title: Maintenance of Mammalian Stem Cell States by Honeybee Royalactin

status: Public on Dec 24 2018

city: Stanford

first: Kevin

last: Wang

state: CA

address: 269 Campus Dr, CCSR 2115a

department: Dermatology

institute: Stanford University

summary: Royal Jelly (RJ) is the queen-maker for the honeybee Apis mellifera, and has documented cross-species effects on longevity, fertility, and regeneration in mammals. We describe novel wound healing and stemness maintenance activities for Royalactin, the major protein component in RJ, in mice and in embryonic and post-natal stem cells, respectively. Royalactin activates a pluripotency gene regulatory network through control of chromatin dynamics to affect a phenotype that mimics ground state pluripotency. We also identified, through a haploid genetic screen, heparan sulfate proteoglycans as the major cell surface binding partners for Royalactin in mammalian cells, and demonstrate important functional interactions between Royalactin and well known pluripotency-regulating pathways. Thus, Royalactin can maintain cellular identity through affecting the dynamic state of stem cells.

overall_design: Each experiment was performed in at least biological duplicate with input or other controls when appropriate.

first: D

last: Wan

first: P

last: Janki

first: A

last: Spencley

first: G

last: Shankar

first: T

first: S

last: Morgan

first: N

last: Mariano

first: Y

last: Luo

last: Dana

first: C

last: Dovey

first: J

last: Lumb

first: L

first: K

middle: V

last: Brown

first: R

last: Luong

last: Pitteri

first: H

last: Tu

last: Nusse

last: Rando

last: Carette


title: Gene expression analysis of mouse liver after bile duct ligation (BDL) treated or not with anti-miR-873

status: Public on Dec 25 2018

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

type: Expression profiling by high throughput sequencing

summary: Background & Aims. Glycine N-methyltransferase (GNMT) is an essential regulator of the total transmethylation flux in the mammalian liver. Distinct DNA methylation patterns are characteristic of liver development, hepatic de-differentiation and liver disease progression, processes in which the levels of GNMT decrease dramatically by mechanisms still poorly understood. Interestingly, putative binding sites for the microRNA miRNA-873-5p were identified in the 3´UTR of GNMT suggesting a potential role for miRNA-873-5p in GNMT regulation.   Results. We have identified that the hepatic expression of miRNA-873-5p was increased in a cohort of cirrhotic and liver cancer patients associated with a down-regulation of GNMT levels. Moreover, during liver development, hepatic de-differentiation and fibrosis, the elevation of miRNA-873-5p coincided with the reduction of GNMT expression, indicating that miRNA-873-5p specifically targets the expression of GNMT. Under these circumstances, inhibition of miRNA-873-5p induced GNMT levels and decreased global CpG methylation and transmethylation flux. Indeed, reestablishment of GNMT expression by miRNA-873-5p inhibition reduced hepatocyte de-differentiation, and abolished completely the mortality produced after bile duct ligation as a result of decreased proinflamatory and profibrogenic markers.  miRNA-873-5p knockdown-mediated antifibrotic effect was significantly blunted if its effect on GNMT was blocked.   Conclusion. Taken together, our studies highlight the role of miRNA-873-5p as a key regulator of GNMT expression, paving the way for new therapeutical approaches in liver de-differentiation and fibrosis.

overall_design: Genome-wide changes in gene Expression in mouse livers from BDL treated or not with anti-miR-873 were generated by RNAseq.

first: Maria

middle: L

last: Martínez Chantar


title: Transcriptomic analysis of the early phase of BoMac cell stimulation with a viral and a bacterial pathogen associated molecular patterns.

status: Public on Dec 22 2018

city: Basseterre

first: Felix

last: Toka

address: West Farm

department: Biomedical Sciences

country: Dominica

institute: Ross University School of Veterinary Medicine

summary: Purpose: To examine differential expression of genes in bovine macrophages under the influence of Toll-like receptor agonists. Goal: to study and understand the early phase of transcriptomic changes induced by Toll-like receptor in bovine macrophage cell line.

overall_design: Examination of the effect of CpG and poly I:C on gene expression in BoMac cell line.

middle: N

first: Kiera

last: Dunaway

first: Felicia

last: Smaltz

first: Lidia-Szulc

last: Dabrowska

first: Magdalena

last: Bossowska-Nowicka

first: Matylda

last: Mielcarska

first: Matthias

last: Schweizer


title: Polycomb Group Proteins EZH2 and EED Directly Regulate Androgen Receptor in Advanced Prostate Cancer

city: Houston

first: Guangyu

last: Wang

address: 6670 Bertner Ave

country: USA

institute: Houston methodist research institute

summary: Polycomb group proteins are important epigenetic regulators for organ development, cell proliferation and differentiation, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including EZH2, promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells. The canonical function of EZH2, along with its essential binding partners EED and SUZ12, is to methylate histone H3K27 and repress its downstream targets. In this study, we discover that EZH2 regulates androgen receptor (AR) expression levels and AR signaling in prostate cancer. Targeting EZH2 with the newly identified EZH2 inhibitor, astemizole, could effectively inhibit the progression of castration-resistant prostate cancer.

overall_design: Examination of mRNA profiles level in 5 cell types

first: Qipeng

last: Liu

first: Qi

last: Cao

first: Kaifu

last: Chen


title: MLL-PTD and RUNX1-knockout cooperate to induce MDS phenotypes

status: Public on Dec 23 2018

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: The MLL-PTD mutation is found in patients with MDS and AML, and not in other hematological malignancies. Previously, we showed that Mll-PTD knock-in heterozygous mice (MllPTD/WT mice) present with several MDS-associated features. However, these phenotypes are insufficient to constitute bona fide MDS. MllPTD/WT mice do not generate MDS or AML in primary or transplant recipient mice. This suggests that additional genetic and/or epigenetic defects are necessary for transformation to MDS or AML. In secondary AML and de novo AML, MLL-PTD mutation is significantly associated with mutations in RUNX1 and with the FLT3-ITD mutations. In fact, the combination of MLL-PTD with the FLT3-ITD allele leads to AML in mice. We combined the MLL-PTD with RUNX1 mutant proteins, in order to generate a new mouse model for MDS. We generated MllPTD/WT/Runx1Flox/Flox/Mx1-Cre mice to model loss-of-function RUNX1 mutations. To test the significance of HIF-1α in this model, we also generated MllPTD/WT/Runx1Flox/Flox/Hif-1αFlox/Flox/Mx1-Cre mice and genetically eliminated Hif-1α expression. We analyzed gene expression variations in the HSPCs comparing the MllPTD/WT/Runx1∆/∆ with or without HIF-1α abrogation.

overall_design: Expression profiles of mRNA in HSPCs from MLL-PTD/Runx1-KO mice with or without HIF-1α

first: Yoshihiro

last: Hayashi

first: Kashish

last: Chetal

last: Leighton Grimes

first: Gang

last: Huang


title: RNA sequencing (RNA-SEQ) of Human endothelial cells (HUVEC) in LFS, sFRP2OE, and WT conditioned media

city: New York

first: Seungyeul

last: Yoo

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary:
Purpose: To understand molecular and cellular effects of secreted sFRP2 to endothelial cells
Methods: We performed RNA sequencing of 9 samples from HUVEC cultured in WT, sFRP2OE, LFS conditioned media for 16 hours
Conclusion: apoptosis and angiogenetic molecular factors are activated in HUVEC by secreted sFRP2

overall_design: cDNA library preparation and sequencing were performed at Novogen (http://www.novogen.com/home). Briefly, RNA quality was determined with an Agilent Bioanalyzer (RNA integrity number [RIN] > 7.0 for all samples). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, and double stranded cDNA synthesized using random hexamers, M-MuLV Reverse Transcriptase (RNase H), and DNA Polymerase I. NEBNext Adaptor with hairpin loop structure were ligated to the cDNA in preparation for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Library of 150-200 bp fragments at an effective concentration of > 2nM were loaded onto an Illumina HiSeq 4000 for sequencing

first: Huen

middle: S

last: Kim

first: Jun

last: Zhu


title: PLZF limits enhancer activity during hematopoietic progenitor aging

status: Public on Dec 21 2018

city: Marseille

first: Mathilde

last: Poplineau

address: 27 BOULEVARD LEI ROURE CS 30059

country: France

institute: INSERM

type: Genome binding/occupancy profiling by high throughput sequencing

summary: PLZF (promyelocytic leukemia zinc finger) is a transcription factor acting as a global regulator of hematopoietic commitment. PLZF displays an epigenetic specificity by recruiting chromatin-modifying factors but little is known about its role in remodeling chromatin of cells committed towards a given specific hematopoietic lineage. In murine myeloid progenitors, we decipher a new role for PLZF in restraining active genes and enhancers by targeting acetylated lysine 27 of Histone H3 (H3K27ac). Functional analyses reveal that active enhancers bound by PLZF are involved in biological processes related to metabolism and associated with hematopoietic aging. Comparing the epigenome of young and old myeloid progenitors, we reveal that H3K27ac variation at active enhancers is a hallmark of hematopoietic aging. Taken together, these data suggest that PLZF, associated with active enhancers, appears to restrain their activity as an epigenetic gatekeeper of hematopoietic aging.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: ChIP-seq for PLZF-Flag and input on 416b cells transduced by PLZF-Flag or empty vector. ChIP-seq for H3K4me3, H3K4me1, H3K27me3, H3K27ac and input on 416b transduced by PLZF-Flag or empty vector. RNA-seq performed on total RNA purified from 416b transduced by PLZF-Flag or empty vector. ATAC-seq performed on genomic DNA purified from 416b transduced by PLZF-Flag or empty vector. ChIP-seq for H3K4me3, H3K4me1, H3K27me3, H3K27ac and input on WT and Zbtb16lu/lu GMPs, young GMPs and old GMPs.  RNA-seq performed on total RNA purified from primary graft of WT and Zbtb16lu/lu GMPs.

first: Julien

last: Vernerey

first: Nadine

last: Platet

first: Lia

last: N’guyen

first: Michaela

last: Esposito

first: Andrew

last: Saurin

first: Christel

last: Guilouf

first: Atsushi

last: Iwama

first: Estelle

last: Duprez


title: Sub-populations in the mammary repopulating units

city: Rehovot

first: Dan

last: Ben-Avraham

address: Herzl 234

department: G-INCPM

country: Israel

institute: Weizmann Institute of Science

summary: Elucidating the top of the mammary epithelial cell hierarchy is highly important for understanding its regeneration capabilities and identifying target cells for transformation. Aiming for enriched mammary epithelial stem cell population, CD200highCD200R1high epithelial cells were identified. These cells represent ~50% of the mammary repopulating units (MRUs, CD49fhigh CD24med ) and termed MRUCD200/CD200R1. Gene expression of these cells was compared to all other MRU cells, termed MRUnot CD200/CD200R1, as well as individual CD200+ population (MRU-CD200R1-) and CD200R1+ population (MRU-CD200-).

overall_design: Gene expression from mammary epithelial cells carrying sorted by CD200, CD200R1 markers and MRU markers. Four populations were sequenced: MRU-positive CD200 positive and CD200R1 positive; MRU-positive and not CD200 positive CD200R1 positive; not MRU CD200 positive CD200R1 negative; not MRU CD200 negative CD200R1 positive. There are 5 replicates from 5 individual mice.

first: Gat

last: Rauner

first: Gilad

last: Shlomit

first: Tania

last: Kudinov

first: Gil

last: Hornung

first: Itamar

last: Barash


title: IMP1 re-expression in adult hematopoietic stem cells RNA Sequencing

city: Oxford

first: Claus

last: Nerlov

address: WIMM

country: United Kingdom

institute: University of Oxford

summary: The onco-fetal RNA-binding protein IMP1 is expressed in fetal liver HSCs, but down-regulated in adult BM HSCs. We here show that when IMP1 is re-expressed in adult HSCs it induces a significant part of the fetal HSC gene expression signature. In addition, IMP1 re-expression leads to the expansion of phenotypic long term (LT-)HSCs, and increased generation of fetal peritoneal B1a B-cells and thymic γδ-T-cells. Finally, IMP1 expressing adult LT-HSCs show dramatically improved self-renewal in serial transplantations compared to their normal counterparts. To assess the effect of IMP1 re-expression on the molecular properties of adult HSCs we performed RNA sequencing of total RNA isolated from Control and IMP1 HSCs sorted from primary recipient mice, transplanted with control or IMP1+ total bone marrow cells.

overall_design: To achieve re-expression of IMP1 in adult mice we generated a conditional knock-in of IMP1 into the Rosa26 locus. In order to achieve selective IMP1 re-expression in hematopoietic cells, we transplanted whole bone marrow (CD45.2 allotype) from Rosa26II+;Mx1-Cretg/+ (IMP1 mice) and Rosa26+I+;Mx1-Cretg/+ (Control mice) into lethally irradiated CD45.1/2 mice. The expression of IMP1 was then induced by inducing the expression of the Mx1-Cre transgene by poly(I-C) injection. For RNA sequencing 200 CD45.2+ LT-HSCs, were sorted from primary recipients, 8 weeks after last PolyIC injection, directly into lysis buffer supplemented with RNase Inhibitor (Clontech). 3 biological replicates were generated from each genotype. Samples were prepared using the SMARTer™ Ultra Low RNA kit for Illumina Sequencing (Clontech) as previously described (Ramskold et al., 2012)

first: Adriana

last: Gambardella

first: Nikolaos

last: Barkas

first: Alice

last: Giustacchini

first: Ruggiero

last: Norfo

first: Sten

middle: E

last: Jacobsen

first: Liliana

last: Minichiello


title: RNA sequencing (RNA-SEQ) of RRD1 knockout yeast strains with Rapamycin treatment

first: Seungyeul

last: Yoo

summary:
Purpose: We develop a multivariate polynomial temporal genetic association (MPTGA) approach for detecting temporal genetic loci of quantitative traits monitored over time in a population. To dissect causal regulators under each temporal genetic locus, we develop a temporal genetic causality test (TGCT) for inferring causal relationships between traits linked to the locus.  We applied MPTGA and TGCT to simulated data sets and a yeast population that was molecularly profiled over six time points in response to treatment with the drug rapamycin.  We demonstrate significantly increased power to detect genetic loci modulating gene expression traits over time in this population and to resolve the causal regulators of dynamic expression quantitative loci hot spots, thereby increasing the power to elucidate regulatory networks. We experimentally validated a teQTL (temporal expression Quantitative Trait Locus) hot spot locus interacting with rapamycin treatment over time, which could only be identified using our temporal genetic association procedure. We experimentally validated RRD1, a cis regulated gene in this locus, as the causal regulator for this teQTL hot spot.
Methods: The wild type strain BY4730 and RRD1 knockout strain YSC6273-201925697 were obtained from Thermo Scientific Open Biosystems.  Yeast was grown in YPD medium to log-phase in shaken flasks at 30°C.  Total RNA was extracted as described previously.  For rapamycin treatment, 100nM rapamycin (Cayman Chemical, Ann Arbor, MI) was added to the medium after yeast grew to log-phase. After culture for 50 minutes, total RNA was extracted the same as above.  All experiments were repeated 3 times on three different days.   Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument with 100nt single read setting according to the manufacturer's instructions. Sequence reads were aligned to yeast genome assembly using Tophat . Total 6,932 yeast transcripts were quantified using Cufflinks, and 5,542 of them overlap with transcripts on Yeast Genome 2.0 Arrays from Affymatrix, which was used for generating the yeast F2 time course data.  The 5,542 transcripts were used in further analysis.  Differentially expressed genes were defined by CuffDiff.  At q-value <0.01, 64 and 581 were in RRD1 ko signature without rapamycin (RRD1 ko  no treatment vs. wild type no treatment) and RRD1 ko signature with rapamycin (RRD1 ko  with rapamycin vs. wild type with rapamycin), respectively.
Conclusions: Integration of temporal and genetic data has the potential to enhance the power to resolve causal relationships and to provide a more accurate view of regulatory networks in complex biological systems.

overall_design: For each of wild type and RRD1 KO strains, 3 untreated and 3 treated with Rapamycin were used and analyzed. To identify RRD1 KO signatures, cuffdiff was performed.

first: Jun

last: Zhu


title: Single cell RNA sequencing of kidney tubuloids and the tissue that the tubuloids were derived from

status: Public on Dec 20 2018

city: Utrecht

first: Frans

last: Schutgens

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute / UMC Utrecht

summary: Adult Stem Cell (ASC )-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney tubular epithelial organoids (‘tubuloids’). Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). The structures retain a normal number of chromosomes. Human tubuloids represent proximal as well as distal nephron segments, as evidenced by gene expression, immunofluorescence and tubular functional analyses. BK virus infection of tubuloids recapitulates in vivo phenomena. "Tumoroids" can be established from Wilms nephroblastoma. Kidney tubuloids from urine from a subject with Cystic Fibrosis (CF) allows ex vivo assessment of treatment efficacy. Finally, tubuloids cultured on microfluidic organ-on-a-chip plates adopt a tubular conformation and display active (trans-)epithelial transport function. Adult kidney-derived epithelial tubuloids allow studies of hereditary, infectious and malignant kidney disease in a personalized fashion.

overall_design: We generated single cell transcriptome data of kidney tubuloids and the tissue that the tubuloids were derived from

first: Maarten

middle: B

last: Rookmaaker

first: Carola

last: Ammerlaan

first: Jitske

last: Jansen

first: Marco

last: Viveen

first: Linda

last: Gijzen

first: Annelotte

last: Vonk

first: Karin

middle: M

last: de Winter-de Groot

first: Benedetta

last: Artegiani

first: Ruben

last: van Boxtel

first: Edwin

last: Cuppen

first: Antoni

middle: P

last: Hendrickx

first: Marry

last: van den Heuvel-Eibrink

first: Ellen

last: Heitzer

first: Henriette

last: Lanz

first: Jeffrey

last: Beekman

first: Jean-Luc

last: Murk

first: Rosalinde

last: Masereeuw

first: Jarno

last: Drost

first: Marianne

middle: C

last: Verhaar

first: Hans

last: Clevers


title: Response of Lactobacillus plantarum WCSF1 to the Gram-negative pathogen-associated quorum sensing molecule N-3-oxododecanoyl homoserine lactone.

status: Public on Dec 19 2018

city: Washington

first: Scott

middle: Nathan

last: Dean

state: DC

address: 4555 Overlook Ave SW

institute: Naval Research Laboratory

summary: The bacterial quorum sensing (QS) phenomenon has been well studied since its discovery and has traditionally been considered to include signaling pathways recognized exclusively within either Gram-positive (Gm+) or Gram-negative (Gm-) bacteria. The Gm+ bacteria are known to utilize quorum sensing pathways mediated by various small autoinducing peptides (AIP), while the Gm- bacteria use small molecules known collectively as acyl-homoserine lactones (AHL). Distinct structural differences between the types of signaling molecules have historically implied a lack of cross-talk among Gm+ and Gm- QS systems. Recent investigations, however, have demonstrated the ability for AIPs and AHLs to be produced by noncanonical organisms, implying QS systems may be more universally recognized than previously hypothesized. With that in mind, our interests were piqued by the organisms Lactobacillus plantarum, a Gm+ commensal probiotic known to participate in AIP-mediated QS, and Pseudomonas aeruginosa, a characterized Gm- pathogen whose virulence is controlled by AHL-mediated QS. Both health-related organisms are known to inhabit the human gut in various instances, both are characterized to elicit distinct effects on host immunity, and some studies hint at the putative ability of L. plantarum to degrade AHLs produced by P. aeruginosa. We therefore wanted to determine if L. plantarum cultures would respond to the addition of N-(3-oxododecanoyl)-L-homoserine lactone (3OC12) from P. aeruginosa by analyzing changes on both the transcriptome and proteome over time. Based on the observed upregulation of various two-component systems, response regulators, and native quorum sensing related genes, the resulting data provide evidence of an AHL recognition and response by L. plantarum.

overall_design: L. plantarum was treated with 3OC12. Changes in the transcriptome were measured at three time points.

first: Joseph

middle: R

last: Spangler

first: Dagmar

middle: H

last: Leary

middle: A

last: Walper


title: Distal ileal antibiotic infusion affects the expressions of neurotransmitters in the hypothalamus of piglets

city: Nanjing

first: Kan

last: Gao

address: No.1 Weigang Road

country: China

institute: Nanjing Agricultural University

summary:
Purpose: Gut microbiota-brain axis serves as an emerging pathway affecting brain function. Hindgut has a higher proportion of microbes than foregut, however whether alteration in hindgut microbiota is related to brain functional change remains unclear. The present study used antibiotics to modulate the hindgut microbiota, to investigate the changes in the functions of porcine hypothalamus.
Methods: Twelve piglets (12.08 ± 0.28 kg) fitted with T-cannula at the distal ileum were fed a standard diet and randomly assigned to two groups (n=6) for ileal infusions of saline (control group) and an antibiotic mix (ampicillin, gentamycin and metronidazole; antibiotic group), respectively. After the 25-day experiment, the microbiota and metabolites in feces, concentrations of amino acids and neurotransmitters in hypothalamus and blood, and transcriptomics profiles of hypothalamus were analyzed.
Results: The results showed that the antibiotic infusion resulted in an increase in aromatic amino acids (AAA)-utilizing genera, notably Lactobacillus, and a decrease in the concentrations of AAAs including tryptophan, tyrosine and phenylalanine in feces. Correspondingly, concentrations of AAAs in the blood and hypothalamus also decreased. In the hypothalamus, the concentrations of AAAs related neurotransmitters 5-HT and dopamine decreased. Meanwhile, the compensatory upregulations of neurotransmitter transporter genes such as SERT, DAT and synthesis-related genes TPH2 and AADC were observed (adjusted P < 0.001). Furthermore, the concentrations of 5-HT and dopamine decreased in the blood.
Conclusion: In conclusion, the results revealed that the ileal antibiotic infusion could affect the expressions of neurotransmitters in the porcine hypothalamus. The changes of hindgut microbial composition, circulating AAA profile and hypothalamic neurotransmitter expressions indirectly suggested that the hindgut microbiota may affect the brain functions.

overall_design: Hypothalamic mRNA profiles of pigs in control and ileal antibiotic infusion groups were generated by deep sequencing, control group with 4 replicates, antibiotic group with 3 replicates, using Illumina HiSeq 2000.

first: Weiyun

last: Zhu


title: A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients [RNA-seq]

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

institute: Academic Medical Center Amsterdam

summary:
The Illumina NextSeq500 was used to sequence the gene expression profiles of 21 ileal fibroblast samples. Samples included 6 control samples and 15 Crohn’s disease samples. The Crohn’s disease samples can be further subdivided into inflamed (4), non-inflamed (6) and stenotic (5) samples.

This experiment together was performed in conjunction with a DNA methylation experiment (GSE99788). Use Supplemental Table 2 of the manuscript to quickly find the samples that were present in both experiments.

overall_design: RNA from 21 samples were sequenced on the Illumina NextSeq500

first: A

middle: Y

last: Li Yim

first: J

last: de Bruyn

first: N

middle: W

last: Duijvis

first: C

last: Sharp

first: E

last: Ferrero

first: W

middle: J

last: de Jonge

first: M

last: Wildenberg

last: Mannens

last: Buskens

first: G

last: D’Haens

first: P

last: te Velde


title: Fasting Imparts a Switch to Alternative Circadian Transcriptional Pathways in Liver and Muscle

status: Public on Dec 18 2018

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

institute: University of California, Irvine

summary: The circadian gene expression in peripheral tissue displays rhythmicity which is driven by the circadian clock and feeding-fasting cycle in mammals. In this study, circadian transcriptome was performed to investigate how fasting influences circadian gene regulation.

overall_design: 8-week-old, male C57BL/6 mice were subjected to 24-hr fasting (FAST) or to ad libitum normal chow feeding (FED) under 12hr light/ 12hr dark schedule. Liver and gastrocnemius muscle were harvested every 4 hours over the circadian cycle at ZT0, 4, 8, 12, 16, 20 (n=3 per time point per group). Total RNA was extracted from liver and gastrocnemius muscle, and used for RNA-seq.

first: Kenichiro

last: Kinouchi

first: Nicholas

last: Ceglia

first: Yu

last: Liu

first: Marlene

last: Cervantes

first: Pierre

last: Baldi

first: Selma

last: Masri

first: Paolo

last: Sassone-Corsi


title: Early pathological characterization of murine dissecting abdominal aortic aneurysms

status: Public on Dec 15 2018

city: West Lafayette

first: Evan

last: Phillips

state: IN

address: 206 S. Martin Jischke Dr

department: Weldon School of Biomedical Engineering

institute: Purdue University

summary: We report on the early pathological development of a well-established murine model of aortic dissection / abdominal aortic aneurysm.

overall_design: Suprarenal aorta and aneurysm tissues were harvested and total RNA extracted for pooling into one of three treatment cohorts. The total number of reads per library were between 35 and 43 million. Differentially expressed genes were found among cohorts of apolipoprotein E-deficient mice infused transiently with angiotensin II (treatment) or saline (control). Angiotensin II-infused mice were either sacrificed within 24 hours of identification of a dissecting abdominal aortic aneurysm or, if no aneurysmal lesion was found, by day 10 after the implantation of pumps infusing angiotensin II.

first: Adam

last: Lorch

first: Abigail

last: Durkes

first: Craig

last: Goergen


title: Control of Th17 cell development by Class IIa HDAC4 and HDAC7 through transcriptional repression of negative regulators

status: Public on Dec 16 2018

first: Rajal

last: Sharma

address: 1425 Madison Ave., Room 16-52

institute: ISMMS

summary: We analyzed the genome wide distributions of HDAC1, HDAC4, HDAC7 in Th17 cells. We find that majority of HDAC4 and HDAC7 binding sites are HDAC1 bound. TMP269 inhibits HDAC4 and HDAC7 at promoter sites of Th17 negative regulator genes, leading to their upregulation through increased H3, H4 acetylation.

overall_design: ChIP-seq study of HDAC1, HDAC4, and HDAC7 in Th17 cells.  The Th17 cells are differentiated for 48hrs and ChIP with the corresponding antibodies and ChIP-seq libraries are made.

first: K

last: Cheung

last: Zhou


title: Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [Bisulfite-Seq]

status: Public on Dec 17 2018

city: Baltimore

first: Andrew

middle: P.

last: Feinberg

state: MD

address: 855 N. Wolfe St

institute: Johns Hopkins University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucleus accumbens, BA9-dorsolateral prefrontal cortex, BA24-anterior cingulate cortex, and HC-hippocampus) in both sorted nuclei and intact tissues. We isolated neuronal and non-neuronal (glial) nuclei from the same six individuals for each tissue via FACS using the neuronal marker, NeuN. Additionally, we performed WGBS from non-sorted tissues from these same brain regions in a total of 12 individuals (BA9 n = 9; BA24 n = 5; HC n = 6; NAcc n = 7). To complement our DNA methylation analyses, we measured gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in neuronal and non-neuronal nuclei from the nucleus accumbens and dorsolateral prefrontal cortex from six more individuals. We then performed an integrative analysis to understand how the epigenome contributes to brain region-specific function.

overall_design: 72 WGBS libraries were sequenced (from intact tissue (27 libraries) and NeuN+ and NeuN- flow sorted nuclei (45 libraries)) from hippocampus, nucleus accumbens, prefrontal cortex (BA9), and anterior cingulate gyrus (BA24). RNA-seq (20 libraries) and ATAC-seq (23 libraries) data from NeuN+ and NeuN- flow sorted nuclei from the nucleus accumbens and prefrontal cortex (BA9) were also obtained.

first: L

middle: F

last: Rizzardi

last: Hickey

middle: D

last: Hansen

first: A


title: Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [RNA-Seq]

first: P


title: The effect of iron dextran on the transcriptome of hippocampus in Rongchang piglet

city: Chongqing

first: Ling

last: Gan

address: 160#Xue Yuan Road,RongchangCounty

department: 1The Department of Veterinary Medicine

institute: Southwest University

summary: The chain of events leading from oxidation stress is still barely understood. With the emergence of high-throughput sequencing, it is now possible to discover many different biological components simultaneously. Using RNA-seq technology, we sequenced the complete transcriptome of hippocampus of Rongchang piglets exposed to iron dextran (FeDex) treatment, a potent inducer of oxidation stress. Total RNAs from hippocampus of Rongchang piglet were sequenced and 11.5 Gb sequencing data was obtained. This analysis revealed regulatory molecules involved in oxidation stress through the identification of 362 differentially expressed genes (DEGs) and the functional analysis of DEGs. Furthermore, 76 neuropeptide gene transcripts, 60 neuropeptide receptor gene transcripts, were identified in hippocampus of Rongchang piglets, even though mRNA levels of only six neuropeptide genes were significantly changed. Totally, by using the RNA-seq we elucidated for the first time the transcriptomic changes directly caused by the injection of iron dextran. This system enabled the characterization of the transcriptional response triggered by oxidation stress in hippocampus of Rongchang piglet.

overall_design: Transcriptional profiles of Rongchang pig hippocampus treatmented by iron dextran  were generated by deep sequencing, using  Hiseq 2500.


title: Widespread RNA editing dysregulation in Autism Spectrum Disorders [RNA-Seq]

status: Public on Dec 14 2018

city: Los Angeles

first: Grace

last: Xiao

address: 610 Charles E. Young Drive S

department: UCLA Department of Integrative Biology and Physiology

institute: UCLA

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disease with complex heterogeneity and aberrations in multiple levels of neurobiology. Recently, our understanding of the molecular abnormalities in ASD has been greatly expanded through transcriptomic analyses of postmortem brains. However, a crucial molecular pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here we profiled the global patterns of adenosine-to-inosine (A-to-I) editing in a large cohort of ASD cortices and cerebella. Strikingly, we observed a global bias of hypoediting in ASD brains, common to different brain regions and involving many genes with critical neurological function. The large-scale RNA editing changes allowed us to reveal novel insights of RNA editing regulation. Through genome-wide protein-RNA binding analyses and detailed molecular assays, we show that the Fragile X proteins, FMRP and FXR1P, interact with ADAR protens and modulate A-to-I editing. Furthermore, we observed convergent patterns of RNA editing alterations between ASD and Fragile X syndrome, thus establishing RNA editing as a novel molecular link underlying these two highly related diseases. Our findings support a role for RNA editing dysregulation in ASD pathophysiology and highlight novel mechanisms for RNA editing regulation.

overall_design: RNA-seq to examine RNA editing in Fragile X patients

first: Stephen

last: Tran

first: Hyun-Ik

last: Jun

first: Jae

last: Bahn

first: Adel

last: Azghadi

first: Gokul

last: Ramaswami

first: Eric

last: Van Nostrand

first: Thai

last: Nguyen

first: Yun-Hua

last: Hsiao

first: Chang

last: Lee

first: Gabriel

last: Pratt

first: Gene

last: Yeo

first: Daniel

last: Geschwind

first: Xinshu


title: Widespread RNA editing dysregulation in Autism Spectrum Disorders [eCLIP-seq]

overall_design: eCLIP-seq in HepG2 and K562 Cells


title: Differential gene expression in EpCAM+ pancreatic cancer cells with Lifr deficiency

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary:
The goal of this study is to investigate the molecular mechanisms of LIFR signaling in pancreatic cancer cells isolated from the classical pancreatic ductal adenocarcinoma mouse model KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice
EpCAM+ pancreatic cancer cells were isolated by FACS from pancreatic tumors developed in Lifrf/f;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre or LifrWT;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice respectively and directly lysed for RNA extraction

overall_design: Tumors were resected from Lifrf/f;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre or LifrWT;KrasLSL-G12D/+;Trp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice at 44~49 days of age

first: Yu

last: Shi

first: Tony

last: Hunter


title: Widespread RNA editing dysregulation in Autism Spectrum Disorders

first: Grace

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

overall_design: Refer to individual Series


title: Differential Wnt-mediated Programming and Arrhythmogenesis in Right versus Left Ventricles

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine


title: Differential Wnt-mediated Programming and Arrhythmogenesis in Right versus Left Ventricles [wntgof]

summary: Several inherited arrhythmias primarily affect the right ventricle, including Brugada syndrome and arrhythmogenic cardiomyopathy, however the molecular basis of this chamber predilection is not well understood. Right and left ventricular cardiomyocytes derive from distinct progenitor populations. Here, we show that Hrt2, a gene associated with Brugada syndrome, is a direct target of Wnt signaling in the right ventricle and Notch signaling in the left ventricle. Perturbations of Wnt and Notch signaling during development and in the adult lead to chamber-specific transcriptional effects on Hrt2 expression associated with distinct binding patterns to Hrt2 enhancers. Differential enhancer binding is present at early developmental stages when the signaling pathways are active and persists into adulthood. Consistent with chamber-specific regulation, mice deficient in Wnt transcriptional activity dysregulate only a small fraction of transcripts in common between ventricles. Wnt target gen  es important for cellular electrophysiology are differentially regulated, resulting in perturbed cardiac conduction and cellular electrophysiological parameters only within the right ventricle. Ex vivo and in vivo physiologic stimulation of the right ventricle is sufficient to induce ventricular tachycardia in Wnt transcriptionally inactive hearts, while left ventricular stimulation has no effect. Taken together, these data delineate mechanisms underlying ventricular-specific arrhythmia susceptibility due to embryonic programming.

overall_design:
RNA-seq data of Wnt GOF ventricles from e12.5 embryonic hearts
n=6 for each group (control ventricles, wntgof ventricles)

first: Aditi

last: Khandekar

first: Rich

middle: G

last: Li

first: Stacey

last: Rentschler


title: Identification of mRNA subsets interacting to RNA binding proteins in regenerating axons

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: The goal of this study is to compare the mRNA interactome of different RBPs in regenerating axons utilizing RNA-immunoprecipitation (RIP). Interacting mRNAs to each target RBPs were co-immunoprecipitated from axoplasm of sciatic nerve, injured 7 days ago. Interactome of each RBPs were identified by Next-generation sequencing (NGS).

overall_design: SD rats underwent crush injury of the sciatic nerve. 7 days after injury, proximal sciatic nerve was excised and axoplasm was extruded with detergent free, isotonic buffer. After clarification with centrifugation (20,000 xg, 20 min) and subsequent preclearing with Protein A/G dynabeads, RBP and associated mRNA was precipitated by specific antibodies against La/SSB, hnRNP H1, hnRNP F, hnRNP K and FLAG (n=3 respectively) and Protein A/G dynabeads.

first: Jeffery

last: L. Twiss

first: Seung

first: Giovanni

last: Coppola


title: Comparative RNAseq analyses between P. acidipropionici WGS7 and P. acidipropionici ATCC 55737

city: Brisbane

first: Carlos

middle: Horacio

last: Luna Flores

state: QLD

address: Cnr College Rd and Cooper Rd

country: Australia

institute: AIBN

summary: Propionic acid (PA) is a three-carbon molecule commonly used as a food preservative and increasingly, as a precursor for the synthesis of monomers. Propionibacterium spp. are the best biological producers of PA. In fact, a recent report showed that if a yield of 0.6 g/g is achieved, biological production of PA would be economically competitive with petrochemical production. To achieve that yield, a library of Propionibacterium strains was used to generate a new strain that can achieve the commercially desirable yield from sucrose. The genome of the new strain was sequenced and a series of SNPs were found to be responsible for the improved phenotype. Using a combination of transcriptomics the relevant mutations were expounded. Differential RNA-sequencing between the wild-type and the mutant strain identified the relevant genomic changes responsible for the PA yield improvement. Notably, an increase in the specific consumption rate of sucrose was attributed to a SNP in the promoter region of a sugar transporter. Similarly, a mutation in a polar amino acid transporter improved acid tolerance, and an improvement in the electron transport system rewired the metabolism to yield an improved PA phenotype. These changes resulted in a lower acetic acid by-product generation and a higher PA yield. The productivity of the new strain was augmented with the design of a fed-batch process to achieve titres of 70 g/L through the use of a mathematically design fed-strategy.

overall_design: Differential transcriptome expression was used to analyse changes leading to high propionic acid production.

last: Luna-Flores

first: Lars

middle: K

last: Nielsen

first: Esteban

last: Marcellin

first: Chris

last: Stowers

first: Brad

last: Cox


title: In vivo response of EpCAM+ pancreatic cancer cells to gemcitabine plus anti-LIF neutralizing antibody treatment

first: Galina

summary:
The goal of this study is to investigate the molecular mechanisms of LIF action on pancreatic cancer cells in the classical pancreatic ductal adenocarcinoma mouse model KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice
EpCAM+ pancreatic cancer cells were isolated from pancreatic tumors developped in KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice treated with either gemcitabine plus control IgG or gemcitabine plus anti-LIF antibody by FACS

overall_design: The KrasLSL-G12D;Tp53f/f;Rosa26LSL-Luc;Pdx1-Cre mice at 42~43 days of age were treated with either gemcitabine plus control IgG or gemcitabine plus anti-LIF antibody for five days (50mg/kg BW gemcitabine on day 1 and day4, 25 mg/kg BW control IgG or anti-LIF mAb on day 1,3,5), and whole tumors from each treated mice were individually dissected out on day 6, dissociated into single cell suspension by enzyme digestion, and EpCAM+ pancreatic cancer cells were purified by FACS


title: Prediction and Expression Analysis of miRNAs Associated with Oxidative Stress in RongChang pig’s Hippocampus

first: Ling

last: Gan

type: Non-coding RNA profiling by high throughput sequencing

summary: Oxidative stress is involved in the human diseases and developmental retardation of animals. The molecular mechanisms that mediate the response of neuron to oxidative stress have been extensively studied. MicroRNAs (MiRNAs) are a type of small non-coding RNAs that regulate nearly all aspects of nerve development and survival, including apoptosis. However, the effect of oxidative stress on the expression of miRNAs of hippocampus of Rongchang piglets, which are regarded as the good production animal and biomedical model has not been investigated. In this study, oxidative stress was induced in newborn piglets by means of intra-muscular injection of iron. Injection of iron significantly increased several markers of oxidative stress in serum of Rongchang piglets. RNA-sequencing (RNA-seq) technology and bioinformatics were used to uncover the differently expressed miRNAs and target genes induced by oxidative stress in the ventral hippocampus (VH) and dorsal hippocampus (DH) of Rongchang piglets, respectively. Results revealed 2790 conserved miRNAs belonging to 279 miRNA families, 326 known miRNAs and 702 novel miRNAs. The sub-tissue specificity was displayed with 54 differentially expressed miRNAs being found between VH and DH. At the same time, the injection of iron induced 59 and 46 differentially expressed miRNAs in VH and DH, respectively. The analysis of target genes showed that 6 known miRNAs (ssc-miR-183, ssc-miR-383, ssc-miR-193a-5p, ssc-miR-182, ssc-miR-7138-5p and ssc-miR-1271) commonly targeted to ADM2. In addition, GO and KEGG pathway analysis showed that these differentially expressed miRNAs induced by the injection of iron were involved in the pathways that regulate the expression of genes associated with oxidative stress. Our study provided an overview of miRNAs expression profile of functional sub-region of hippocampus in Rongchang piglets and shed light into the significantly changed miRNAs after the injection of iron, which will lead to further understanding of the important roles of miRNAs in hippocampus of Rongchang piglets during the process of oxidative stress.

overall_design: Four small mRNA profiles of vehippocampus Rongchang piglets treatmented by iron dextran were generated by deep sequencing, using Illumina Hiseq 2500.

first: Binyu

last: Yang


title: Transcriptional changes and H3K27ac occupancy associated with resistance to JQ1 treatment in MYCN-amplified neuroblastoma

status: Public on Dec 13 2018

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute


title: Membrane stress and perturbed nutrient homeostasis as common attributes of heterogeneous aneuploidy

status: Public on Dec 12 2018

first: Hung-Ji

last: Tsai

state: Maryland

address: 855 N Wolfe Street

department: Cell Biology

institute: Johns Hopkins University

summary: Aneuploidy, the state of having unbalanced chromosome copy numbers, represents a large repertoire of genome alteration that leads to phenotype variation and enables eukaryotic microbes and cancer cells to adapt to stress or acquire drug resistance. Distinct pattern of gene expression and phenotypes associated with individual karyotype have prevented easy identification of common properties caused by aneuploidy. In this study, we conducted a unique transcriptomic analysis aimed to eliminate the direct DNA dosage effect on gene expression across heterogeneous aneuploid populations. This analysis uncovered a gene expression signature associated with heterogeneous aneuploidy that strongly resembles those previously identified for cell populations under hypo-osmotic stress. Cell biological and biophysical measurements confirmed the presence of plasma membrane stress in heterogeneous aneuploid cell populations, which impairs endocytosis. Through a genome-wide screen for gene deletions that alter the growth of heterogeneous aneuploid populations, we identified a genetic dependency of aneuploid growth on members of the arrestin family that promote endocytic recycling of nutrient transporters in the plasma membrane. Experimental measurements and mathematical modeling demonstrated a dysregulation of nutrient homeostasis as a common defect that results from the biophysical ailment of aneuploid cells.

overall_design: Used RNA-Seq to identify an aneuploidy-associated gene expression signature by comparing the transcriptomes of karyotypically heterogeneous aneuploid populations to euploid control populations.

first: Hung

first: Anjali

last: Nelliat


title: Glutamine 5 serotonylation on histone H3 is a permissive modification that functions combinatorialy with H3K4me3 to potentiate TFIID interactions

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Chemical modifications of histone proteins, along with the ?writers,? ?erasers? and ?readers? of these modifications, are capable of mediating a diverse set of DNA-templated processes including gene transcription1-7. Here, we provide evidence for a new class of histone posttranslational modification (PTM), serotonylation of glutamine, which occurs at position 5 (Q5ser) on histone H3 in serotonin (5-hydroxytryptamine, 5-HT) producing organisms. We demonstrate that the tissue Transglutaminase 2 (TGM2) enzyme, a transamidase that is both necessary and sufficient to deposit the mark, can serotonylate H3 on lysine 4 tri-methylated (H3K4me3) nucleosomes resulting in the presence of combinatorial H3K4me3Q5ser in vivo. H3K4me3Q5ser displays a ubiquitous pattern of tissue expression in mammals, with predicted enrichment observed in brain and gut, two organ systems responsible for the bulk of 5-HT production. Genome-wide analyses of its enrichment in human serotonergic neurons, developing mouse brain and cultured serotonergic cells, using an H3K4me3Q5ser specific antibody, indicate that the mark is enriched in euchromatin, is sensitive to cellular differentiation and correlates with permissive gene expression, phenomena that are linked to the mark?s potentiation of TFIID8-10 interactions with H3K4me3. Cells ectopically expressing an H3 mutant that cannot be serotonylated display significantly altered expression of H3K4me3Q5ser target loci leading to deficits in differentiation. Taken together, these data identify a direct role for 5-HT, independent from its contributions to neurotransmission and cellular signaling, in the mediation of permissive gene expression in mammalian cells, and further define its biophysical activities as a putative co-regulator of TFIID recruitment to H3K4me3 marked chromatin.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Investigation of H3K4me3 and H3K4me3Q5ser marks in RN46A-B14 cells; Investigation of associations of H3K4me3 and H3K4me3Q5ser marks with gene expression and TAF3 recruitment to chromatin in RN46A-B14 cells; Investigation of H3K4me3 and H3K4me3Q5ser marks in embryonic rodent brain; Investigation of associations of H3K4me3 and H3K4me3Q5ser marks with gene expression in embryonic rodent brain; Investigation of the H3K4me3Q5ser marks in human PSCs vs. 5-HT neurons; investigation of associations of H3K4me3Q5ser in human PSCs vs. 5-HT neurons with gene expression.

first: Lorna

last: Farrelly

first: Robert

middle: E

last: Thompson

first: Shuai

last: Zhao

first: Ian

last: Maze


title: Identification of differentially expressed genes in tolerant and susceptible potato cultivars in response to Spongospora subterranea f. sp. subterranea tuber infection

status: Public on Dec 11 2018

city: Pretoria

first: Moleboheng

last: Lekota

state: Choose a State

address: Corner of Lynwood Road & Roper street

department: Plant and soil sciences

country: South Africa

institute: University of Pretoria

summary: We report the application of RNA- sequencing technology for high-throughput profiling of histone modifications in mammalian cellsor identification of expressed genes upon infection by Spongospora subterranea. Using RNA-sequencing (RNA-seq), 2058 differentially expressed genes (DEGs) were identified from two potato cultivars (tolerant and susceptible) in response to Sss infection. Analysis of the expression patterns of ten selected defense-response genes was carried out at two different stages of tuber growth using RT-qPCR to validate the RNA-seq data. Several defense related genes showed contrasting expression patterns between the tolerant and susceptible cultivars, including marker genes involved in the salicylic acid hormonal response pathway (StMRNA, StUDP and StWRKY6). Induction of six defense related genes (StWRKY6, StTOSB, StSN2, StLOX, StUDP and StSN1) persisted until harvest of the tubers, while three other genes (StNBS, StMRNA and StPRF) were highly up-regulated during the initial stages of disease development. The results of this study suggested that the tolerant potato cultivar employs quantitative resistance and salicylic acid pathway hormonal responses against tuber infection by Sss. The identified genes have the potential to be used in the development of molecular markers for selection of powdery scab resistant potato lines in marker assisted breeding programs.

overall_design: Examination of 2 different potato cultivars, inoculated and un-inoculated with Spongospoora subterranea.

first: Jacquie

last: van der Waals

first: Norman

last: Muzhinji


title: Genome wide binding of BCL6 and LSD1 In GC derived lymphoma B cells

first: Katerina

last: Hatzi

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

summary: Using ChIP-seq we identified the genome wide targets of BCL6 and LSD1 in lymhpoma cells (OCI-Ly1) with control siRNA or siRNA targeted to BCL6

overall_design: ChIP-seq  was performed in lymphoma cells under baseline conditions, treated with control siRNAs or treated with BCL6 targeted siRNAs


title: c-Maf-dependent Treg cell control of intestinal TH17 cells and IgA establishes host–microbiota homeostasis

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

summary: Foxp3+ regulatory T (Treg) cells are essential for immunological tolerance and homeostasis. In peripheral tissues, Treg cells acquire enhanced suppressive functions and co-opt distinct transcriptional modules, allowing context and tissue-dependent immune regulation. Here we show that the transcription factor c-Maf was highly expressed by effector Treg cells and controlled their IL-10 production. In the intestine, c-Maf was required for the differentiation of RORgt+ microbiota-dependent Treg cells, and restricted their production of inflammatory cytokines. Consequently, Treg cell-specific loss of c-Maf resulted in perturbed intestinal homeostasis, microbial dysbiosis and a selective failure to control Th17 responses during homeostasis and upon chemically induced epithelial damage. Molecular profiling revealed that c-Maf regulated expression of key genes of the transcriptional signature of intestinal Treg cells, including Rorc and Il10. Thus, our study identifies a key role of c-Maf in preserving the identity and function of intestinal Treg cells, essential for the control of intestinal immune homeostasis.

overall_design: Transcriptional profiling of control (Foxp3Cre-YFP, "WT") and Maf-KO (Maffl/fl x Foxp3Cre-YFP, "KO") Treg cells sorted from Gut and Spleen

first: Yang

last: Liao

first: Yifang

last: Hu

first: Christian

last: Neumann

first: Mir-Farzin

last: Mashreghi

first: Alexander

last: Scheffold

first: Axel

last: Kallies


title: Differential Wnt-mediated Programming and Arrhythmogenesis in Right versus Left Ventricles [wntlof]

first: Bo

last: Zhang

overall_design:
RNA-seq data of Wnt LOF RV and LV
n=3 for each group (control lv, control rv, wntlof lv, wntlof rv)

first: Aditi

last: Khandekar

first: Rich

last: Li

first: Stacey

last: Rentschler


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses[SMRT sequencing Nipponbare]

status: Public on Dec 10 2018

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

institute: Chinese Academy of Agricultrual Sciences

summary: N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.

overall_design: SMRT sequencing in 3-week-old Nipponbare

first: Qian

first: Zhe

last: Liang

first: Xuean

last: Cui

first: Changmian

last: Ji

first: Pingxian

first: Jingrong

last: Liu

first: Adeel

last: Riaz

first: Pu

last: Yao

first: Min

first: Yunpeng

last: Wang

first: Tiegang

last: Lu

first: Hao

last: Yu

first: Hongkun

last: Zheng


title: Enhancer remodeling promotes resistance to epigenetic-targeted therapy and engenders tumor cell vulnerabilities

first: Gabriela

last: Alexe

summary: Drug resistance is a major clinical challenge in achieving durable responses to targeted cancer therapeutics.  Resistance mechanisms to new classes of epigenetic-targeted drugs entering the clinic remain largely unexplored.  We used BET inhibition in MYCN-amplified neuroblastoma as a prototype to model innate and acquired resistance to chromatin remodeling inhibitors in cancer. Genome-scale, pooled lentiviral ORF and CRISPR knockout rescue screens nominated the PI3K pathway as a key signaling node that mediates resistance to BET inhibition.

overall_design: ChIP-seq for H3K27Ac and input on JQ1 resistant and naive SK-N-BE(2)-C neuroblastoma cells  engineered to overexpress either GFP control or PI3K,  treated with vehicle or JQ1 for 24 hours, 1 biological replicate per condition;   ChIP-seq for H3K27Ac and input on JQ1 resistant and naive Kelly  neuroblastoma cells   treated with vehicle or JQ1 for 24 hours, 1 biological replicate per condition; ChIP-seq for BRD4 and input on JQ1 resistant and naive SK-N-BE(2)-C neuroblastoma cells  treated with vehicle or JQ1 for 24 hours, 1 biological replicate per condition.

first: Kimberly

last: Stegmaier


title: Transcriptional changes associated with resistance to JQ1 treatment in MYCN-amplified neuroblastoma

summary: Drug resistance is a major clinical challenge in achieving durable responses to targeted cancer therapeutics.  Resistance mechanisms to new classes of epigenetic-targeted drugs entering the clinic remain largely unexplored.  We used BET inhibition in MYCN-amplified neuroblastoma as a prototype to model innate and acquired resistance to chromatin remodeling inhibitors in cancer. Genome-scale, pooled lentiviral ORF and CRISPR knockout rescue screens nominated the PI3K pathway as a key signaling node that mediates resistance to BET inhibition.  RNA-seq profiling of BET inhibitor resistant cells revealed that global enhancer and super-enhancer remodeling leads to differential cell state commitment and the upregulation of receptor tyrosine kinases upstream of PI3K signaling, engendering a vulnerability to receptor tyrosine kinase (RTK) and PI3K inhibition.  Large-scale, unbiased, chemical combinatorial screening with BET inhibitors identified PI3K inhibitors among the most synergistic upfront combinations with JQ1, a finding validated in vivo.  These studies provide a comprehensive roadmap to elucidate resistance to epigenetic-targeted cancer therapeutics and inform efficacious combination therapies for second-generation clinical trials.

overall_design:
RNA-sequencing of JQ1 resistant and naive SK-N-BE(2)-C neuroblastoma cells treated with vehicle or JQ1 for 24 hours, 3 biological replicates per condition, and RNA-sequencing of SK-N-BE(2)-C cells engineered to overexpress either GFP control or PI3K, 3 biological replicates per condition.

RNA-sequencing of JQ1 resistant and naive Kelly neuroblastoma cells treated with vehicle or JQ1 for 24 hours, 3 biological replicates per condition.


title: Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damage

status: Public on Dec 08 2018

city: Oxford

first: Monika

last: Gullerova

address: South Parks Road

department: Sir William Dunn School of Pathology

institute: University of Oxford

summary: The endonuclease Dicer is a key component of the human RNA interference (RNAi) pathway and known for its role in cytoplasmic micro RNA (miRNA) production. Recent findings suggest that non-canonical Dicer generates small non-coding RNA (ncRNA) to mediate the DNA damage response (DDR). Here we show that human Dicer is phosphorylated in the platform-PAZ-connector helix cassette (S1016) upon induction of DNA damage. Phosphorylated Dicer (p-Dicer) accumulates in the nucleus and is recruited to DNA double-strand breaks (DSBs). We further demonstrate that turnover of damage-induced nuclear dsRNA requires additional phosphorylation of carboxy-terminal Dicer residues (S1728 and S1852). DNA damage-induced nuclear Dicer accumulation is conserved in mammals. Dicer depletion causes spontaneous DNA damage and delays DNA repair. Taken together, we place Dicer in context of the DDR by demonstrating DNA damage-inducible phospho-switch that causes localised processing of nuclear dsRNA by p-Dicer to promote DNA repair.

overall_design: We have analysed ChIP samples from damaged and non-damaged cells, using an anti-Dicer antibody. Non-damaged sample serves as physiological control.

first: Kaspar

last: Burger

first: Margarita

last: Schlackow

first: Svenja

middle: S

last: Hester

first: Shabaz

last: Mohammed


title: Transcriptional Changes in Germinal Center (GC) B cells from LSD1 conditional knockout mice

first: Katerina

last: Hatzi

summary: Using RNA-seq we identified the gene expression changes in GC B cells from LSD1 wild-type or LSD1-deficient mice immunized with T cell dependent antigens (Sheep Red Blood cells)

overall_design: RNA seq of sorted GC B cell populations from 3 littermate mice per genotype (3 wild-type, 3 knockout)


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [RNA-Seq Nipponbare]

first: Xiaofeng

last: Gu

overall_design: RNA-seq in Oryza sativa Nipponbare wild-type, two replicates.

first: Qian

last: Zhang

first: Zhe

last: Liang

first: Xuean

last: Cui

first: Changmian

first: Pingxian


title: Direct reprogramming of fibroblasts into antigen-presenting dendritic cells

status: Public on Dec 07 2018

city: Cantanhede

first: Andreia

last: Gomes

address: Parque Tecnológico de Cantanhede, Núcleo 4, lote 8

department: CNC

country: Portugal

institute: Universidade de Coimbra

summary: Ectopic expression of transcription factors has been used to reprogram differentiated somatic cells toward pluripotency or to directly reprogram them to other somatic cell lineages. This concept has been explored in the context of regenerative medicine. Here, we set out to generate dendritic cells (DCs) capable of presenting antigens from mouse and human fibroblasts. By screening combinations of 18 transcription factors that are expressed in DCs, we have identified PU.1, IRF8, and BATF3 transcription factors as being sufficient to reprogram both mouse and human fibroblasts to induced DCs (iDCs). iDCs acquire a conventional DC type 1–like transcriptional program, with features of interferon-induced maturation. iDCs secrete inflammatory cytokines and have the ability to engulf, process, and present antigens to T cells. Furthermore, we demonstrate that murine iDCs generated here were able to cross-present antigens to CD8+ T cells. Our reprogramming system should facilitate better understanding of DC specification programs and serve as a platform for the development of patient-specific DCs for immunotherapy.

overall_design: Single cell mRNAseq profiling on single cells generated after transduction of mouse embryonic fibroblasts (MEFs) with Pu.1, Irf8, Baft3 at day 3, day 7 and day 9. mRNAseq profiling of MEFs and splenic dendritic cells CD11c+ MHC-II+ CD8a+ single cells were used as controls. Each sample represents a single cell. Bulk mRNAseq profiling on populations generated after transduction of mouse embryonic fibroblasts (MEFs) with lentivirus encoding Pu.1, Irf8, Baft3 at day 5, day 7, day 8 and day 9. mRNAseq profiling of MEFs and CD11c+ MHC-II+ CD8a+ cDC1s, CD11c+ MHC-II+ CD11b+ cDC2s and MHC-IIIntSiglecH+Bst2+ B220+ pDCs isolated from spleen were used as controls.

middle: M

first: Ilia

last: Kurochkin

first: Fábio

last: Fiúza Rosa

first: Cristiana

last: Pires

first: Carlos-Filipe

last: Pereira

first: Alexandra

last: Ferreira


title: Profiling the transcriptome of layer 5 intratelencephalic-projection neurons (IT-PNs) in the mature mouse motor cortex

status: Public on Dec 06 2018

city: Dunedin

first: Alison

middle: Jane

last: Clare

state: Otago

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

summary: Low input RNA-seq analysis of fluorescently activated cell sorted IT-PNs from layer 5 of the mature mouse motor cortex. Comparison of two distinct IT-PN subtypes previously described by Tantirigama et al. (2014) identifies unique gene expression.

overall_design: A Fezf2-Gfp reporter mouse model was injected at postnatal day 23 - 25 with the retrograde tracer, cholera toxin subunit b conjugated to Alexa 647, in M1 of the left hemisphere (n = 5). Five to seven days after injection, the layer 5 of the right hemisphere M1 was dissected and dissociated for FACS-purification of Fezf2+ and Fezf2- IT-PNs. A novel approach to low-input RNA-seq was used to generate cDNA libraries before sequencing.

first: Robert

middle: C

last: Day

first: Ruth

last: Empson

first: Steph

last: Hughes


title: Walking along chromosomes with super-resolution imaging, contact maps, and integrative modelling

city: houston

first: Cynthia

middle: Perez

last: Estrada

state: TEXAS

address: 1 Baylor Plaza  Room 906B

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary:
Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments identified with chromosome conformation capture, with our imaging we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of an entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method – integrative modeling of genomic regions (IMGR) – to increase the genomic resolution of our traces to 10 kb.

Grant: 1DP2OD008540: Exploring how the genome folds through proximity ligation and sequencing
Grant: 4DP2OD008540: Exploring how the genome folds through proximity ligation and sequencing
Grant: U01HL130010: Beyond Pairwise DNA Contacts: Exploring Higher-order Genome Structure Using Proximity Ligation NIH/4D Nucleome Consortium
Grant: UM1HG009375: Genome-wide mapping of loops using in situ Hi-C

overall_design: Hi-C maps of 10 library replicates and a mega map

last: Pérez Estrada

first: Erez

last: Lieberman Aiden

first: Sheikh

last: Russel


title: The role of SIRT1 deacetylase in neuromuscular aging and amyotrophic lateral sclerosis

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

summary: SIRT1 deacetylase functions in a variety of cells and tissues to mitigate age- and disease-induced damages. However, it remains unknown if SIRT1 also acts to prevent pathological changes that accrue in motor units, and specifically alpha-motor neurons, with advancing age and during the progression of amyotrophic lateral sclerosis (ALS).  Here, we show that SIRT1 expression decreases in the spinal cord of wild type mice with advancing age.  Using mouse models that overexpress or inactivate SIRT1 in motor neurons, we discovered that SIRT1 prevents age-related degeneration of motor neurons’ presynaptic sites at neuromuscular junctions (NMJs). We also found that increasing SIRT1 in motor neurons delays degeneration of presynaptic sites at NMJs and extends the lifespan of SOD1G93A mice.  Thus, SIRT1 has a similar effect on aging and ALS-affected motor neurons, two conditions in which a remarkable number of transcripts are similarly altered in the spinal cord.  These include genes involved in inflammatory and immune responses and genes with known function at synapses.  These findings show that SIRT1 functions to mitigate pathological changes induced by aging and ALS, two conditions with a surprising degree of overlap in the spinal cord.

overall_design: Eight replicates spinal cords from mice aged 18-24 months, eight replicates of spinal cords from mice aged 3-4 months, 3 replicates of spinal cords from ALS symptomatic mice aged 5-6 months and 3 replicates of spinal cords from wt controls aged 5-6 months.

first: A

middle: Z

last: Herskovits

first: T

last: Hunter

first: N

last: Maxwell

first: K

middle: A

first: G

last: Valdez

first: L

last: Guarente


title: Single-cell transcriptome profiling during the in vitro differentiation of mouse ESCs (mESCs) into epiblast-like cells (EpiLCs).

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

summary: We performed single-cell RNA sequencing (RNA-seq) during the in vitro transition of mouse ESCs (mESCs) from a naïve pluripotent state into epiblast-like cells (EpiLCs), a primed pluripotent state. We derived pseudotime expression trajectories  to investigate transcript dynamics of key metabolic regulators, with the aim to identify metabolic pathways that potentially impact on early embryonic cell state transitions.

overall_design: Single-cell RNA-seq during the in vitro differentiation of mouse embryonic stem cells (ESCs) in 2i culture conditions (time point t=0h) into epiblast-like cells (EpiLCs) at time points t=24h and t=48h.

first: Julia

last: Tischler

middle: R

first: M

last: Surani


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [BiSulfite-seq]

first: Xiaofeng

last: Gu

overall_design: BS seqencing of Nip and 93-11

first: Qian

last: Zhang

first: Zhe

last: Liang

first: Xuean

last: Cui

first: Changmian

last: Ji

first: Yun

last: Li

first: Pingxian

first: Jingrong

last: Liu

first: Adeel

last: Riaz

first: Pu

last: Yao

first: Min

first: Yunpeng

last: Wang

first: Donglie

last: Yang

first: Tiegang

last: Lu

first: Hongkun

last: Zheng


title: Induced human forebrain neurons overexpressing MAPT demonstrate chromatin structure alterations

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary: We assessed whether forebrain neurons from human induced pluripotent stem cells (iNs) could recapitulate the tau-related epigenomic changes that we found in human brain H3K9ac data (Synapse ID: syn4896408). We used an existing iN model system whereby we can virally transduce NGN2-induced neurons with lentivirus to modulate expression of specific genes. Here, we overexpressed the 4R isoform of human MAPT, which induces AD-related features such as the intracellular accumulation of phosphorylated tau. To characterize the epigenomic changes in our model system, we used the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to map genome accessibility. Finally, we utilized the iN model system to assess whether a drug compound (17-DMAG) might attenuate the tau effect on chromatin organization.

overall_design:
We generated n=9 MAPT OE and n=9 control iNs in 3 batches of independent differentiations. The second and third batch of experiments contained additional iNs treated with 1, 3, or 10 nM 17-DMAG for 24 hours prior to collection. Further, the third batch contained additional control iNs cultured in concentration-matched DMSO solution for 24 hours prior to collection.

The main purpose of the study was to detect domains (or peaks) that were different between the n=9 MAPT OE iNs and n=9 control iNs. Therefore, a set of common peaks was defined in the n=2x9 iNs samples, then the numbers of reads in these peaks were counted, and finally, peaks were tested for differences between MAPT OE iNs and control iNs. The processed data provided in this series consist of a bed file with peak locations and a matrix file with read counts for each peak and sample. While the peaks were defined on the initial n=2x9 iNs, the matrix file also contains read counts for the 17-DMAG treated iNs.

first: Cristin

last: McCabe

first: Elizabeta

last: Gjoneska

first: Sarah

last: Sullivan

first: Belinda

middle: J

last: Kaskow

first: Anna

last: Tang

first: Robert

middle: V

last: Smith

first: Jishu

last: Xu

first: Andreas

last: Pfenning

first: Bradley

last: Bernstein

first: Alexander

last: Meissner

first: Julie

last: Schneider

first: Sara

last: Mostafavi

first: Li-Huei

last: Tsai

first: Tracy

middle: L

last: Young-Pearse

first: David

last: Bennett

first: Philip

last: De Jager


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [RNA-seq]

first: Xiaofeng

last: Gu

overall_design: RNA-seq in Oryza sativa  (Nip) wild-type and ddm1a-1/ddm1b-1, three replicates for each sample

first: Qian

last: Zhang

first: Zhe

last: Liang

first: Xuean

last: Cui

first: Changmian

last: Ji

first: Yun

last: Li

first: Pingxian

first: Jingrong

last: Liu

first: Adeel

last: Riaz

first: Pu

last: Yao

first: Min

first: Yunpeng

last: Wang

first: Donglie

last: Yang

first: Tiegang

last: Lu

first: Hongkun

last: Zheng


title: Histone demethylase LSD1 is required for germinal center formation and BCL6 driven lymphomagenesis

first: Katerina

last: Hatzi

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

overall_design: Refer to individual Series


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [SMRT sequencing 93-11]

overall_design: SMRT sequencing in 3-week-old 93-11

first: Hao

last: Yu


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [MeDIP-seq Nipponbare]

first: Xiaofeng

overall_design: 6mA IP-seq in 3-week-old Nipponbare wild-type with two replicates.


title: Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA binding factor Rbm15/Spenito to other components of the m6A machinery

status: Public on Dec 04 2018

city: Lausanne

first: Jean-Yves

last: Roignant

address: genopode building

country: Switzerland

institute: University of Lausanne

summary: m6A is catalyzed by the activity of Mettl3, which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 as a novel interactor of m6A methyltransferase complex components in mouse. Like other components of this complex, Zc3h13 controls m6A levels.

overall_design: We performed m6A-RIP-seq on oligo-dT selected mRNA from wild type, Mettl3-/-, and Zc3h13-/- mESCs. Similar to Mettl3 KO cells, ablation of Zc3h13 resulted in a drastic reduction of m6A enrichment, particularly at the 3’ end of target mRNAs

first: Philip

last: Knuckles

first: Tina

last: Lence

first: Irmgard

middle: U

last: Haussmann

first: Dominik

last: Jacob

first: Nastasja

last: Kreim

first: Marco

last: Biggiogera

first: Marc

last: Helm

last: Bühler

first: Sarah

middle: H

last: Carl

first: Irene

last: Masiello

last: Hares

first: Rodrigo

last: Villaseñor

first: Daniel

last: Hess

first: Miguel

last: Andrade-Navarro

first: Matthias

last: Soller


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals GcvB sRNA targetome.

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

country: Canada

institute: University of Sherbrooke

summary: Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we perform MAPS with GcvB, a sRNA involved in amino acid metabolism.

overall_design: Identification of RNAs co-purified with MS2-GcvB in a rne131 ΔgcvB strain. GcvB (without MS2) was used as control.

first: David

last: Lalaouna


title: RNASEQ Analysis of sh-TRC and sh-MIR100HG in the triplex negative breast cancer

city: Kunming

first: Honglei

last: Zhang

address: 1076 Yuhua Road, Chenggong District, Kunming, Yunnan Province

institute: Yunnan university of Chinese Medicine

summary: Purpose:The goals of this study are using next generation sequencing to identify differentially expressed genes by analyzing knockdown of MIR100HG in triple-negative breast cancer

overall_design: Knockdown MIR100HG with two shRNAs in triple negative breast cancer MDA-MB231 cells

first: Shaowei

last: Wang

first: Baowei

last: Jiao


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

first: Xiaofeng

last: Gu


title: Human iPSC derived glomeruli facilitate accurate modelling of podocytopathy

city: Parkville

first: Belinda

last: Phipson

address: 1G Royal Parade

department: Bioinformatics

institute: WEHI

summary: Podocytes are the highly specialised cells within the glomeruli of the kidney that maintain the filtration barrier by forming interdigitating foot processes and slit-diaphragms. Disruption to these features result in proteinuria. Studies into podocyte biology and disease has been hampered by a paucity of in vitro models of this non-proliferative cell type. Here we characterise sieved glomeruli from kidney organoids derived from human pluripotent stem cells. Compared to conditionally immortalised podocytes, organoid-derived glomeruli show superior podocyte-specific gene and protein expression, morphology and functional properties. Using CRISPR-derived MAFB reporter iPSC lines, homozygous MAFB mutant organoids recapitulated the anticipated disease related transcriptional changes. Culture of kidney organoids on chicken chorioallantoic membrane resulted in glomerular vascularisation, glomerular filtration barrier assembly, formation of slit diaphragms and fenestrated endothelial cells. This definitively demonstrates that human iPSC kidney organoid-derived glomeruli can serve as an accurate model of human podocytopathies and glomerular disease in vitro.

overall_design: Gene expression profiling of three immortalised podocyte line samples at 33 degrees celsius, three immortalised podocyte line samples at 37 degrees celsius and three day 25 kidney organoid derived glomeruli


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [MeDIP-seq 93-11]

overall_design: 6mA IP-seq in 3-week-old 93-11 wild-type with two replicates.

first: Qian

first: Zhe

last: Liang

first: Xuean

last: Cui

first: Changmian

last: Ji

first: Pingxian

first: Jingrong

last: Liu

first: Adeel

last: Riaz

first: Pu

last: Yao

first: Min

first: Yunpeng

first: Tiegang

last: Lu

first: Hao

last: Yu

first: Hongkun

last: Zheng


title: N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses [RNA-Seq 93-11]

overall_design: RNA-seq in Oryza sativa 93-11 wild-type, two replicates.


title: Transcriptional changes in lymphoma cells induced by LSD1 depletion

first: Katerina

last: Hatzi

summary: Using RNA-seq we identified the gene expression changes in lymhpoma cells (OCI-Ly1) expressing LSD1 targeted shRNA and control shRNA

overall_design: RNA-seq was performed in biological  triplicates from cells selected with puromycin to express non-targeted pLKO1 shRNA against LSD1 (TRCN0000046068 or TCRN0000046072) and cotnrol non-targeted shRNA


title: Salmonella persisters undermine host immune defences during antibiotic treatment

city: London

first: Peter

last: Hill

address: Kensington

institute: Imperial College London

summary: Many bacterial infections are hard to treat and tend to relapse, possibly due to the presence of antibiotic-tolerant persisters that are considered dormant cells when bacteria are grown in laboratory medium. Non-growing persisters also form following uptake of Salmonella by macrophages but their nature is little understood. Here we show that Salmonella persisters arising during macrophage infection maintain an active state. Persisters reprogram macrophages by means of effectors secreted by the SPI-2 Type 3 Secretion System (T3SS), thereby dampening pro-inflammatory innate immune responses and inducing anti-inflammatory macrophage polarisation. Reprogramming allows non-growing Salmonella to survive for extended periods in their host. Persisters undermining the host immune defences might confer an advantage to the pathogen during relapse once the antibiotic pressure is relieved.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium

overall_design: Transcriptome profiling of macrophages/Salmonella in distinct subpopulations by dual RNA-Seq

first: Daphne

last: Stapels


title: H3K9ac data from mouse models suggest structural changes in the murine brain epigenome that involve the nuclear lamina

first: Hans-Ulrich

last: Klein

summary: To explore whether tau-related epigenomic changes that we found human brain H3K9ac data  (Synapse ID: syn4896408) are recapitulated in mouse models known to accumulate tau, we generated hippocampal H3K9ac ChIP-seq profiles from two different mouse models each at an early and a late stage of neurodegeneration. Specifically, we studied 6 and 11 months old mutant tau mice (MAPT P301S), which start to accumulate phosphorylated tau in neurons by 6 months. Wild-type mice of the same age were used as controls. The second mouse model was the CK-p25 model, which is characterized by increased amyloid-β levels early after p25 induction followed by increased tau phosphorylation and neuronal loss at later stages. Three months old CK-p25 mice were studied 2 weeks and 6 weeks after p25 induction and compared with CK littermate controls.

overall_design: H3K9ac profiles were generated for mutant tau mice at the ages of 6 and 11 months and compared with wild type controls. H3K9ac profiles of the CK-p25 mouse model were generated 2 and 6 weeks after p25 induction and compared with controls. The main purpose of the study was to detect differential H3K9 acetylation between AD mice and control mice. Therefore, a common set of peaks was defined, then the number of reads in these peaks was counted, finally peaks were tested for different read counts between AD mice and controls. The processed data provided under this series contains a bed file with peak locations and a matrix file with read counts for each sample and peak. Samples of input DNA (without ChIP) were sequenced and used as negative controls during peak calling, but are not represented in the matrix file.

first: Cristin

last: McCabe

first: Elizabeta

last: Gjoneska

first: Sarah

last: Sullivan

first: Belinda

last: Kaskow

first: Anna

last: Tang

first: Robert

last: Smith

first: Jishu

last: Xu

first: Andreas

last: Pfenning

first: Bradley

last: Bernstein

first: Alexander

last: Meissner

first: Julie

last: Schneider

first: Sara

last: Mostafavi

first: Li-Huei

last: Tsai

first: Tracy

last: Young-Pearse

first: David

last: Bennett

first: Philip

last: De Jager


title: Functional genomics for the oleaginous yeast Yarrowia lipolytica

city: IRVINE

first: James

last: Yu

state: ca

address: Med Sci D262

department: Biological Chemistry

institute: University of California Irvine

summary: Oleaginous yeasts are valuable systems for biosustainable production of hydrocarbon-based chemicals. Yarrowia lipolytica is one of the best characterized of these yeast with respect to genome annotation and flux analysis of metabolic processes. Nonetheless, progress is hampered by a dearth of genomewide tools enabling functional genomics. The Hermes DNA transposon was expressed to achieve saturation mutagenesis of the Y. lipolytica genome. Over 535 thousand independent insertions were identified by next-generation sequencing. Poisson analysis of insertion density classified ~22% of genes as essential. As expected, most essential genes not only have homologues in Saccharomyces cerevisiae and Schizosaccharomyces pombe, but the majority of those are also essential. As an obligate aerobe, Y. lipolytica has significantly more respiration - related genes that are classified as essential than do S. cerevisiae and S. pombe. The findings provide insights into biosynthetic pathways, compartmentalization of enzymes, and distinct functions of paralogs. Contributions of nonessential genes to fitness were determined in log growth cultures with glucose and glycerol carbon sources. Fluorescence-activated cell sorting identified mutants in which lipid accumulation is increased. Biological contributions of genes to growth were used to evaluate two recent genome-scale models Y. lipolytica metabolism. This study is the first functional genomic analysis of an oleaginous yeast and provides an important resource for modeling and bioengineering of Y. lipolytica.

overall_design: Transposon mediated mutagenesis is utilized to determine the essentiality of every gene in the Yarrowia lipolytica CLIB89 genome.

first: Kurt

last: Patterson

first: Suzanne

last: Sandmeyer


title: Whole blood transcriptome analysis of Septic shock patients according to early therapy response

status: Public on Dec 03 2018

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

summary: Septic shock is the most severe complication of sepsis, associated with high mortality. The patient’s response to supportive therapy is very heterogeneous and the underlying mechanisms are still elusive. In order to identify which are the actors (genes and pathways) that play a role in establishing the response, we investigate the whole blood transcriptome in septic shock patients with positive and negative responses to early supportive hemodynamic therapy, assessed by changes in SOFA scores within the first 48 hours from ICU admission. We pinpointed genes and pathways that are differently modulated and enriched respectively within 48hrs between responders and non-responders.

overall_design: We analyzed 31 patients (17 Responders and 14 Not Responders to early therapy). For each patient, 2 samples were collected. In particular the first sample (T1) collected within 16 hours from ICU admission whereas the second (T2) collected within 48 hours from ICU admission. Experimental groups (Responders and Not Responders) are defined accordingly with SOFA scores improvements within 48 hours.

first: Daniele

last: Braga

first: Cristina

last: Barlassina


title: DNA accessibility in CD8+  tumour-infiltrating T cells treated with Phenelzine.

status: Public on Dec 05 2018

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

institute: University of Canberra

summary: Phenelzine treatments were conducted in tumour-bearing Balb/c mice and then 4T1 tumours were acquired. CD8+ tumour-infiltrating T cells were positively selected by using mouse CD8a (Ly-2) microbeads and isolated by autoMACS Separator with recommended programs. Then isolated CD8 T cells were stimulated by PMA and Ionomycin. Global ATAC-seq analysis was performed to identify the dynamic changes in chromatin accessibility of tumour-filtrating CD8 T cells after phenelzine treatment.

overall_design: 4 individual samples, no replicates.

first: Wen

last: Tu

first: Abel

last: Tan

first: Sudha

last: Rao


title: RNA-seq expression profiling of Grhl2-deficient and control murine lung epithelium at embryonic day E16.5

first: Matthew

last: Ritchie

state: Victoria

department: Epigenetics and Development Division

institute: The Walter and Eliza Hall Institute of Medical Research

summary: Epithelial (CD31-CD45-EpCAM+) cells were isolated by FACS from Grhl2-deficient (Shh-Cre;Grhl2f/-) and control (Shh-Cre;Grhl2f/+) embryonic lungs at day E16.5 (3 biological replicates/genotype). Total RNA extracted from the samples was subjected to next-generation sequencing (NGS) library preparation using standard Illumina protocols. Completed libraries from individual samples were sequenced on a HiSeq2500 at the Australian Genome Research Facility.

overall_design: RNA-seq was performed on Grhl2-deficient and control epithelium isolated from the lungs of E16.5 embryos (n=3 replicates/genotype/cell population).

first: Ariena

last: Kersbergen

first: Sarah

last: Best

first: Kate

middle: D

last: Sutherland


title: Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs (Bisulfite-Seq)

city: Bethesda

first: Andrew

last: Oler

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

summary: To better understand the paternally inherited epigenome and transcriptome, we profiled multiple histone modifications, histone H3.3 variant, cytosine DNA methylation at base-pair resolution, and small RNA transcriptomes. We report new and surprising features of enhancers, pluripotency factor targets, spermiogenesis genes, piRNA clusters, CpG islands, partially methylated domains, imprinted loci, repetitive elements and sex chromosomes. First, we find that enhancers for embryonic transcription factors bear H3K27me3, but low H3K14ac and DNA methylation -- consistent with poising for future activation -- whereas enhancers near genes active in gametogenesis have high H3K27ac/H3K14ac, consistent with past activation. Second, binding site regions (in ES cells) for the pluripotency factors SOX2 and NANOG are DNA methylated in sperm, suggesting a need for zygotic demethylation/reprogramming. Unexpectedly, genes for spermiogenesis (but not spermatogenesis), and almost half of piRNA cluster promoters, bear both H3K4me3 and DNA methylation, a co-incidence not previously observed in mammals. Furthermore, we find major assymetries in H3.3 and H3K9me3 density between the X and Y chromosomes after MSCI. Lastly, deep sequencing reveals >10-fold increase in the known repertoire of retained/inherited miRNAs and piRNAs than previous estimates. Thus, the paternal epigenome contributes a mosaic of epigenetic regions that reflect past gametogenesis or poising for subsequent embryonic developmental regulation -- and a complex repertoire of small RNAs.

overall_design: Sperm from two fertile donors were subjected independently to genome-wide bisulfite sequencing.

first: Saher

last: Hammoud

last: Nix

first: Douglas

last: Carrell

first: Bradley

last: Cairns


title: Human Sperm Epigenomes and Transcriptomes Reveal Novel Features of Enhancers, Sex Chromosomes, piRNAs, Gametogenesis, and Inherited Small RNAs (ChIP-Seq)

overall_design: Sperm from four fertile donors was pooled. One or two replicate ChIP libraries (H3K9me3, H3.3, H3K36me3, H3K4me1, H3K14ac, H3K27ac) were sequenced on the Illumina GAII.

first: David


title: Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming

city: New York

first: Betty

last: Chang

state: NY

address: 1425 Madison Ave

institute: Mount Sinai School of Medicine

summary: During development, hematopoietic stem/progenitor cells (HSPCs) arise from specialized endothelial cells by a process termed endothelial-to-hematopoietic transition (EHT). The genetic program driving human HSPC emergence remains largely unknown. We previously reported that the generation of hemogenic precursor cells from mouse fibroblasts recapitulates developmental hematopoiesis. Here, we demonstrate that human fibroblasts can be reprogrammed into hemogenic cells by the same transcription factors. Induced cells display dynamic EHT transcriptional programs, generate hematopoietic progeny, possess HSPC cell surface phenotype and repopulate immunodeficient mice for three months. Mechanistically, GATA2 and GFI1B interact and co-occupy a cohort of targets. This cooperative binding is reflected by engagement of open enhancers and promoters, initiating silencing of fibroblast genes and activating the hemogenic program. However, GATA2 displays dominant and independent targeting activity during the early phases of reprogramming. These findings shed light on the processes controlling human HSC specification and support generation of reprogrammed HSCs for clinical applications.

overall_design: mRNAseq profiling on adult human dermal fibroblasts (HDFa) at the population and single cell level and on neonatal foreskin fibroblasts (BJ) generated after transdution with GATA2, GFI1b, cFOS at day 2, day 15 and day 25. mRNAseq profiling of HDFa, BJ and Umbilical Cord Blood (UCB) Lin-Cd34+ single cells were used as controls. Examination of global occupancy for GATA2, GFI1b and FOS together or individually at day 2 of reprogramming.

first: Andreia

last: Gomes

first: Carlos-Filipe

last: Pereira

first: Kateri

last: Moore

first: Ihor

last: Lemischka


title: Chromatin immunoprecipitation and expression analysis in WT and hrr25 mutant cells

status: Public on Dec 02 2018

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by genome tiling array

overall_design: Refer to individual Series


title: The transcriptome of Tetraselmis suecica reveals new insights on green algae response to nitrogen starvation

status: Public on Dec 01 2018

city: Verona

first: Massimo

last: Delledonne

address: Strada le Grazie 15

institute: Universita' degli Studi di Verona

summary: Nitrogen starvation is an efficient environmental pressure used to increase lipid accumulation and oil droplet formation in microalgal cells. Various studies focused on metabolic changes occurring in microalgae in nitrogen starvation conditions, but the mechanisms at the basis of these changes are not completely understood. Between microalgae, green algae, with more than 7000 species growing in a variety of habitats, have been frequently studied for energy purposes, but also as source of bioactive extracts/compounds. In this study, de novo transcriptome of the green algae Tetraselmis suecica has been performed in order to (1) deeply study its response to nitrogen starvation, (2) to look for enzymes with antioxidant capacity and for polyketide synthases (PKSs), (3) if present, to evaluate if nutrient starvation can influence their expression levels.

overall_design: Tetraselmis suecica was cultured in two conditions, i.e. Nitrogen-starved or -repleted (control) conditions. Cells were harvested at the end of the stationary phase and used for RNA extraction. Triplicate samples of both conditions were sequenced and differential expression analysis was performed. In addition, enzymes with biotechnological interest were identified.

first: Lauritano

last: Chiara

first: Adrianna

last: Ianora


title: Impact of plastic leachates on marine Prochlorococcus strains

city: Sydney

first: Sasha

last: Tetu

state: NSW

address: Macquarie University

department: Molecular Sciences

institute: Macquarie University

summary: Examining the impact of short term exposure to HDPE and PVC plastic leachates on gene transcription in Prochlorococcus cultures in vitro

sample_organism:
Prochlorococcus marinus str. NATL2A
Prochlorococcus marinus str. MIT 9312

overall_design: Prochlorococcus MIT9312 and NATL2A strains grown in vitro were exposed to diluted HDPE and PVC leachate and harvested after short term exposure for RNA collection. Samples were collected from each of 3 biological replicate cultures of Proclorococcus control (no leachate) and leachate exposed cultures

middle: G

first: Liam

last: Elbourne


title: Genome-Wide Identification of ABA Responsive microRNAs in the Root of Populus euphratica

city: Beijing

first: Conglong

last: Lian

address: 35 Tsinghua Eastern Road

institute: Beijing Forestry University

summary: More then 10 million raw reads were acquired. In total, 238 unique mature sequences which contain 142 conserved miRNA and 96 novel miRNAs were identified.

overall_design: Nine sRNA libraries derived from three groups (control, ABA for 1 day and ABA for 4 days) with three librariesas biological replicate.

first: Xinli

last: Xia


title: Polycomb- and Methylation-Independent Roles of EZH2 as a Transcription Activator

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

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


title: Genome-Wide Identification of ABA Responsive microRNAs in the root and stem of Populus euphratica