes in gene expression upon acute PRDM15 deletion

overall_design: Three biological replicates of primary mouse lymphoma cells were harvested for RNAseq preparation.

middle: H

first: Slim

last: Mzoughi


title: Gene expression profiling of neural crest cells from E10.5 mouse embryos with basal p53 or activated p53

first: Margot

last: Bowen

summary: To investigate the mechanisms by which p53 activation triggers developmental defects, we generated a mouse model in which p53 is activated in neural crest cells due to the expression of a mutant p53 protein (p53-25,26) that can bind to and stabilize wild-type p53. Here, we performed gene expression profiling on neural crest cells isolated from these embryos, to identify the transcriptional response to p53 activation during embryogenesis.

overall_design: RNA-seq was performed on neural crest cells isolated from E10.5 mouse embryos expressing a stabilized p53 protein (Wnt1Cre;Trp53LSL-25,26/+;R26mTmG/+) and littermate controls (Wnt1Cre;Trp53+/+;R26mTmG/+). n=5 embryos per genotype.

first: Laura

last: Attardi


title: Single base mapping of m6A by an antibody-independent method

city: Guangzhou

first: Zhang

last: Zhang

state: Guangdong

address: Xingangxi Roda 135#

country: China

institute: Sun Yat-sen University

summary: N6-methyladenosine (m6A) is one of the most abundant mRNA modifications in eukaryotes, related to pivotal RNA metabolism processes. The most popular high-throughput m6A identification method relies on the commercial m6A antibody but suffers from poor reproducibility and limited resolution. Exact location of m6A site is of great vital for understanding the dynamics, functions and machinery of RNA methylation. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease–Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic single base m6A map generated by m6A-REF-seq displayed a typical distribution pattern with enrichment adjacent to stop codon. Ligase-based and qPCR validation methods were used to confirm the individual m6A sites and quantify the methylation level, reinforcing the high accuracy of m6A-REF-seq. We applied m6A-REF-seq on five tissues from three mammals, showing that m6A sites were conserved and tend to gather together among species. (m6A-REF-seq had been named as Aim-seq.)

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: For human HEK293T cell line, three pairs of replicates with MazF treatment and negative control were provided. For the samples of human tissues (brain, liver and kidney), mouse tissues (brain, liver, heart, testis and kidney) and rat tissues (brain, liver and kidney), MazF treatment and negative control were provided.

first: Liqian

last: Chen

first: Guanzheng

last: Luo


title: Dissecting the transcriptome landscape of human neural retina and retinal pigment epithelium by Single-cell RNA sequencing analysis

city: Beijing

first: Boqiang

middle: John

last: Hu

address: 5th Yiheyuan Road

department: bio-dynamic imaging center

institute: Peking university

summary: The developmental pathway of the neural retina (NR) and retinal pigment epithelium (RPE) has been revealed by extensive research in mice. However, the molecular mechanisms underlying the development of the human NR and RPE, as well as the interactions between these two tissues, have not been well defined. Here, we analyzed 2,421 individual cells from human fetal NR and RPE using single-cell RNA sequencing (RNA-seq) technique and revealed the tightly regulated spatiotemporal gene expression network of human retinal cells. We identified major cell classes of human fetal retina and potential crucial transcription factors for each cell class. We dissected the dynamic expression patterns of visual cycle and ligand-receptor interaction related genes in the RPE and NR. Moreover, we provided a map of disease-related genes for human fetal retinal cells and highlighted the importance of retinal progenitor cells as potential targets of inherited retinal diseases. Our findings captured the key in vivo features of the development of the human NR and RPE and offered insightful clues for further functional studies.

overall_design: Here we performed single cell RNA-seq analysis for human embryonic neural  retina and retinal pigment epithelium, covering the developmental stages of 5-24 weeks after gestation.

first: Yuqiong

first: Xiaoye

last: Wang

first: Yunuo

last: Mao

first: Yidong

first: Liying

last: Yan

first: Jun

last: Yong

first: Ji

last: Dong

first: Yuan

last: Wei

first: Wei

first: Lu

last: Wen

first: Jie

last: Qiao

first: Fuchou

last: Tang


title: Transcriptome-wide analysis of adipose circular RNAs reveals their dynamic regulation in obesity and functional role in adipogenesis

first: Roger

last: Foo

address: 60 Biopolis Street

institute: Genome Institute of Singapore

type: Non-coding RNA profiling by high throughput sequencing

summary: Non-coding RNAs are emerging as novel regulators in adipocyte differentiation and function. Circular RNAs (circRNAs) are a new class of non-coding transcripts generated across all eukaryotic tissues, but their function in adipose biology remains unknown. Here we perform deep sequencing of visceral and subcutaneous fat to discover thousands of adipose circRNAs, many of which are species-conserved, tissue-specific and dynamically regulated during adipogenesis and obesity. We identified circTshz2-1 and circArhgap5-2 as indispensable regulators of adipogenesis in vitro. To characterize the function of circRNAs in vivo, we injected adenoviral shRNA targeting circArhgap5-2 into mouse inguinal tissue and found that the expression of this circRNA was essential in maintaining the global adipocyte transcriptional programme involved in lipid biosynthesis and metabolism. Furthermore, we demonstrated that the pro-adipogenic function of circArhgap5-2 is conserved in human adipocytes. Our results provide important evidence that circRNAs serve as important regulators in adipocyte differentiation and metabolism.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Discovery of circular RNA in adipocytes using RNA-seq

first: Sun

last: Lei

first: Camille

last: Arcinas


title: A Physiological Biomimetic Culture System for Pig and Human Heart Slices

city: Louisville

first: Tamer

last: Mohamed

state: KY

address: 580 S. Preston St., Baxter II Bldg., Room 122

department: Cardiology

institute: University of Louisville

summary: We have developed and optimized a reliable medium-throughput culture system for pig and human heart slices as a platform for testing the efficacy of novel heart failure therapeutics and reliable testing of cardiotoxicity in a 3D heart model.

overall_design: Temporal transcriptome analysis using RNAseq at day 2, 6, and 10 in culture confirmed overall maintenance of normal gene expression for up to 6 days, while over 500 transcripts were differentially regulated after 10 days.


title: LncRNA NONHSAT113026 represses renal cell carcinoma tumorigenesis through interacting with NF-κB/p50 and SLUG

city: Urumqi

first: yan

last: pu

state: State...

address: Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011, P.R. China

institute: Institute of Cancer Research

summary: We provide evidence that NOAT113026 inhibits renal cancer proliferative and mobility potential by blocking NF-κB/p50 and SLUG expression, which consequently inhibiting the production of oncogenic chemokines and metastasis-promoting genes. Our findings manifest that NOAT113026 may become a critical and feasible target for RCC treatment because of its anti-proliferative and anti-metastatic properties and emerge as an important biomarker for the detection of overall survival and disease-free survival.

overall_design: We reported a long non-coding RNA (lncRNA), NONHSAT 113026 (NOAT113026), that may play an important role in the pathogenesis of RCC. The expression level of NOAT113026 was estimated by qPCR from 76 pairs of RCC and NT samples. The correlation of NOAT113026 to clinical data of RCC patients was analyzed. NOAT113026 was overexpressed in 786-O and ACHN cell lines by lentivirus-mediated technology, and the oncological behavioral changes of RCC cells were observed, as well as, tumorigenicity in experimental nude mice. Compared to the adjacent tissues, NOAT113026 was obviously downregulated in RCC. Survival analysis showed that the lower the expression level of NOAT113026, the shorter the disease-free survival and overall survival in RCC. Overexpression of NOAT113026 can decrease the ability of cell migration, invasion, proliferation, and colony formation by regulating NF-κB/p50 and SLUG through a mechanism that involves lncRNA-mRNA interactions.

first: Huibin

last: Liu

first: Yan

last: Pu

first: Yu

last: Xia

first: Mengmeng

last: Zhang

first: Jianzhong

last: Song

first: Jing

last: Han


title: Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [day28 acute vs chronic]

first: Dietmar

last: Zehn

summary:
Chronic CD8 T-cell stimulation in persisting infections or tumors can induce a stable gene expression program, known as T-cell dysfunction or exhaustion, that limits the cell’s effector functions and anti-viral and anti-tumor immunity. Thus far, the underlaying molecular mechanisms that induce and stabilize this phenotype are vaguely understood. We report here that establishing this program requires the thymocyte selection-associated high mobility group-box protein (Tox). Genetic disruption of Tox augments effector function, decreases the expression of PD-1, and significantly enhances immunopathology. These changes are linked to a failure in fixing the dysfunctional phenotype in the critical Tcf1+ progenitor population and to impaired epigenetic programing. Surprisingly, the gains in effector function co-incide with declining numbers of Tcf1+ cells and result ultimately in reduced total numbers of pathogen-specific T-cells. Thus, we establish Tox as a critical factor for the development of T-cell dysfunction and establish a clear link between CD8 T-cell intrinsic suppression of effector function and protection against immune-pathology.
The term 'chronic' refers to P14 T-cells isolated from mice chronically infected with LCMV clone-13.  'Acute' are P14 T cells that were primed by in a specific LCMV-clone-13 infection setup in which P14 T cells are exposed to low antigen levels. In this setup, T cells retain a phenotype that resembles T-cells found in acutely resolved infection. Both samples were side by side compared.

overall_design: 2*10^3 wt P14 T-cells were transferred into C57BL6 host, infected with 2x10^6 PFU LCMV c13 wt or 0.4x10^6 PFU wt clone-13 mixed with 1.6x106 PFU gp33-deficient LCMV clone-13 mutant strain and collected on day 28. P14 T-cells were isolated and FACS-sorted and sent to IMGM Laboratories to generate Microarray gene expression profiles.

first: Francesca

last: Alfei

first: Daniel

last: Utzschneider

first: Patrick

last: Roelli

first: Ming

last: Wu


title: Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [day 8 acute vs chronic]

summary:
Chronic CD8 T-cell stimulation in persisting infections or tumors can induce a stable gene expression program, known as T-cell dysfunction or exhaustion, that limits the cell’s effector functions and anti-viral and anti-tumor immunity. Thus far, the underlaying molecular mechanisms that induce and stabilize this phenotype are vaguely understood. We report here that establishing this program requires the thymocyte selection-associated high mobility group-box protein (Tox). Genetic disruption of Tox augments effector function, decreases the expression of PD-1, and significantly enhances immunopathology. These changes are linked to a failure in fixing the dysfunctional phenotype in the critical Tcf1+ progenitor population and to impaired epigenetic programing. Surprisingly, the gains in effector function co-incide with declining numbers of Tcf1+ cells and result ultimately in reduced total numbers of pathogen-specific T-cells. Thus, we establish Tox as a critical factor for the development of T-cell dysfunction and establish a clear link between CD8 T-cell intrinsic suppression of effector function and protection against immune-pathology.
The terms acute and chronic samples refer to P14 T-cells that were initially activated in acute LCMV (Armstrong) or chronic LCMV (clone-13) infections. 4 weeks later, the P14 T cells were collected, transferred into naive mice, and both then re-expanded in acute LCMV (Armstrong) infection. 8 days later P14 T-cells were collected and analysed.

overall_design: 2*10^3 wt P14 T-cells were transferred into C57BL6 host, infected with 2x10^5 PFU LCMV Armstrong or 2x10^6 PFU LCMV-c13 and collected on day 28. P14 T-cells were isolated and FACS-sorted, before being tranferred in a naive host,infected then with 2x105 PFU LCMV Armstrong. P14 were isolated and FACS-sorted on day 8 and sent to IMGM Laboratories to generate Microarray gene expression profiles.


title: RNA sequencing for PDX1, NGN3 and MAFA transduced iPSCs cell

city: Rochester

first: Yasuhiro

last: Ikeda

address: 200 First Street SW

institute: Mayo Clinic

summary: Global gene expression profiling identifies accelerated induction of genes upon PDX1, NGN3 and MAFA transduction.

overall_design: Examination of differentially expressed genes among PN-treated and control cells, and PNM-treated and control cells.

first: Ikeda

last: Yasuhiro

first: Yaxi

last: Zhu


title: Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [RNA_seq_Whole]

city: Darlinghurst

first: Stephen

last: Bradford

state: NSW

address: 384 Victoria St

country: Australia

institute: Garvan Institute of Medical Research

summary: To understand the molecular differences between adipocytes and their contribution to cell-type specific function, we comprehensively characterised the transcriptomes and DNA methylomes using WGBS of isolated adipocytes from the SAT and VAT from normal weight individuals

overall_design: WGBS, RNA-seq, and microarrays were used to study epigenetics and transcriptomics human cancer isolated subcutaneous (abdominal - SA) and vieceral (omental - VA) adipocyte, peripheral blood leukocytes (PBL) and visceral adipose tissue (VAT).

first: S


title: Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [microarrays]

type: Methylation profiling by genome tiling array


title: Tox reinforces the phenotype and longevity of exhausted T-cells in chronic viral infection [ATAC-seq]

first: yiping

last: fan

summary: Chronic CD8 T-cell stimulation in persisting infections or tumors can induce a stable gene expression program, known as T-cell dysfunction or exhaustion, that limits the cell’s effector functions and anti-viral and anti-tumor immunity. Thus far, the underlaying molecular mechanisms that induce and stabilize this phenotype are vaguely understood. We report here that establishing this program requires the thymocyte selection-associated high mobility group-box protein (Tox). Genetic disruption of Tox augments effector function, decreases the expression of PD-1, and significantly enhances immunopathology. These changes are linked to a failure in fixing the dysfunctional phenotype in the critical Tcf1+ progenitor population and to impaired epigenetic programing. Surprisingly, the gains in effector function co-incide with declining numbers of Tcf1+ cells and result ultimately in reduced total numbers of pathogen-specific T-cells. Thus, we establish Tox as a critical factor for the development of T-cell dysfunction and establish a clear link between CD8 T-cell intrinsic suppression of effector function and protection against immune-pathology.

overall_design: C57BL/6 mice engrafted with wt or Tox∆Ex5 2x10^3 P14 T-cells were infected with 2x10^6 PFU of LCMV clone-13. On day 8 post infection, splenic wt and Tox∆Ex5 P14 T-cells were sorted into Tim-3+ and Tim-3- T-cells and whole-genome DNA methylation analysis was performed as previously described (Ghoneim, et al. Cell 2017, PMID: 28648661).  On day 8 and day 13 post infection, ATAC-seq was performed on splenic wt and Tox∆Ex5 P14 T-cells.

first: Hazem

last: Ghoneim

first: Yiping

last: Fan

first: Benjamin

last: Youngblood


title: Effects of Electroacupuncture on the CircRNA of Plasma Exosomes in Diabetic Mice: Based on RNA Sequencing Technique

status: Public on Jul 02 2019

city: Shanghai

first: Yi

last: Shou

address: Haining Road 100

department: Department of Acupuncture-Moxibustion

institute: Shanghai General Hospital

summary:
Aim: To study the effect of electroacupuncture (EA) on circRNA expression of plasma Exosomes and signal pathway of type 2 diabetic mice (T2DM).
Methods: 10 mice were randomly selected as normal group. 20 mice were for T2DM model preparation and then were randomly divided into model and model + EA group. Mice in model + EA group were given EA treatment. The changes of fasting blood glucose (FBG) and the Islet structure were evaluated. Plasma exosomes of mice were subjected to RNA sequencing. Bioinformatics analysis on differentially expressed circRNA was performed. 12 differentially expressed circRNA were confirmed for real-time quantitative PCR (qPCR).
Results: EA treatment reduced the FBG, preserved islets structure and reduced the islet β cell apoptotic rate of T2DM mice. RNA-sequencing analysis showed EA treatment lead to significant change of 165 circRNA expressions. GO and KEGG revealed that the effects of EA on T2DM mainly focus on regulating the functions and pathways related to multi-link metabolism, cell growth and organ development. Especially, the thyroid hormone signaling pathway was actively regulated by EA. circRNA/miRNA interactions analysis revealed that that mmu-mir-7092-3p was closely combined with circINPP4B, suggesting phosphatidylinositol signaling pathway was affected by EA. 12 circRNAs were identified to have significant differences by qRT-PCR.
Conclusion: EA intervention can significantly protect islet function and improve FBG in T2DM, which may be related to the regulation on thyroid hormone and Phosphatidylinositol signaling pathway.

overall_design: CircRNA profiles of Plasma Exosomes in Diabetic Mice were generated by deep sequencing, using Illumina 4000.

first: Yin

first: Li

last: Hu


title: Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [Bisulfite-Seq]


title: Circular RNA expression profile in the spinal cord of morphine tolerated rats and screen of putative key circRNAs

city: Changsha

first: Jiali

last: Shao

state: Hunan

address: 281 Tongzipo Road, Changsha, Hunan, China

department: Department of Anesthesiology

institute: The affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

summary: Microarray analysis for circRNA expression in the spinal cord was conducted and compared between 4 morphine tolerated rats and 4 normal rats

overall_design: Adult male Sprague-Dawley rats in the morphine tolerance group (MT group) received 10 μg intraperitoneal morphine (1 μg/1 μL) twice a day at 08:00–09:00 and 16:00~17:00 for 7 consecutive days.Their cohorts in the normal saline group (NS group, n = 8) received equal volumes of normal saline following the identical protocol.  On the 8 th day, one hour after the injection with morphine or saline in the morning,the rats were decapitated under deep anesthesia, and the lumbar enlargements were collected for analysis.

first: Yingqi

last: Weng

first: Jing

first: Ling

last: Li

first: Yiqi

last: Lizheng

first: Meiling

last: Deng

first: Wangyuan

last: Zou


title: Transcriptome of tumor biopsy sample of patient with non-small-cell lung adenocarcinoma, ALK rearrangement positive

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

type:
Expression profiling by array
Third-party reanalysis

summary: We profiled gene expression in formalin-fixed, paraffin-embedded (FFPE) tumor biopsy sample of the patient with non-small-cell lung adenocarcinoma, ALK rearrangement positive.

overall_design: Microrray analysis was performed for single biopsy sample. Sample was evaluated by a pathologist to confirm the diagnosis and estimate the tumor cell content (sample should contain at least 80% of tumor cells).

first: Irina

last: Kochergina-Nikitskaya


title: The Role of Histone H3 Lysine 36 Methylation in Reprogramming of fibroblasts and on Induced Pluripotent stem Cell Generation

city: Istanbul

first: Tamer

last: Onder

address: Rumelifeneri Yolu Sariyer

department: School of Medicine

country: Turkey

institute: Koc University

summary: SETD2 downregulation via two independent shRNA infection significantly modulated expression profile of dH1f cells in preOSKM and postOSKM samples such that 186/121 genes were down and 135/66 were up-regulated in preOSKM, and 467/544 were down and 313/586 were up-regulated in postOSKM cells significantly  (padj<0.001 and log2 fold change>0.5).

overall_design: Examination of SETD2 downregulation effect on gene expression profile of dH1f cells in pre- and 6 days postOSKM samples. 2 sets of samples were prepared for shSETD2-1/shSETD2-3 preOSKM and 3 sets of samples were prepared for shCntrl preOSKM, shSETD2-1/ shSETD2-3 and shCntrl postOSKM conditions.

last: Önder

first: Burcu

last: Özçimen

first: Kenan

last: Sevinç

first: Fırat

last: Uyulur

first: Udo

last: Oppermann

first: Martin

last: Philpott

first: Adam

last: Cribbs


title: RasV12 blocks DNA synthesis and DNA damage response

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

summary: Transcriptional profile of RasV12 expressing cells shows an upregulation of RTK signalling genes and a downregulation in genes involved in DNA sintesis and DNA damage response.

overall_design: mRNA expression profiles of GFP-i  and RasV12 expressing drosophila wing imaginal cells. Transgenes where expressed for 3 days at 29ºC under the control of the Ap>Gal4 driver. Cells where labelled by the expression of myristolated Tomate and FACS sorted based on this expression.

first: Marta

last: Clemente-Ruiz

first: Lada

last: Murcia

first: Marco

last: Milán

last: Reina

first: Jose

last: Ignacio Pons


title: Identification of the m6Am Methyltransferase PCIF1 Reveals the Location and Functions of m6Am in the Transcriptome

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

summary: mRNAs are regulated by nucleotide modifications that influence their cellular fate. Two of the most abundant modified nucleotides are N6-methyladenosine (m6A), found within mRNAs, and N6,2′-O-dimethyladenosine (m6Am), which is found at the first transcribed nucleotide. Distinguishing these modifications in mapping studies has been difficult. Here, we identify and biochemically characterize PCIF1, the methyltransferase that generates m6Am. We find that PCIF1 binds and is dependent on the m7G cap. By depleting PCIF1, we generated transcriptome-wide maps that distinguish m6Am and m6A. We find that m6A and m6Am misannotations arise from mRNA isoforms with alternative transcription start sites (TSSs). These isoforms contain m6Am that maps to “internal” sites, increasing the likelihood of misannotation. We find that depleting PCIF1 does not substantially affect mRNA translation but is associated with reduced stability of a subset of m6Am-annotated mRNAs. The discovery of PCIF1 and our accurate mapping technique will facilitate future studies to characterize m6Am’s function.

overall_design: Putatitive N6-methyltransferases were investigated to find the m6Am writer. This revealed PCIF1 as the only m6Am writer. We generated knockout HEK293T cell lines to study transcript stability, translation rates, and performed miCLIP.

first: Konstantinos

last: Boulias

first: Diana

last: Toczydłowska-Socha

first: Ben

middle: R

last: Hawley

first: Noa

last: Liberman-Isakov

first: Ken

last: Takashima

first: Sara

last: Zaccara

first: Théo

last: Guez

first: Jean-Jacques

last: Vasseur

first: Françoise

last: Debart

first: L

last: Aravind

first: Eric

middle: L

last: Greer


title: Linear and circular long noncoding RNAs regulate cellular reprogramming by sponging multiple miRNAs

city: Harbin

first: Xiaolei

last: Zhang

address: No.59 Mucai street

institute: Northeast Agricultural University

summary: Using a doxycycline inducible expression of Yamanaka factors (Oct4, Sox2, Klf4 and c-Myc) to generate induced pluripotent stem cells (iPSCs) from mouse embryonic fibroblasts (MEFs), we investigated the dynamic changes of miRNAs, long intergenic noncoding RNAs (lincRNAs) and noncoding circular RNAs (circRNAs) from cells collected at early reprogramming stage. We found that the pools of miRNAs highly expressed in MEFs remain unchanged from day 0 to day 6 after doxycycline induction; unexpectedly, many genes targeted by these miRNAs were actually up-regulated during reprogramming; meanwhile, lincRNAs and circRNAs which have complementary binding sites with the miRNAs were also highly expressed in the reprogramming MEFs (rMEFs). Intriguingly, we found that knockdown of lincRNAs and circRNAs sharing the miRNA binding sites with Oct4 mRNA resulted in down-regulation of Oct4 expression, and significantly decreased the colony formation during reprogramming. Our results suggest that the ceRNA network plays an important role in reprogramming somatic cells to pluripotent stem cells.

overall_design: Examination of dynamic changes of miRNAs, mRNAs lincRNAs and circRNAs during reprogramming.

first: Qingran

last: Kong

first: Duancheng

last: Wen


title: Cardiomyocyte Dedifferentiation and Proliferation Revealed by Massive Parallel Single-Nucleus Transciprotmic Analysis in Adult Mouse Hearts

city: Honolulu

first: Yiqiang

state: HI

address: 651 Ilalo St BSB-311D

department: Anatomy, Biochemistry and Physiology

institute: University of Hawaii Manoa

summary: We have demonstrated previously that adult cardiomyocytes can dedifferentiate and proliferate when cultured in vitro.  To determine if cardiomyocyte dedifferentiation and cell cycling/proliferation happens in vivo, we applied here a novel multi-reporter transgenic mouse model (aMH-CMerCreMer;mT/MG;aMHC-H2BBFP) carrying reporter genes for permanent cardiomyocyte lineage mapping and maturity (dedifferentiation) reporting. With this new model, we deciphered the cellular sources and processes of cardiomyocyte dedifferentiation and proliferation in adult hearts. In this study, we used single-nucleus RNA-sequencing to tackle the challenges in analyzing the highly heterogeneous heart cell populations, and obtained datasets for a large number of cardiac single nuclei (both myocytes and non-myocytes) for control and post-infarct hearts. We identified specific cell populations in the heart using distinct transcriptomic clusters, transgenic reporters for ACM lineage and dedifferentiation, as well as cell cycle markers.   The results demonstrated that the dedifferentiation and cell cycle progression of pre-existing CMs was augmented in post-infarct hearts, with a number of signaling pathways and gene sets affected. This is the first study dissecting the transcriptomic profiles and signaling pathways associated with cardiomyocyte dedifferentiation and cycling/proliferation in vivo using unbiased high-throughput single-nucleus RNA-Seq analysis, in junction with novel  cell lineage (e.g. cardiomyocyte) and phenotyping (e.g. dedifferentiation) transgenic model systems.

overall_design: Massive parallel single-nucleus RNA profiles of whole-ventricular nuclei containing all heart cell populations from novel transgenic mouse model aMH-CMerCreMer;mT/MG;aMHC-H2BBFP; Included a control and two 5-day post-infarct hearts; data generated by deep sequencing with 10x Genomics platform and Illumina sequencer.


title: Innate Immune Gene Profiling of the Chick Embryo to Newcastle Disease Virus Infection

city: University Park

first: Vivek

last: Kapur

state: PA

address: 205 Wartik Lab

department: Animal Science

institute: Pennsylvania State University

summary: Lung tissues were harvested from chick embryos 72 hours post inoculation (inoculation at 18 days) with NDV LaSota. Control chick embryos were inoculated with 1X PBS.

overall_design: qRT-PCR gene expression profiling of the innate immune response in the chick embryo to NDV

first: Megan

last: Schilling


title: DNA-methylation of GGCC motifs via M.Ssp6803II is linked to DNA repair in the cyanobacterium Synechocystis sp. PCC 6803 [sll0729 suppressor mutant]

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

summary: DNA methylation plays a crucial role for gene regulation among eukaryotes, but its regulatory function is less understood in bacteria. In the cyanobacterium Synechocystis sp. PCC 6803 five DNA methyltransferases have been identified. Among them, M.Ssp6803II is responsible for the specific methylation of the first cytosine in the frequently occurring motif GGCC, leading to N4-methylcytosine (GGm4CC). The mutation of the corresponding gene sll0729 led to a strong phenotype, including a lowered chlorophyll/phycocyanin ratio, impaired growth, and alterations of the expression of two genes encoding hypothetical proteins. However, prolonged cultivation revealed instability of the initially obtained phenotype, with colonies showing normal pigmentation and wild-type-like growth appearing regularly and in high frequencies on agar plates. These colonies represent suppressor mutants, since the sll0729 gene was still completely inactivated and the GGCC sites remained un-methylated. Two suppressor clones were further characterized and showed a smaller cell size and lowered DNA content per cell. Moreover, they exhibited a decreased tolerance against UV stress compared to wild type. Proteomics revealed the reduction of DNA topoisomerase in suppressor mutant cells. Collectively, these results indicate that GGm4CC methylation is involved in the regulation of gene expression, in the fine-tuning of DNA replication, and DNA repair mechanisms.

overall_design: We analyzed gene expression in sll0729 suppressor mutants compared to Synechocystis sp. PCC 6803 WT.

first: Katrin

last: Gärtner

first: Satoru

last: Watanabe

first: Stefan

last: Mikkat

first: Ingeborg

last: Scholz

first: Wolfgang

last: Hess

first: Martin

last: Hagemann


title: Axitinib exposure triggers endothelial cells senescence through ROS accumulation and ATM activation

city: Bologna

first: Fabrizio

last: Ferrè

address: Via Selmi 3

department: Pharmacy and Biotechnology

country: Italy

institute: University of Bologna

summary: Here we report that Axitinib, an inhibitor of VEGFRs currently in use as a second line treatment for advanced renal cell carcinoma, promotes senescence of human endothelial cells in vitro. Mechanistically, this requires oxidative stress-dependent activation of the Ataxia Telangiectasia Mutated (ATM) kinase. Induction of oxidative stress-related genes  distinguishes the response of endothelial cells to Axitinib from that to doxorubicin

overall_design: RNA-seq analysis of Human Umbilical Vein Endothelial Cells (HUVEC) treated with Axitinib and Doxorubicin pulses

first: Maria

last: Falchetti

last: Mongiardi

first: Andrea

last: Levi


title: RNA-sequencing analysis of differentially expressed genes (DEGs) induced by STC2 overexpression in colorectal cancer cells

city: Hangzhou

first: Jingjing

last: Wu

state: Zhejiang

address: 866 Yuhangtang Road

department: pathology

institute: Zhejiang University

summary: To identify STC2-regulated downstream target genes, we compared the results of RNA-seq analysis between colorectal cancer cells without STC2 (SW480-NC) and cells with STC2 (SW480-STC2).

overall_design: Colorectal cancer cells SW480 were transfected with negative control (named SW480-NC) or STC2 overexpression vectors (named SW480-STC2). Then cells were harvested for RNA isolation for RNA-seq analysis.

first: Jian

last: Wang

first: Shaojun

last: Yu


title: Arginine methylation controls cell proliferation by integrating E2F activity with the splicing machinery (RNA-seq data set)

city: St. Petersburg

first: Alexander

last: Kanapin

address: 7/9 University Emb.

department: Institute for Translational Biomedicine

institute: St Petersburg Universoty

summary: Residue-specific arginine methylation (meR) on the E2F1 subunit plays an essential role in determining whether cell cycle progression or apoptosis ensues, although the molecular pathways underpinning the effects of methylation remain obscure.  We report here that the methylation events on E2F1 have a direct impact on the mechanisms which underpin gene expression control. Specifically, the PRMT5-mediated symR mark not only influences the transcription repertoire of genes targeted by E2F1, but also endows E2F1 with the ability to regulate RNA splicing. This occurs through tudor domain protein p100/TSN which reads the symR mark on E2F1, and thereby enables a distinct set of RNA to be alternatively spliced. The p100/TSN-E2F1 complex binds alternatively spliced RNAs, with many RNAs derived from E2F target genes connected with proliferation and cancer.

overall_design: The U2OS Tet-ON inducle, stable cell line system was used to generate cell lines expressing WT E2F1, or meR deficient derivatives R109K and R111/113K (KK).  An empty vector cell line (pTRE) was used as a control, reference sample.  mRNA was enriched from three biological replicates and sequenced by Illumina NextSeq platform.

first: Alice

last: Roworth

first: Nicholas

middle: B

last: La Thangue


title: Investigation of target molecule alterations by a cDNA microarray in ATO-treated HCC cells

city: Beijing

first: Jun-Nian

last: Zhou

address: 27# Taiping Road

institute: Institute of Health Service and Transfusion Medicine

summary:
BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) has a high mortality rate due to the lack of effective treatments and drugs. Arsenic trioxide (As2O3, ATO, arsenious acid), which has been proved to successfully treat acute promyelocytic leukemia (APL), was recently reported to show therapeutic potential in solid tumors including liver cancer. Although the mechanistic effects of ATO in APL are established, its anticancer mechanism of action in HCC is still unclear. METHODS: We established an HCC subcutaneous xenograft and intrahepatic metastasis mouse model. In CSC models, tumorspheres and the flow cytometry analysis of CSC markers together with limiting dilution and serial transplantation were used. We compared mRNA expression profiles of the ATO-treated and control cells with mRNA microarray. The expression of target molecule or a clinical correlation was analyzed by immunohistochemistry staining in tissues from ATO-treated mouse and 76 HCC patients. We generated five stable minichromosome maintenance protein 7 (MCM7)-knockdown and two stable MCM7-overexpression HCC cell lines. The chromatin immunoprecipitation (ChIP) assays, immunoprecipitation (IP) assays, the dual luciferase reporter assays, a green biarsenical labeling reagent (FlAsH-EDT2) and a “competing endogenous RNA” (ceRNA) analysis were used.

RESULTS: ATO could inhibit the liver tumor-initiating capacity and distant metastasis and prolongs survival in mice. We then screened and found that ATO downregulates the overexpression of MCM7 which is correlated with the progression and prognosis in HCC patients. Knockdown of MCM7 expression recapitulates the inhibition function of ATO on self-renewal of cancer stem cells (CSCs), while overexpression of MCM7 abolishes the inhibition function of ATO on tumorsphere formation. Most importantly, we revealed that ATO directly binds to the MCM7 protein and disturbs the interaction between serum response factor (SRF) and MCM7, resulting in downregulation of MCM7 transcription. A ceRNA analysis also indicated the alterations of endogenous MCM7-associated gene networks involved in stemness-related signaling pathways and cell differentiation.

CONCLUSIONS: Here, for the first time, we report that ATO inhibits liver CSCs through blocking the interaction between SRF/MCM7 and suppressing MCM7 autoregulation activity.

overall_design: The profiles of differentially expressed mRNAs were analyzed in SMMC-7721 cells and Huh7.5.1 cells treated with 3.6 μM arsenic trioxide (48 hours) or PBS as controls.

first: Hai-Yang

first: Biao

last: Zhang

first: Wen

last: Yue

first: Xue-Tao

last: Pei


title: Transcriptome analysis by expression microarrays of rectal cancer derived from the Cancer Institute Hospital of Japanese Foundation for Cancer Research

city: Koto

first: Akihisa

last: Takahara

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

summary: We performed the expression microrarray experiments for mRNA of rectal cancer tissue.

overall_design: Messenger RNA were extracted from primary tumor of 90 rectal cancer patients, hybridized and scanned with Affymetrix PrimeView Human Gene Expression Array. There are 91 samples because one sample was hybridized twice, once in each batch, and is represented by GSM2928780 and GSM2928794.

first: Takashi

last: Akiyoshi


title: Arginine methylation controls cell proliferation by integrating E2F activity with the splicing machinery

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

overall_design: Refer to individual Series


title: Knock down of MTHFD2 of lung adenocarcinoma cell line H322

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

summary: Lung cancer is leading cause of cancer-related death in the world, because of high recurrence rate and acquired resistance to targeting drugs such as gefitinib. Here we uncover a critical MTHFD2 enzyme-mediated purine synthesis pathway in mitochondria in poor prognostic lung cancer. Expression of MTHFD2 was induced by epidermal growth factor (EGF) stimulation. It was overexpressed in gefitinib-resistant cancer cells and high-grade tumor tissues. Knockdown of MTHFD2 significantly decreased not only in vitro and in vivo cell growth but also tumor sphere formation and tumor initiating activity, properties of cancer stem-like cells. Integrated analysis of metabolome and transcriptome of MTHFD2 knocked-down cells revealed significant accumulation of the nucleotide intermediates before MTHFD2-mediated one carbon transfer and marked deficiency of purine nucleotides required for cell growth. Thus we provide evidence that MTHFD2 pathway is critical for growth of both cancer cells and cancer stem-like cells as an Achilles heel to eradicate tumors in poor prognostic lung cancer.

overall_design: Comaprison between negative control cells and MTHFD2 knocked down cells. There are three biological replicates for each conditions.

first: Tatsunori

last: Nishimura

first: Asuka

last: Nakata

first: Makiko

last: Meguro-Horike

first: Shini-chi

last: Horike

first: Kaori

last: Saitoh

first: Keiko

last: Kato

last: Igarashi

first: Susumu

last: Kohono

first: Chiaki

last: Takahashi

first: Tomoyoshi

last: Soga

first: Arinobu

last: Tojo

first: Noriko

last: Gotoh


title: Effects of pre-pubertal DSS treatment on mouse ovary

city: Haifa

first: Philippa

last: Melamed

address: Technion City

institute: Technion-Israel Institute of Technology

summary: We report the changes on ovarian gene expression that follow pre-pubertal colitis in mice

overall_design: Young female sexually immature mice were given 3% DSS in their drinking water for 7 days, with littermate controls. After reaching sexual maturity ovaries were harvested for transcriptome analysis.

first: Ben

last: Sade


title: NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

summary: The advent of quantitative approaches that enable interrogation of transcription at single nucleotide resolution has allowed a novel understanding of transcriptional regulation previously undefined. To better map transcription genome-wide at base pair resolution and with transcription/elongation factor dependency we developed an adapted NET-seq protocol called NET-prism (Native Elongating Transcription by Polymerase-Regulated Immunoprecipitants in the Mammalian genome). NET-prism introduces an immunoprecipitation to capture RNA Pol II – associated proteins, which reveals the interaction of these proteins with active RNA Pol II.  Application of NET-prism on different Pol II variants (Pol II S2ph, Pol II S5ph), elongation factors (Spt6, Ssrp1), splicing factors (Sf1), and components of the pre-initiation complex (PIC) (TFIID, and Mediator) reveals diverse Pol II signals, at a single nucleotide resolution, with regards to directionality and intensity over promoters, splice sites, and enhancers/super-enhancers. NET-prism will be broadly applicable as it exposes transcription factor/Pol II dependent topographic specificity and thus, a new degree of regulatory complexity.

overall_design: NET-prism profiles were generated for Pol II S2ph, Pol II S5ph, Spt6, Ssrp1, Sf1, TFIID, and Mediator

first: Constantine

last: Mylonas


title: Analysis of MACC1 dependent gene expression regulation in CRC cells

city: Berlin

first: Mathias

last: Dahlmann

address: Robert-Rössle-Str. 10

department: Experimental and Clinical Research Center

institute: Charité University Medicine

summary: We employed whole genome expression profiling to identify differential gene expression in the colorectal cancer (CRC) cell line SW480 (ATCC - CCL-228), dependent on the expression level of MACC1 (Metastasis Associated in Colon Cancer 1). SW480 cells with endogenously low expression levels of MACC1 were transfected either with CMV-promoter driven MACC1-cDNA or the empty vector, and selected for stable expression.

overall_design: Total RNA of two biological replicates of both MACC1 overexpressing cells and vector control cells, respectively, was isolated and subjected to whole genome expression profiling.

first: Felicitas

last: Schmid

first: Quing

last: Wang


title: Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [RNA-Seq]

city: Darlinghurst

first: Stephen

last: Bradford

address: 384 Victoria St

institute: Garvan Institute of Medical Research

summary: To understand the molecular differences between adipocytes and their contribution to cell-type specific function, we comprehensively characterised the transcriptomes and DNA methylomes using WGBS of isolated adipocytes from the SAT and VAT from normal weight individuals

overall_design: WGBS, RNA-seq, and microarrays were used to study epigenetics and transcriptomics human cancer isolated subcutaneous (abdominal - SA) and vieceral (omental - VA) adipocyte, peripheral blood leukocytes (PBL) and visceral adipose tissue (VAT).

first: S


title: Single-Cell Imaging and Transcriptomic Analyses of Endogenous Cardiomyocyte Dedifferentiation and Cycling

first: Yiqiang

last: Zhang


city: Yokohama

first: Takaharu

last: Sasaki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Thurumi-ku

department: Center for Integrative Medical Sciences

institute: RIKEN

summary: Transcriptomal comparison between group 2 innate lymphoid cells (ILC2s) in the murine small intestine (SI-ILC2s) and those in white adipose tissue (WAT-ILC2s).

overall_design: mRNA profiles of group 2 innate lymphoid cells (ILC2s) sort-purified from small intestinal lamina propria and mesenteric white adipose tissue of 9-week-old wild type (WT) mice were generated by sequencing, in duplicate, using Illumina HiSeq1500.

first: Hiroshi

last: Ohno

first: Kazuyo

last: Moro


title: Gene expression profiling  of  CD25High and CD25Low regulatory T cell populations from mice lacking autophagy in their dendritic cells and their littermate controls.

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

summary: The goal of this study is to compare the transcriptome profiling (RNA-seq) of two CD25 regulatory T cell subsets isolated from secondary lymphoid organs of mice lacking autophagy in their dendritic cells. CD25High and CD25Low  regulatory T cells were isolated from Atg5 flox/flox CD11c Cre +/-  (Atg5 -/- DC) mice and their littermate controls, Atg5 flox/flox CD11c Cre -/- (Atg5 +/+ DC), under steady state conditions.

overall_design: Transcriptome profile analysis of two different regulatory T cell (T reg) populations (CD25 High and CD25 Low) from mice which lack autophagy in their DC (Atg5 -/- DC) and their litter mate controls (Atg5 +/+ DC). Samples were run in triplicates. cDNA were used for library preparation using the Nextera XT kit from Illumina

first: Monique

last: Gannage

first: Jennifer

last: Niven

first: Assunta

last: Caruso

first: Nicolas

last: Page


title: Transcriptomic Signatures of Mouse Cardiomyocyte Dedifferentiation In vitro (Affymetrix)

summary: Adult cardioyocytes undergo remarkable dedifferentiation and cell cycle reprogramming/reentery when cultured in mitogen-rich medium, continuously, and give rise to cardiac progenitor cells (CPCs). Using microfluidic device for single-cell capture and whole-transcriptomic amplification, we analyze the whole-genome transcriptomic profile in adult mouse cardiomyocytes (Ctl) and in their derived CPCs, and validate the gene expression by single-cell PCR and PCR array. Using two platforms for DNA methylation profiling: NimbleGen DNA methylation array and CHARM array, the whole-genome DNA methylation profile in myocytes (Ctl) and CPCs were compared and their regulations in relationship to the transcriptomics profile were analyzed. The results demonstrated remarkable molecular reprogramming pertaining to dedifferentiation, loss of cardiac contractile, structure, and function molecules, and reactivation of cell cycle and proliferation genes, significant changes in metabolisms. The reduction of cardiac function and structure genes are highly related to their hypermethylation of the promoter regions. GO and Pathway enrichment analysis revealed distinct coordianted transcriptomic and epigenetic regulation in the CPCs derived from cardiomyocytes.

overall_design: Mouse single cardiomyocytes (Ctl) and their derievd single CPCs were captured using microfluidic deviced and cDNA synthesized and amplified and labelled using NuGENE kits, and regular Affymetrix hybridization and wash protocols were used to process the mouse whole-genome array GeneChip 430 2.0.

first: Charles


title: Asparaginase 2 gene expression as a biomarker in response to nitrate ans sucrose during bud outgrowth in Rosa hybrida

status: Public on Jul 01 2019

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRA

summary: Axillary bud outgrowth is an essential process of plant branching to set-up its architecture. Nitrogen is implicated in the development of young organs such as secondary axes (axes II) resulting from bud outgrowth. We have previously shown in planta that asparagine concentration increases in the sap and in the tissues during axes II elongation. In vitro, we demonstrated that this amino acid is the sole at its physiological concentration able to evoke an efficient elongation of axes II in the presence of different sugars. To go further, we performed in this work a transcriptomic analysis through RNA sequencing and obtained 848 annotated sequences that are potentially implicated in bud outgrowth in response to nitrate in the presence of sucrose. Among them, the expression of Asparaginase 2 gene takes place during dormancy while, in contrast, Asparagine synthase 2 gene is active during bud outgrowth. So we have established through qRT-PCR the expression level of the main growth regulators related genes in the permissive condition in the presence of asparagine and sucrose. We confirmed using conceptually different experiments that asparagine has a strong involvement in bud outgrowth and demonstrated that the genes implicated in its metabolism could be consider as new biomarkers in the process in rosebush.

overall_design: Median nodes cultivated in vitro on sucrose medium supplemented with nitrate were compared to a control without nitrate. 30 nodes per sample were pooled for each sequencing.

first: M

last: Le Moigne

last: Bahut


title: Translocation of dense granule effectors across the parasitophorous vacuole membrane in Toxoplasma-infected cells requires the activity of ROP17, a rhoptry protein kinase

city: Stanford

first: Adit

last: Naor

state: CA

address: 300 Pasteur Drive Stanford, D305 Fairchild Building

institute: Stanford

summary: Toxoplasma gondii tachyzoites co-opt host cell functions through introduction of a large set of rhoptry- and dense granule-derived effector proteins. These effectors reach the host cytosol through different means: direct injection for rhoptry effectors and translocation across the parasitophorous vacuolar membrane (PVM) for dense granule (GRA) effectors.  The machinery that translocates these GRA effectors has recently been partially elucidated, revealing 3 components, MYR1, MYR2 and MYR3. To determine if other proteins might be involved, we returned to a library of mutants defective in GRA translocation and selected one that has a partial defect, suggesting it might be in a gene encoding a new component of the machinery. Whole-genome sequencing showed that this mutant indeed has a missense mutation in a gene encoding a known serine/threonine protein kinase, ROP17, which has not previously been reported to be involved in GRA translocation. ROP17 resides at the PVM in infected cells and has previously been known for its activity in phosphorylating and, thereby, inactivating host immunity-related GTPases. Here, we show that null or catalytically dead mutants of ROP17 are defective in GRA translocation across the PVM, and that translocation across the PVM surrounding a Δrop17 mutant can be rescued “in trans” by ROP17 delivered by other tachyzoites infecting the same host cell. This strongly argues for a role for ROP17 at the PVM, not within the parasites or parasitophorous vacuole space. Hence, ROP17 plays a crucial part in GRA translocation, adding another function to the role it plays in modulating the interaction of Toxoplasma tachyzoites and the infected host cell.

overall_design: RNASeq of human foreskin fibroblasts, infected with Toxoplasma, harvested 6 hours post infection. Samples are: Mock infected, infected with a WT RH, RH∆myr1,  RH∆rop17

first: John

last: Boothroyd

first: Michael

middle: W

last: Panas


title: Gene expression alteration regulated by BCAA-metabolism in human acute leukemia

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

institute: Kyushu University


title: Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes

first: Stephen

last: Bradford


title: Landscape of ribosome-engaged alternative transcript isoforms across neuronal cell classes

city: Basel

first: Geoffrey

last: Fucile

address: Spitalstrasse 41

department: sciCORE

institute: University of Basel

summary: The goal of this project was to assess how alternative splicing programs are arrayed across neuronal cells types. We systematically mapped ribosome-associated transcript isoforms in genetically-defined neuron types of the mouse forebrain. The endogenous ribosomal protein Rpl22 was conditionally HA-tagged in glutamatergic neurons (using CamK2-cre for most neocortical pyramidal cells and Scnn1a-cre for spiny stellate and star pyramid layer 4 cells), and GABAergic interneurons [with somatostatin-cre (SST), parvalbumin-cre (PV) and vasointestinal peptide-cre (VIP)]. Within the hippocampus, we further targeted Cornu ammonis 1 (CA1) neurons (CamK2-cre), CA3 neurons (Grik4-cre), and SST-positive interneurons (SST-cre). Four replicates were deep sequenced (~100 million reads) using an Illumina platform. We find that neuronal transcript isoform profiles reliably distinguish even closely-related classes of pyramidal cells and inhibitory interneurons in the mouse hippocampus and neocortex, positing transcript diversification by alternative splicing as a central mechanism for the functional specification of neuronal cell types and circuits.

overall_design: We systematically mapped ribosome-associated transcript isoforms in genetically-defined neuron types of the mouse forebrain. The ribosome-associated RNA profiles were generated by paired-end deep sequencing, with four replicates, using an Illumina platform.

first: Elisabetta

last: Furlanis

first: Lisa

last: Traunmüller

first: Peter

last: Scheiffele


title: Arginine methylation controls cell proliferation by integrating E2F activity with the splicing machinery (RIP-seq data set)

first: Alexander

last: Kanapin

overall_design: U2OS cells were transfected with siRNA targeting p100/TSN or non-targeting siRNA for 72h.  Cells transfected with siE2F1 were used as a reference sample for specificity.  An E2F-1 antibody was used in a RNA immunoprecipitation (RIP) reaction and RNA was extracted and DNAse treated from duplicate biological replicates. Samples underwent ribodepletion prior to sequencing on Illumina NextSeq.

first: Alice

last: Roworth

first: Nicholas

last: La Thangue


title: Antagonistic interaction between Ezh2 and Arid1a coordinates root patterning and development via Cdkn2a in mouse molars

city: Los Angeles

first: junjun

last: jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California


title: Environmental conditions influence the expression of the Streptococcus pyogenes R28 surface protein promoting the colonization in the female genital tract

city: Ann Arbor

first: Taylor

last: Nye

address: 1105 N University Ave

department: MCDB

institute: University of Michigan

summary: We used Illumina NGS to measure mRNA levels and perform subsequent differential expression analysis between wild type and RM system deficient strains of Streptococcus pyogenes

overall_design: Examination of mRNA levels across wild type and a RoaR deficient strain of Streptococcus pyogenes

middle: M

first: Lyle

last: Simmons

middle: E

last: Watson Jr


title: NAD tagSeq, a new method for transcriptome-wide identification and quantification of NAD+-capped RNAs, revealed that NAD+-capped RNAs are produced from a large number of protein-coding genes in Arabidopsis

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

summary: The 5’ end of a eukaryotic mRNA generally has a methyl guanosine cap (m7G cap) that not only protects the mRNA from degradation but also mediates almost all other aspects of gene expression. Some RNAs in E. coli, yeast, and mammals were recently found to contain an NAD+ cap at their 5’ ends. Here we report development of a new method – NAD tagSeq – for transcriptome-wide identification and quantification of NAD+-capped RNAs (NAD-RNAs). The method uses first an enzymatic reaction and then a click chemistry reaction to label NAD-RNAs with a synthetic RNA tag. The tagged RNA molecules can be enriched and directly sequenced using the Oxford Nanopore sequencing technology. NAD tagSeq not only allows more accurate identification and quantification of NAD-RNAs but can also reveal sequences of whole NAD-RNA transcripts. Using NAD tagSeq, we found that NAD-RNAs in Arabidopsis are mostly produced from a few thousand protein-coding genes, with over 60% of them from fewer than 200 genes. The top 2,000 genes that were found to produce the highest numbers of NAD-RNAs were enriched in the gene ontology terms of responses to oxidative stress and other stresses, photosynthesis, and protein synthesis. For some Arabidopsis genes, over 10% of their transcripts could be NAD-capped. The NAD-RNAs in Arabidopsis have similar overall sequence structures to their canonical m7G-capped mRNAs. The identification and quantification of NAD-RNAs and revealing their sequence features provide essential steps toward understanding functions of NAD-RNAs.

overall_design:
The identification and quantification of NAD-RNAs in Arabidopsis thaliana

ADPRC = adenosine diphosphate ribosylcyclase

first: Hailei

last: Zhang

last: Zhong

first: Yiji

last: Xia


title: Human Thoracic Duct Lymph Contains Circulatory Intermediates T Follicular Helper Cells [RNA-Seq]

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

summary: T follicular helper CD4 T cells (Tfh) provide requisite help to B cells in the germinal centers (GC) of lymphoid tissue. GC Tfh are identified by high expression of the chemokine receptor CXCR5 and the inhibitory molecule PD-1. Although more accessible, blood contains lower frequencies of CXCR5+ and PD-1+ cells that have been termed circulating Tfh (cTfh). However, it remains unclear whether GC Tfh exit lymphoid tissues and populate this cTfh pool. To examine exiting cells, we assessed the phenotype of Tfh present within the major conduit of efferent lymph from lymphoid tissues into blood, the human thoracic duct. Unlike blood, we consistently identified a CXCR5-Bright PD-1-Bright (CXCR5BrPD-1Br) Tfh population in thoracic duct lymph (TDL). These CXCR5BrPD-1Br TDL Tfh shared phenotypic and transcriptional similarities with GC Tfh. Moreover, components of the epigenetic profile of GC Tfh could be detected in CXCR5BrPD-1Br TDL Tfh, and the transcriptional imprint of this epigenetic signature was enriched in an activated cTfh subset known to contain vaccine-responding cells. Together with data showing shared TCR sequences between the CXCR5BrPD-1Br TDL Tfh and cTfh, these studies identify a population in TDL as a circulatory intermediate connecting the biology of Tfh in blood to Tfh in lymphoid tissue.

overall_design: Transcriptional features of germinal center Tfh were detected in a population of Tfh in the efferent lymph of the human thoracic duct and can be traced to an activated subset of circulating Tfh in blood.

first: Laura

last: Vella

middle: J

last: Wherry


title: Human Thoracic Duct Lymph Contains Circulatory Intermediates T Follicular Helper Cells


title: Antagonistic interaction between Ezh2 and Arid1a coordinates dental root patterning via Cdkn2a [ChIP-Seq]

summary: We performed H3K27me3 CHIP sequencing of mouse molars from three-day-old wildtype mice.

overall_design: CHIP DNA from mouse molars of three-day-old wildtype mice were generated for CHIP sequencing

first: Junjun

last: Jing

first: Jifan

last: Feng


title: Identification of Radiosensitivity Gene Signatures Induced by Enzalutamide in Prostate cancer cells

city: Montreal

first: Thierry

last: Muanza

address: 3755 Chemin de la Côte-Sainte-Catherine,

institute: McGill Univeristy

summary: This study aimed to identify gene signatures induced by enzalutamide (ENZA) in hormone-sensitive (LNCaP) and hormone-resistant prostate cancer (PCa) cells. LNCaP and C4-2 cells were treated with ENZA alone or  in combination with androgen deprivation therapy (ADT) and radiation (XRT). Through gene expression profiling, we identified that ENZA alone or in combination with ADT enhanced the effect the effect of XRT through immune-related pathways in LNCaP cells and metabolic pathways in C4-2 cells.Kaplan-Meier curve and Cox propotional hazard models showed that low expression of all the candidate genes except PTPRN2 were associated with tumor progression and recurrence in a PCa cohort.

overall_design: Total RNA was extracted from LNCaP (hormone-sensitive PCa cells) and C4-2 (hormone-resistant PCa cells) under eight conditions, control, enzalutamide, ADT, enzalutamide+ADT, radiation , enzalutamide+Radiation, ADT+Radiation, enzalutamide+ADT+radiation.There were three biological replicate for each condition.Total number of sample is 48.


title: Antagonistic interaction between Ezh2 and Arid1a coordinates dental root patterning via Cdkn2a [RNA-Seq]

summary: We sequenced mouse molar mRNA from three-day-old Ezh2fl/fl and Osr2KI-Cre;Ezh2fl/fl mice to compare their gene expression profile

overall_design: mRNA from mouse molars of three-day-old Ezh2fl/fl and Osr2KI-Cre;Ezh2fl/fl mice were generated for RNA sequencing


title: Bone Morphology is Regulated Modularly by Global and Regional Genetic Programs

city: Rehovot

first: Dena

last: Leshkowitz

department: Bioinformatics Unit, Life Sciences Core Facilities

institute: Weizmann Institute of Science

summary: Comparative transcriptomic analysis of different Sox9+/Scx+ progenitor populations identified genes potentially involved in patterning of bone superstructures. Moreover, this analysis shows that the genetic program includes both proximal and distal regulatory modules.

overall_design: Comparative transcriptomic analysis of proximal and distal Sox9+/Scx+ progenitor populations was performed. Sox9+/Scx+ progenitor populations were isolated by FACS sorting genetically co-labeled Sox9-CreERT2;Rosa26-tdTomato+;ScxGFP+ cells from E13.5 dissected forelimbs.

first: Shai

last: Eyal

first: Shiri

last: Kult

first: Sarah

last: Rubin

first: Sharon

last: Krief

first: Tomer-Meir

last: Salame

first: Yoseph

last: Addadi

first: Kyriel

last: Pineault

first: Deneen

last: Wellik

first: Elazar

last: Zelzer


title: Intracellular Zn2+ transients modulate global gene expression in dissociated rat hippocampal neurons

city: Boulder

first: Lynn

last: Sanford

state: CO

address: UCB 596

department: Biochemistry

institute: University of Colorado Boulder

summary: Zinc (Zn2+) is an integral component of many proteins and has been shown to act in a regulatory capacity in different mammalian systems, including as a neurotransmitter in neurons throughout the brain. While Zn2+ plays an important role in modulating neuronal potentiation and synaptic plasticity, little is known about the signaling mechanisms of this regulation. In dissociated rat hippocampal neuron cultures, we used fluorescent Zn2+ sensors to rigorously define resting Zn2+ levels and stimulation-dependent intracellular Zn2+ dynamics, and we performed RNA-Seq to characterize Zn2+-dependent transcriptional effects upon stimulation. We found that relatively small changes in cytosolic Zn2+ during stimulation altered expression levels of 931 genes, and these Zn2+ dynamics induced transcription of many genes implicated in neurite expansion and synaptic growth. Additionally, while we were unable to verify the presence of synaptic Zn2+ in these cultures, we did detect the synaptic vesicle Zn2+ transporter ZnT3 and found it to be substantially upregulated by cytosolic Zn2+ increases. These results provide the first global sequencing-based examination of Zn2+-dependent changes in transcription and identify genes that may mediate Zn2+-dependent processes and functions.

overall_design: 3 replicates of each of 3 conditions (KCl treatment, KCl/Zn treatment, KCl/TPA treatment), none of which are control conditions. KCl treatment was used as the reference condition for all comparisons. TPA = tris(2-pyridylmethyl)amine, a Zn2+ chelator.

first: Amy

last: Palmer


title: Human Thoracic Duct Lymph Contains Circulatory Intermediates T Follicular Helper Cells [ATAC-Seq]

first: E

last: WHERRY

overall_design: Epigenetic features of germinal center Tfh were detected in a population of Tfh in the efferent lymph of the human thoracic duct and can be traced to an activated subset of circulating Tfh in blood.

last: Vella

first: Josephine

last: Giles

first: Marcus

last: Buggert


title: Expression data of AML cells treated with out without H4

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

summary: Safer and more efficient therapy for patients with acute myeloid leukemia (AML) is needed and differentiation therapy is an appealing option to eradicate leukemic stem cells blocked in differentiation. With the aim of identifying new AML differentiating agents/molecules, we screened 528 natural compounds on primary AML samples. Compounds that upregulated the expression of the myeloid differentiation markers CD11b/CD15 were considered as positive hits. Among those, a macrocyclic diterpenecalled H4 upregulated expression of CD11b (DMSO 22±5%, H4 66±8% SEM), which was accompanied with a clear decrease in nuclear-cytoplasmic ratio, on patient cells with AML subtype M5. To identify the mechansim AML cells were treated with H4 for 16 hrs followed by gene expression analysis.

overall_design: Comparing primary acute Myeloid leukemia traeated with the H4 molecule

first: Simon

last: Hultmark


title: mRNA expression profile of mouse CD4 T cells (treated vs. untreated with PM2.5 suspension)

city: Shanghai

first: Sun

last: Licheng

address: No. 399, wanyuan road

institute: Fudan University

summary:
Purpose: PM2.5 can impact mouse TH17 cell differentitation. To Investigator the genes altered by PM2.5 during TH17 differentiation, mRNA-seq was performed.
Methods: Naïve T cells were isolated from mouse spleen by magnetic beads. These naïve T cells were stimulated by CD3/CD28 antibodies and cultured under TH17 polarization conditions for 4 days before harvested. For PM2.5 group, 100ug/ml of PM2.5 suspensions were added to culture medium 6 hours after stimulation. The total RNA was extracted using the TRIzol reagent (Invitrogen). The library construction and sequencing was performed by Illumina Xten at Shanghai Biotechnology Corporation.

overall_design: PM2.5 treated group was compared to control group. Each group has 3 samples.

first: Yufeng

last: Zhou

first: Licheng

last: Sun


title: MYC deregulates TET1 and TET2 expression to control global DNA (hydroxy)methylation and gene expression to maintain a neoplastic phenotype in T-ALL

city: Augusta

first: Jan

last: van Riggelen

state: GA

address: 1410 Laney Walker Blvd.

country: USA

institute: Augusta University

summary: We performed methylation, hydroxymethylation, and gene expression profiling using MeDIP-seq, hMeDIP-seq, and RNA-seq, respectively, to investigate the role of TET1 and TET2 in MYC-driven tumor maintenance. We compared T-ALL tumor cells before and upon MYC inactivation and revealed genome-wide changes in the DNA methylation and hydroxymethylation patterns. Furthermore, TET1 knock-down or ectopic TET2 expression in T-ALL revealed genome-wide changes in DNA methylation and hydroxymethylation patterns corresponding to changes in gene expression.

overall_design: Samples used in this study correspond to T-cell acute lymphoblastic leukemia (T-ALL) cell lines derived from EμSRα-tTA;tet-o-MYC mice (6780) and human CCRF-CEM.

first: Candace

last: Poole