title: CNOT6L Couples the Selective Degradation of Maternal Transcriptsto Meiotic Cell Cycle Progression in Mouse Oocyte

status: Public on Nov 23 2018

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

overall_design: Refer to individual Series


title: CNOT6L Couples the Selective Degradation of Maternal Transcriptsto Meiotic Cell Cycle Progression in Mouse Oocyte [total RNA-seq]

country: China

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goals of this study are to study the function of Cnot6l during oocyte maturation and the differences between loss of Cnot6l and Btg4 during oocyte maturation.
Methods:Comparing the degration of transcripts at different stage in  WT, Btg4-/- and Cnot6l-/- oocytes by RNA sequencing.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the mouse genome (build mm9) and identified  23236 transcripts with TopHat workflow.
Conclusions: CNOT6L stimulated degradation of maternal transcriptsto oocyte meiotic maturation.

overall_design: 2 oocytes at GV ,MI, MII stages and zygotes of WT, Btg4-/- and Cnot6l-/- mice are performed RNA sequencing.

first: Qian-Qian

last: Sha

first: Jia-Li

last: Yu

first: Jing-Xin

last: Guo

first: Xing-Xing

last: Dai

first: Jun-Chao

last: Jiang

first: Yin-Li

last: Zhang

first: Chao

first: Shu-Yan

last: Ji

first: Yu

first: Song-Ying

first: Xiang-Hong

last: Ou

first: Heng-Yu

last: Fan


title: Single Nucleotide Resolution Analysis of Nucleotide Excision Repair of Ribosomal DNA in Humans and Mice

status: Public on Nov 24 2018

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

country: USA

institute: University of North Carolina  at Chapel Hill

summary: In the present work we have applied analytical methods to map repair events in rDNA using data generated by the newly developed XR-seq genome-wide single nucleotide repair technology. We find that in human and mouse cell lines, rDNA is not subject to TCR of damage caused by UV or by cisplatin.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We perform XR-seq in mouse skin fibroblast under UV irradiation and collect cells after incubation 3 hours. For human cell lines NHF1, CSB and XPC, we perform XR-seq under UV irradiation and collect cells after incubation 1 hour. For GM12878, we perform XR-seq under cisplatin and collect cells after incubation 2 hours. Then we mapped all the reads to rDNA or DHFR.
This dataset includes re-analysis of five GSE67941 Samples and two GSE82213 Samples.

first: Jinchuan

last: Hu

first: Christopher

middle: P

last: Selby

first: Wentao

last: Li

first: Askar

last: Yimit

first: Yuchao

first: Aziz

last: Sancar


title: Osmostress induced changes of chromatin architecture and transcription in mammalian cells [ChIP-Seq]

city: Barcelona

first: Francesc

last: Posas

address: Carrar Baldiri Reixac 10

country: Spain

institute: Cell Signaling Group, IRB Barcelona

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Osmostress causes chromatin compaction and simultaneously triggers a massive transcriptional response in eukaryotic cells that is required for adaptation and cell survival. However, thus far it was unknown how changes of chromatin organization and ongoing DNA transcription are linked under hyper-osmotic conditions. In this study, we focused on elucidating the extent of chromatin reoganization upon hyper-osmotic shock, its reversibility and its link with active transcription in human T47D cells.

overall_design: T47D cells were subjected to 100 mM NaCl for defined periods of time and both total RNA as well as chromatin were collected in several batches. RNA steady state levels between stressed and untreated T47D cells were compared using RNA-seq at 1 h, 3 h and 6 h of exposure to NaCl. Changes of active transcription / Pol II occupation were determined by ChIP-seq of Pol II, again comparing unstressed and stressed cells (1 h stress). We used HiC to study chromatin organization before and after NaCl treatment (1 h) as well as when inhibiting transcription by pre-treating cells with 500 nM of triptolide for 2 h prior stress or no stress, resulting in a total inhibition time of 3 h prior to sequencing. In addition, recovery of the initial chromatin interaction profiles was assessed by shifting cells back to isotonic conditions for 1 h after NaCl exposure, both with and without triptolide addition. We also assessed CTCF binding to chromatin after 7.5 min, 30 min and 60 min compared to basal conditions using ChIP-seq. ChIP-seq was also used to evaluate RAD21 binding after 1 h of stress as well as 1 h of stress plus 1 h of recovery (in line with HiC experiments) compared to control. Lastly, both CTCF and RAD21 ChIP-seq with and without stress (1 h) as well as recovery of chromatin binding after 1 h of stress were also performed when inhibiting transcription by triptolide pre-treatment (2 h, 500 nM).

first: Ramon

last: Amat

first: René

last: Böttcher

first: François

last: le Dily

first: Enrique

last: Vidal

first: Javier

last: Quilez

first: Yasmina

last: Cuartero

first: Eulàlia

last: de Nadal

first: Miguel

last: Beato


title: Osmostress induced changes of chromatin architecture and transcription in mammalian cells

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


title: Osmostress induced changes of chromatin architecture and transcription in mammalian cells [RNA-Seq, HiC]

summary: Osmostress causes chromatin compaction and simultaneously triggers a massive transcriptional response in eukaryotic cells that is required for adaptation and cell survival. However, thus far it was unknown how changes of chromatin organization and ongoing DNA transcription are linked under hyper-osmotic conditions. In this study, we focused on elucidating the extend of chromatin reoganization upon hyper-osmotic shock, its reversibility and its link with active transcription in human T47D cells.

overall_design: T47D cells were subjected to 100 mM NaCl for defined periods of time and both total RNA as well as chromatin were collected in several batches. RNA steady state levels between stressed and untreated T47D cells were compared using RNA-seq at 1 h, 3 h and 6 h of exposure to NaCl. Changes of active transcription / Pol II occupation were determined by ChIP-seq of Pol II, again comparing unstressed and stressed cells (1 h stress). We used HiC to study chromatin organization before and after NaCl treatment (1 h) as well as when inhibiting transcription by pre-treating cells with 500 nM of triptolide for 3 h prior to sequencing. In addition, recovery of the initial chromatin interaction profiles was assessed by shifting cells back to isotonic conditions for 1 h after NaCl exposure, both with and without triptolide addition. We also assessed CTCF binding to chromatin after 7.5 min, 30 min and 60 min compared to basal conditions using ChIP-seq. ChIP-seq was also used to evaluate RAD21 binding after 1 h of stress as well as 1 h of stress plus 1 h of recovery (in line with HiC experiments) compared to control.


title: Single cell RNA-sequencing of EpCAM-, CD45-, CD31- NG2- murine mammary tumor fibroblasts

city: Lund

first: Kristian

last: Pietras

address: Medicon Village, Building 404:A3

department: Laboratory Medicine

country: Sweden

institute: Lund University

summary: This study was conducted to determine heterogeneity of cancer-associated fibroblasts (CAFs) in mammary tumors, by unsupervised analysis of single cell transcriptomes.

overall_design: 768 single EpCAM-, CD45-, CD31- NG2- fibroblasts were isolated from mammary tumors of two 14 week old MMTV-PyMT mice. The cells were sequenced following the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013).

first: Michael

last: Bartoschek


title: Therapeutic effects of Rosuvastatin in hypercholesterolemic prediabetic mice in the absence of low density lipoprotein receptor

city: Kuopio

first: Henri

last: Niskanen

department: A.I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

summary: Statins are efficient in preventing cardiovascular disease progression, but their effects in the absence of low density lipoprotein receptor (LDLR) and on the risk of diabetes are not yet well characterized. The aim was to clarify systemic and pleiotropic effects of Rosuvastatin on cardiovascular and diabetic phenotypes in hypercholesterolemic prediabetic mice. The IGF-II/LDLR-/-ApoB100/100 animals were tested for Rosuvastatin effects on plasma glucose, insulin, lipids, atherosclerosis and liver steatosis. To achieve a more comprehensive view, genes differentially expressed in response to Rosuvastatin were identified by RNA sequencing in liver tissue. Rosuvastatin significantly reduced plasma cholesterol in hypercholesterolemic LDLR – deficient mice, but had no effects on atherosclerosis development at aortic sinus level and in coronary arteries. Rosuvastatin also significantly reduced liver steatosis without any pronounced effects on glucose or insulin levels. RNA sequencing revealed that Rosuvastatin – responsive hepatic genes are involved in cholesterol metabolism and in anti-inflammatory response. In addition, significant changes were detected in the expression of Perilipin 4 and 5 which are involved in lipid droplet formation in the liver. For the first time it was shown that Tribbles proteins are affected by Rosuvastatin treatment in the hypercholesterolemic mice. In conclusion, Rosuvastatin treatment had several positive effects in hypercholesterolemic mice showing early signs of diabetes, and many of these outcomes are unrelated to direct effects on cholesterol and lipoprotein metabolism. These results increase our understanding about the systemic and pleiotropic effects of Rosuvastatin in the absence of LDLR expression.

overall_design: Gene expression profiling of mouse liver tissue from Rosuvastatin and placebo fed mice overexpressing IGF-II with a knock-out of LDL-receptor and expressing only ApoB100.

first: Minna

middle: U

last: Kaikkonen

first: Erika

last: Gurzeler


title: Expression data in HUVECs treated with siERG, siFLI1, or both

city: Kumamoto

first: Nao

last: Nagai

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: Endothelial-to-mesenchymal transition (EndMT) in which endothelial cells lose their characteristics and acquire mesenchymal property has recently been recognized as a driver of disease progression in wide range of pathologies. However, the regulatory mechanism of EndMT has not been fully understood. Here, we found that combined knockdown of two ETS family transcription factors, ERG and FLI1, induced EndMT. Hence, we analyzed functions of ERG and FLI1 using gene expression microarray and ChIP-seq to elucidate the regulatory mechanism of EndMT.

overall_design: 8 samples are uploaded. Human umbilical vein endothelial cells (HUVECs) were treated with siControl, siERG, siFLI1 or siERG+siFLI1 for 3 or 7 days.

first: Takashi

last: Minami


title: CNOT6L Couples the Selective Degradation of Maternal Transcriptsto Meiotic Cell Cycle Progression in Mouse Oocyte [polysome RNA-seq]

first: Li

last: Shen

summary:
Purpose: The goals of this study are to study the function of Cnot6l during oocyte maturation .
Methods: Comparing the polysome-bounded transcripts at GV, MI and MII stage in  WT and Cnot6l-/- oocytes by RNA sequencing.
Results: Using an optimized data analysis workflow, we mapped about 15 million sequence reads per sample to the mouse genome (build mm9) and identified  23236 transcripts with TopHat workflow.
Conclusions: CNOT6L stimulated degradation of maternal transcriptsto oocyte meiotic maturation.

overall_design: 2 oocytes at GV ,MI and MII stages  of WT and Cnot6l-/- mice are performed polysome-bounded transcripts by RNA sequencing.

first: Qian-Qian

last: Sha

first: Jia-Li

last: Yu

first: Jing-Xin

last: Guo

first: Xing-Xing

last: Dai

first: Jun-Chao

last: Jun-Chao

first: Yin-Li

last: Zhang

first: Chao

first: Shu-Yan

last: Ji

first: Yu

last: Jiang

first: Song-Ying

first: Xiang-Hong

last: Ou

first: Heng-Yu

last: Fan


title: ERG and FLI1 in endothelial cells


title: Impact of intron deletion on starvation dependent repression of gene expression

city: Sherbrooke

first: Sherif

last: Abou Elela

state: Québec

address: 3201, rue Jean-Mignault

department: Microbiologie et Infectiologie

country: Canada

institute: Université de Sherbrooke

summary: Deleting the introns from either the chromatin remodeling MMS2 gene or the splicing regulator gene YSF3 modified the expression of a common set of genes in the stationary phase of growth.

overall_design: RNA extracted from wild type cells and cells carrying deletion in the intron of two genes with unrelated function was sequenced and their expression pattern compared in different phases of growth.


title: Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling

city: Berlin

first: Aslihan

last: Karabacak

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: DNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions via footprinting. Recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. However, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. Here, we undertake a systematic comparison of the two methods and show that a modification to the ATAC-seq protocol increases its yield and its agreement with DNase-seq data from the same cell line. We demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. Despite differences in footprint shapes, the locations of the inferred footprints in ATAC-seq and DNase-seq are largely concordant. However, the protocol-specific sequence biases in conjunction with the sequence content of TFBSs impacts the discrimination of footprint from background, which leads to one method outperforming the other for some TFs. Finally, we address the depth required for reproducible identification of open chromatin regions and TF footprints.

overall_design:
Open chromatin profiling via ATAC-seq and DNase-seq in HEK293 and K562 cells

Please note that the only difference between high, medium and low depth samples is how they were sequenced. High depth samples were sequenced by themselves on a HiSeq lane, whereas for medium depth samples 2 libraries were multiplexed on one lane (and for low depth samples 4 libraries were multiplexed on one lane).


title: Hobit- and Blimp-1-driven CD4+ P2X7+ tissue resident memory T cells   critically control chronic intestinal inflammation

status: Public on Nov 25 2018

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

summary:
Although tissue resident memory T (TRM) cells have been shown to regulate host protection in infectious disorders, their functional role in inflammatory bowel diseases (IBD) remains to be investigated. Here, we characterized TRM cells in human IBD and addressed their role in experimental models of intestinal inflammation with mice deficient for TRM-associated transcription factors and by TRM depletion.
We show that pro-inflammatory TRM cells are increased in active IBD. Moreover, the presence of CD4+ but not CD8+ TRM cells in IBD patients predicts subsequent development of flares. In vivo, mice deficient in Hobit and Blimp-1 are protected from several models of colitis due to decreased pro-inflammatory cytokine secretion, impaired cytotoxicity and leukocyte chemotaxis. Finally, P2X7-induced TRM depletion via NAD enema leads to suppression of colitis activity.  Taken together, our data argue for a central role of TRM cells in the pathogenesis of IBD and suggest that these cells are an interesting target for future therapeutic approaches.

overall_design: The 4 analyzed samples belong to 2 different groups with 2 biological replicates per group. One of the groups consisted of control samples.

first: Sebastian

last: Zundler

first: Markus

middle: F

last: Neurath

first: Sören

last: Lukassen

first: Arif

middle: B

last: Ekici


title: The gene regulation of FAM198B in lung cancer

city: Taipei

first: Sung-Liang

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

summary:
FAM198B is identified as a novel tumor supressor gene in lung adenocarcinoma. This study aim to investigate the effects of the glycoprotein protein, FAM198B, on the biological behavior and global gene expression profiles of lung cancer cells. Expression microarray and bioinformatics analyses indicated that FAM198B mainly regulated  ERK-mediated MMP1 pathway in CL1-5 cells, which results in tumor metastasus inhibition.
We used microarrays to identify the global gene alterarion in lung cancer CL1-5 cells after ectopic expressing FAM198B

overall_design: Etopic expressing FAM198B-V5 and mock control vector in lung cancer CL1-5 cells

first: Chia-Ying

last: Hsu


title: Genome-wide analysis of ERG- and FLI1-binding in HUVECs, and histone modifications in HUVECs treated with siControl or siERG+siFLI1

first: Nao

last: Nagai

overall_design: 12 samples are uploaded. ChIP was performed for ERG and FLI1 in human umbilical vein endothelial cells (HUVECs); ChIP was performed for H3K4me3 and H3K27Ac in HUVECs treated with siControl or siERG+siFLI1; each sample has two biological replicates.

first: Ryo

last: Nakaki

first: Shogo

last: Yamamoto

first: Takashi

last: Minami


title: Differential roles of Stella in the modulation of DNA methylation during oocyte and zygotic development

status: Public on Nov 22 2018

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

institute: Beijing Institute of Radiation Medicine

type: Methylation profiling by high throughput sequencing

summary: In order to obtain genome-wide profiles, base-resolution methylomes of oocytes and zygotes were generated using the bisulfite sequencing (BS-seq) method for small samples. We find that global loss of DNA methylation during zygotic development in HFD mice. A total of 412 DMRs were identified, of which 294 were hypomethylated (hypo-DMRs; 71.4%) and 118 were hypermethylated (hyper-DMRs; 28.6%) (Fig. 6A and 6B), showing a predominance of hypo-DMRs. Furthermore, we show that hyper-DMRs are significantly depleted from CGI, but enriched in short interspersed elements (SINEs) and non-CGI regions. Strikingly, hypo-DMRs are specifically depleted from SINEs, with a concurrent enrichment in DNA transposons.

overall_design: Examination of DNA methylome in oocyte and zygote from Stella∆ and WT

first: Qiang

last: Wang

first: Jun

last: Zhang

first: Longsen

last: Han

first: Chao

last: Ren


title: RNA Sequencing of three pairs of gastric cancer

city: Shanghai

first: Jie

last: Chen

address: Dongan Road

institute: Fudan University Shanghai Cancer Center

summary: The prognosis after curative resection of gastric cancer (GC) remains unsatisfactory, and thus, the development of treatments involving alternative molecular and genetic targets is critical. Circular RNAs (circRNAs), new stars of the non-coding RNA network, have been identified as critical regulators in various cancers. Here, we aimed to determine the circRNA expression profile and investigate the functional and prognostic significance of circRNA in GC. Using next-generation sequencing profiling, we first characterized an abundant circRNA, hsa_circ_0008549, derived from the OSBPL10 gene, and named it circOSBPL10. The expression of circOSBPL10 was found via quantitative real-time RT-PCR (qRT-PCR) to be upregulated in GC tissues, and silencing of circOSBPL10 significantly inhibited gastric cancer cell growth, migration and invasion in multiple experiments. We further confirmed that miR-136-5p is a downstream target of circOSBPL10 using RNA pull-down and luciferase reporter assays. Rescue experiments confirmed that circOSBPL10 regulates biological functions in GC cells via a circOSBPL10-miR-136-5p-WNT2 axis. In vivo experiments showed that circOSBPL10 promotes tumor growth and metastasis in mice. Furthermore, the level of circOSBPL10 was observed to be a prognostic marker of the overall survival and disease-free survival of patients with GC. Taken together, our findings reveal that circOSBPL10 may serve as a new proliferation factor and prognostic marker in gastric cancer.

overall_design: RNA profiles of three gastric cancer and normal tissues adjacent to gastric cancer were generated by deep sequencing, using Illumina HiSeq 2000.

first: Sen


title: Expression profiling of pancreatic adenocarcinoma and ductal adenocarcinoma cell lines.

city: Houston

first: Samir

last: Hanash

state: TX

address: 6767 Bertner Ave

institute: UT MD Anderson Cancer Center

summary: We characterized baseline gene expression profiles for eleven human pancreatic adenocarcinoma and ductal adenocarcinoma cell lines.

overall_design: Eleven human pancreatic adenocarcinoma (Hs 766T, Panc 03.27, SU.86.86 and SW1990) and pancreatic ductal adenocarcinoma (AsPC-1, BxPC-3, Capan-2, CFPAC-1, HPAF-II, MIA PaCa-2 and PANC-1) cell lines were grown under standard conditions. RNA expression profiling was performed on total cell extracts using Illumina HiSeq 2000 paired-end sequencing to determine baseline gene expression.


title: The Type I interferon response impairs differentiation potential of pluripotent stem cells

city: New York

first: Julie

middle: Anne

last: Eggenberger

state: NY

address: 1 Gustave L. Levy Pl

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

overall_design: Refer to individual Series


title: Mitochondrial hypoxic stress induces RNA editing by APOBEC3G in lymphocytes

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, de novo induction of RNA editing in response to environmental factors is an uncommon phenomenon. While APOBEC3A edits many mRNAs in monocytes/macrophages in response to hypoxia and interferons, the physiological significance of such editing is unclear. Here we show that the related APOBEC3G cytidine deaminase induces site-specific C-to-U RNA editing in natural killer (NK), CD8+ T cells and lymphoma cell lines upon cellular crowding and hypoxia. RNA seq analysis of hypoxic NK cells reveals C-to-U recoding mRNA editing in dozens of genes including multiple translational and ribosomal genes. APOBEC3G promotes Warburg-like metabolic remodeling and reduces proliferation of HuT78 T cells under similar conditions. Hypoxia-induced RNA editing by APOBEC3G can be mimicked by the inhibition of mitochondrial respiration, and occurs independently of HIF-1α. Thus, APOBEC3G induces mRNA editing in lymphocytes to promote adaptation to mitochondrial hypoxic stress.

overall_design: 6 NK cells. 3 normoxia and 3 hypoxia treatment replicates.

first: Shraddaha

last: Sharma

first: Bora

last: Baysal


title: ChIP-seq profiles of primary, metastatic, drug-resistant and drug-holiday cells

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: We employed ChIP-seq to detect poised and active chromatin regions in cisplatin sensitive and resistant head neck squamous cell carcinoma patient derived primary and lymph node cell lines.

overall_design: Examination of chromatin profiles of sensitive and drug-resistant cells from HNSCC

first: Ankur

first: Ramanuj

last: DasGupta


title: Transcriptome-wide analysis links the short-term expression of the b isoforms of T-cell intracellular antigens to protective proteostasis-mediated survival and quiescence

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

summary: Control of gene expression depends on genetics and environmental factors. The T-cell intracellular antigens T-cell intracellular antigen 1 (TIA1), TIA1-like/related protein (TIAL1/TIAR) and human antigen R (HuR/ELAVL1) are RNA-binding proteins that play crucial roles in regulating gene expression in both situations. This study used massive sequencing analysis to uncover molecular and functional mechanisms resulting from the short-time expression of the b isoforms of TIA1 and TIAR and HuR in HEK293 cells.

overall_design: Three comparisons (altered vs control) were carried-out using three biological replicates per sample type. RNA-seq was performed with 100 nt strand-specific and paired-ends reads. Illumina HiSeq 2000 sequencer was used.

first: Isabel

last: Carrascoso

first: Daniel

last: Tabas-Madrid

middle: C

first: José

middle: M

last: Izquierdo


title: Transcriptome of Prmt5-deficient and control mouse activated B cells

city: Montréal

first: Claudia

middle: L

last: Kleinman

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

summary: Quiescent splenic B cells purified from Cg1-cre Prmt5F/F cells and Cg1-cre control mice. Resting B cells were plated on feeder cells expressing CD40L and BAFF and supplemented with IL-4 for activation. Four days later, the resulting activated germinal center-like B cells were purified and RNA extracted and processed for HiSeq. Four independent samples of each genotype were processed and analyzed.

overall_design: 2 Experiments, 2 samples of each genotype per experiment (Exp 1: Samples 1,2,7,8 ; Exp 2: Samples 3,4,5,6)_ PRMT5 FF Cg1cre: Samples 1,2,3,4_ Cg1cre controls: Samples 5,6,7,8

first: Ludivine

last: Litzler

first: Astrid

last: Zahn

first: Steven

last: Hébert

first: Javier

last: Di Noia


title: Flag-Sae2 ChIP seq in yeast

status: Public on Nov 21 2018

city: Austin

first: Tanya

middle: T.

last: Paull

address: 2500 Speedway MBB 2.448

department: Molecular Biosciences

institute: Univ. of Texas at Austin

summary: Flag-tagged Sae2 was immunoprecipitated from G1 or S phase yeast cells, either untreated or treated with camptothecin

overall_design: 4 biological samples: Sae2 in G1, Sae2 in G1 with CPT, Sae2 in S, Sae2 in S with CPT. For each, there are input, bead control (no antibody), and IP (anti-Flag) data


title: RNA sequencing of mutant AKT tumors

city: Salt Lake City

first: Sheri

last: Holmen

state: UT

address: 2000 Circle of Hope Dr.

department: Surgery

institute: University of Utah

summary:
Goal: Comparison of mRNA expression profiles in primary tumors based on activation of different AKT paralogs
Methods: RNA sequencing performed at the High-Throughput Genomics and Bioinformatics Analysis Core at the University of Utah. Detailed procedures available in methods and DNA processing pipline sections.
Results: Focus of study compared mRNA expression profiles of BRAFV600E;Cdkn2a-/-;Pten-/- and  BRAFV600E;Cdkn2a-/-;Pten-/-;AKT1E17K cohorts. PCA and unsupervised heirarchical clustering revealed samples clustered together appropriately. Seventeen of eighteen FA factor genes analyzed were upregulated in the AKT1E17K cohort.
Conclusion: AKT1E17K has a critical role in upregulating a large group of FA factors

overall_design: Thirty primary tumor samples included in analyses: Six BRAFV600E;Cdkn2a-/-, Six BRAFV600E;Cdkn2a-/-;Pten-/-, Six BRAFV600E;Cdkn2a-/-;Pten-/-;AKT1E17K,  Six BRAFV600E;Cdkn2a-/-;Pten-/-;AKT2E17K,  Six BRAFV600E;Cdkn2a-/-;Pten-/-;AKT3E17K

first: David

middle: A

last: Kircher

first: Christopher

last: Stehn


title: Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge (ATAC-Seq)

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

country: Israel

institute: The Weizmann Institute of Science

summary: Microglia are yolk sac-derived macrophages residing in the parenchyma of brain and spinal cord, where they interact with neurons and other glial cells by constantly probing their surroundings with dynamic extensions. After different conditioning paradigms and bone marrow (BM) or hematopoietic stem cell (HSC) transplantation, graft-derived cells seed the brain and persistently contribute to the parenchymal brain macrophage compartment. Here we establish that graft-derived macrophages acquire, over time, microglia characteristics, including ramified morphology, longevity, radio-resistance and clonal expansion. However, even after prolonged CNS residence, transcriptomes and chromatin accessibility landscapes of engrafted, BM-derived macrophages remain distinct from yolk sac-derived host microglia. Furthermore, engrafted BM-derived cells display discrete responses to peripheral endotoxin challenge, as compared to host microglia. In human HSC transplant recipients, engrafted cells also remain distinct from host microglia, extending our finding to clinical settings. Collectively, our data emphasize the molecular and functional heterogeneity of parenchymal brain macrophages and highlight potential clinical implications for HSC gene therapies aimed to ameliorate lysosomal storage disorders, microgliopathies or general monogenic immuno-deficiencies.

overall_design: overall there are 28 samples, from total of 2 experiments. in each experiment there were at least 3 biological repeats (3 individual mice). Sorting of the CD45.1 and CD45.2 populations were performed from the same animal. Animals were either injected with LPS (2.5 mg/kg) or untreated.

first: Anat

last: Shemer

first: Jonathan

last: Grozovski

first: Tuan

last: Tay

first: Jenhan

last: Tao

first: Alon

last: Volaski

first: Patrick

last: Süß

first: Alberto

last: Ardura-Fabregat

first: Mor

last: Gross-Vered

first: Jung-Seok

last: Kim

first: Eyal

last: David

first: Louise

last: Chappell-Maor

first: Lars

last: Thielecke

middle: K

last: Glass

first: Marco

last: Prinz

first: Kerstin

last: Cornils


title: Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge

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


title: Dynamic molecular monitoring reveals that SWI/SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma

city: Melbourne

first: Mark

last: Dawson

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

relation:
SuperSeries of: GSE122509
SuperSeries of: GSE122510


title: Engrafted parenchymal brain macrophages differ from microglia in transcriptome, chromatin landscape and response to challenge (RNA-Seq)

last: Jung

first: Christopher


title: The Type I interferon response impairs differentiation potential of pluripotent stem cells [seq]

first: Julie

last: Eggenberger

summary: Upon virus infection,pluripotent stem cells neither induce nor respond to canonical Type I interferons (IFN-I). To better understand this biology,we characterized induced pluripotent stem cells (iPSCs) as well as their differentiated parental or re-derived counterparts. We confirmed that only iPSCs failed to respond to viral RNA,Type I interferon (IFN-I),or viral infection.  This lack of response could be phenocopied in fibroblasts with the expression of a reprogramming factor which repressed the capacity to induce canonical antiviral pathways. To ascertain the consequences of restoring the antiviral response in the context of pluripotency,we engineered a system to engage these defenses in iPSCs.    Inducible expression of a recombinant virus-activated transcription factor resulted in the successful reconstitution of antiviral defenses through the direct upregulation of IFN-I stimulated genes. Induction of the antiviral signature in iPSCs,even for a short duration,resulted in the dysregulation of genes associated with all three germ layers despite maintaining pluripotency markers. Trilineage differentiation of these same cells showed that engagement of the antiviral defenses compromised ectoderm and endoderm formation and dysregulated the development of mesodermal sublineages. In all,these data suggest that the temporal induction of the antiviral response primes iPSCs away from pluripotency and induces numerous aberrant gene products upon differentiaton. Together these results suggest that the IFN-I system and pluripotency may be incompatible with each other and thus explain why stem cells do not utilize the canonical antiviral system.

overall_design: RNA-Seq data in duplicate for 70 total samples

first: Benjamin

last: tenOever


title: Robust generation of honemogeneous midbrain organoids with in vivo–like cellular composition facilitates neurotoxin-based Parkinson’s disease modeling

city: Seoul

first: Chanhyeok

last: Park

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

country: South Korea

institute: KIST (Korea Institute of Science and Technology)

summary: We could establish the advanced protocol for generating homogeneous and mature midbrain organoids by manipulating SMAD inhibitor combination and in vitro WNT gradient elaborately.

overall_design: Here we perform RNA-Seq experiment in different stage of midbrain organoids generated  by various conditions. hESCs was used as a starting source of midbrain organoids.

first: T

middle: H

last: Kwak

first: J

last: Kang

first: S

last: Hali

first: C

first: Y

middle: J

last: An

first: D

middle: W

last: Han


title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

summary: G-quadruplexes (G4) are secondary nucleic acid structures that have been associated with genomic instability and cancer progression. When present in the promoter of some oncogenes, G4 structures can affect gene regulation and, hence, represent a possible therapeutic target. In this study, RNA-Seq was used to explore the effect of a G4-binding anthraquinone derivative, named AQ1, on the whole-transcriptome profiles of two common cell models for the study of KIT pathways; the human mast cell leukemia (HMC1.2) and the canine mast cell tumor (C2). The highest non-cytotoxic dose of AQ1 (2 µM) resulted in 5441 and 1201 differentially expressed genes in the HMC1.2 and C2 cells, respectively. In both cell lines, major pathways such as cell cycle progression, KIT- and MYC-related pathways were negatively enriched in the AQ1-treated group, while other pathways such as p53, apoptosis and hypoxia-related were positively enriched. These findings suggest that AQ1 treatment induces a similar functional response in the human and canine cell models, and provide news insights into using dogs as a reliable translational model for studying G4-binding compounds.

sample_organism:
Homo sapiens
Canis lupus familiaris

platform_organism:
Homo sapiens
Canis lupus familiaris

overall_design: Examination of 2 different doses of a G-quadruplex-biding ligand (dubbed AQ1) in 2 cell types.

first: Elgendy

last: Ramy

first: Zorzan

last: Eleonora


title: Bulk RNA sequencing of intracortically-projecting neurons at P10

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

summary: Distinct subtypes of intracortically-projecting neurons (ICPN) are present in all layers, allowing propagation of information within and across cortical columns. How the molecular identities of ICPN relate to their defining anatomical and functional properties is unknown. Here we show that the transcriptional identities of ICPN primarily reflect their broad axonal projections rather than their date of birth or laminar position. Thus, conserved circuit-related transcriptional programs are at play across cortical layers, which may preserve canonical circuit features across development.

overall_design: We performed bulk RNA sequencing of P10 layer 4 Tomato+ spiny stellate neurons, and retrogradely labeled callosal projection neurons from deep and superficial layers of the neocortex.

first: A

last: De La Rossa

first: E

last: Klingler


title: The effects of exercise on gene expression in abdominal subcutaneous adipose tissue

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: Exercise improves health and well-being across diverse organ systems, and elucidating mechanisms underlying the beneficial effects of exercise on health can lead to new therapies for disease. We find that exercise training in humans causes profound changes in subcutaneous adipose tissue (scWAT) gene expression, including genes encoding secreted proteins. In addition, we used our previously published microarray dataset derived from scWAT from mice housed in static cages (sedentary controls) or mice housed in cages with running wheels for 11 days. Genes that were significantly changed by exercise training in humans and mice were further selected by annotation for Extracellular Space in Gene Ontology. Of these genes, the most significantly correlated with the total wheel running distance in the trained mice was Tgfb2. We validated that exercise training increased TGFB2 mRNA in scWAT of human subjects using RT-qPCR. This led us to hypothesize that TGF-β2 is an exercise-induced adipokine. To determine the therapeutic potential and mechanism for increased TGF-β2, we investigated mouse models of exercise training and obesity. Our findings indicate that exercise training improves metabolism through inter-organ communication with fat via a TGF-β2 signaling, providing a novel mechanism for counteracting metabolic disease.

overall_design: Biopsies of abdominal abdominal subcutaneous adipose tissue (scWAT) were taken from healthy young male subjects before and after 12 weeks of exercise training. The exercise training protocol consisted of 60-80 minutes cycling/day, 5 days/week.

first: Kristin

last: Stanford

first: Laurie

last: Goodyear


title: Role of interleukin 2 on thymic Foxp3+CD4+ regulatory T (Treg) cell chromatin modeling

city: Bronx

first: Gregoire

middle: S

last: Lauvau

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

summary: Interleukine 2 (IL-2) is still one of the most interesting cytokines in T cell biology with its ability to control immune homeostasis by maintaining the functional identity of Foxp3+ regulatory T (Treg) cells and the expansion of activated conventional T (Tconv) cells. Yet, how IL-2 exactly enables Treg cells to suppress autoreactive Tconv cells and to maintain their identity is unclear. Using a mouse model in which IL-2 signaling via its high affinity receptor CD25 is selectively impaired, the “Il2ramut/mut” mouse, we report that Treg cells that only receive low IL-2 signals keep Il2ramut/mut but not WT Tconv cells “in check”, suggesting equal IL-2 signals in Treg and Tconv cells is essential to safeguard immune homeostasis. Furthermore, the comparative analysis of gene expression and epigenetic landscape of Il2ramut/mut and WT Treg cells support a model in which IL-2 "locks in” Treg cell identity and functions in vivo by controlling their genome-wide chromatin accessibility.

overall_design: Thymuses from ~20 weeks old aged-matched females either Il2ramut/mut (4 mice) or WT (4 mice) Foxp3-RFP+ reporter mice were harvested and RFP+ Treg cells were enriched by negative selection (dynabeads) and flow-sorted (Aria III) before proceeding to extraction of nuclei, transposition and library preparation for sequencing (ATAC-seq).

first: Laurent

last: Chorro

first: Masako

last: Suzuki


title: Role of interleukin 2 on SATB1 binding in SP CD4+ thymocytes

overall_design: Thymus from 6-8 weeks old aged-matched females either Il2ramut/mut (2 mice) or WT (2 mice) mice were harvested and 2x10e6 single positive (SP) CD4+ thymocytes were pre-enriched by negative selection (dynabeads), stained with fluorescent labeled antibodies against CD4 (GK1.5) and CD8α (53-6.7) and flow-sorted (Aria III) before proceeding to fixation (cross-linking), lysis, immunoprecipation against SATB1 and library preparation for sequencing.


title: Differential expression in wild type and mutant HAP1 cells [RNA-seq II]

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary: Characterization of gene expression changes occuring upon knockout of RING1A, RING1B, and BAP1.

overall_design: Four Samples

first: Antoine

last: Campagne

first: Dina

last: Zielinski

first: Ming-Kang

last: Lee

first: Audrey

last: Michaud

first: Stéphanie

last: Le Corre

first: Lara

middle: Z

last: Sahidian

first: Florent

last: Dingli

first: Hong

last: Chen

first: Ivaylo

last: Vassilev

first: Damarys

last: Loew

first: Eric

last: Pasmant

first: Robert

last: Schneider

first: Sophie

last: Postel-Vinay

first: Michel

last: Wassef

first: Raphaël

last: Margueron


title: Dynamic molecular monitoring reveals that SWI/SNF mutations mediate resistance to ibrutinib plus venetoclax in mantle cell lymphoma [ATAC-Seq]

first: Mark

last: Dawson

summary: Ibrutinib plus venetoclax is a highly effective combination in mantle cell lymphoma. However, strategies to enable the evaluation of therapeutic response are required. Our prospective analyses of patients within the AIM study revealed genomic profiles that clearly dichotomized responders and non-responders. Mutations in ATM were present in most patients who achieved a complete response, while chromosome 9p21.1-p24.3 loss and/or mutations in components of the SWI/SNF chromatin remodeling complex were present in all patients with primary resistance and 2/3 patients with relapsed disease. Circulating tumor DNA analysis revealed that these alterations could be dynamically monitored providing concurrent information on treatment response and tumour evolution. Functional modeling demonstrated that compromise of the SWI/SNF complex facilitated transcriptional upregulation of BCL2L1 (Bcl-xL) providing a selective advantage against ibrutinib plus venetoclax. Together these data highlight important insights into the molecular basis of therapeutic response and provide a paradigm for real-time assessment of innovative targeted therapies.

overall_design: Examining the effect of SMARCA4 knockdown and the response to ibrutinib plus venetoclax in mantle cell lymphoma cell lines Z-138

first: Sarah-Jane


title: Investigation of mRNA expression pattern by RAD21 knockdown in hematopoetic stem cells

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

institute: Leibniz Institute on Aging - FLI

summary: Elevated inflammation represents a hallmark of hematopoietic aging and leukemia development but mechanistically its impact on hematopoietic stem and progenitor cell (HSPC) maintenance remains incompletely understood. Here we identify Rad21/cohesin as a major component mediating inflammation-induced NF-kB signaling, which in turn limits self-renewal of HSPCs by induction of differentiation. Disruption of Rad21/cohesin diminishes inflammation-induced loss of self-renewal and induction of differentiation, but these effects are abrogated in NF-kB knockout (p50-/-) HSPCs. During aging, HSPCs exhibit an increased responsiveness to activate NF-kB signaling in response to inflammatory stimuli also resulting in activation of genes encoding for secreted cytokines. These cell intrinsic and extrinsic responses cooperatively enhance differentiation and loss of self-renewal of HSPCs resulting in increased selection of Rad21/cohesin deficient HSPCs exhibiting elevated self-renewal and myeloid skewed differentiation. Together, these results identify cohesin-mediated NF-kB signaling as a major axis connecting cell extrinsic increases in inflammation with the evolution of hallmark features HSC aging characterized by increases in self renewal and myeloid skewed differentiation aggravated by the concomitant selection of cohesin deficient HSPCs.

overall_design: total samples: 12 (6 in vivo: 3 Rad21 knockdown, 3 control; 6 in vitro: 3 Rad21 knockdown, 3 control)

first: Zhiyang

first: Yohei

last: Morita

first: Martin

last: Hölzer

first: K.

last: Rudolph


title: T47D Breast cancer cell line  ChIP-seq data II

city: Barcelona

first: François

last: Le Dily

address: Dr. Aiguader, 88

institute: CRG-Centre for Genomic Regulation

summary: We performed genome-wide  CDK9 ChIP seq experiments in T47D  cells  only expressing HA Tagged amanitin resistant wild type in comparison to R1810A mutant form of RNAP2.

overall_design:
We designed experiment to perform genome wide CDK9 ChIP sequencing in T47D cells expressing HA Tagged amanitin resistant wild type in comparison to R1810A mutant form of RNAP2.We find that PADI2 deiminates R1810 at CTD (C-terminal domian ) of RNAP2  and this is important to regulate the P-TEFb complex association with RNAP2. Therefore in order to investigate precise effect of the RNAP2  R1810A mutantion on CDK9  recruitment, we performed the CDK9 ChIP seq .
Objective was to analyse  chromatin  binding regions of  CDK9 in T47D cells  expressing  wild type (WT) form of RNAP2 was expressed . After 24h of transfections , cells were treated  by 6ug/ml amanitin  to inhibit endogenous form of RNAP2 .So that we could demonstrate specific  CDK9 ChIP seq data  after expressing amanitin resistant wild type form  of RNAP2 .

first: Priyanka

last: Sharma

first: Antonios

last: Lioutas

first: Javier

last: Quilez

first: Jose

last: Caballero

first: Roni

middle: G

last: Wright

first: Chiara

last: Di Vona

first: Roland

last: Schüller

first: Dirk

last: Eick

first: Miguel

last: Beato


title: Differential expression in wild type and mutant HAP1 cells [RNA-seq I]

first: Nicolas

last: Servant

summary: using RNA-seq we characterized gene expression changes occuring upon knockout of BAP1, ASXL1, ASXL2, ASXL1/2 or Polycomb genes RING1B and EZH2. We also investigated the response to retinoic acid treatment in wild-type and BAP1 KO cells.

overall_design: Examination of transcript abundance in wild-type HAP1 cells and in 9 different HAP1-mutated cell lines as well as upon retinoic acid treatment in wild-type and BAP1 KO cells. Two biological replicated were performed for each condition.

first: Raphaël

first: Michel

last: Wassef


title: Genome-wide maps of chromatin modifications in wild-type or mutant HAP1 cells

summary: Using ChIP-seq, we profiled several histone marks associated with active transcription (H3K4me3) or with Polycomb-mediated silencing (H2AK119ub1 and H3K27me3) in wild-type HAP1 cells and in cells mutated in BAP1, ASXL1, ASXL2, EZH2 and RING1B.

overall_design: Examination of 3 different histone modifications in wild-type HAP1 cells and in 5 different HAP1-mutated cell lines. Two biological replicated were performed for each condition.

last: Margueron


title: BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation

overall_design: Refer to individual Series


title: MICRO-RNA AS BIOMARKERS IN POMPE DISEASE

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

type: Non-coding RNA profiling by high throughput sequencing

summary: We studied microRNAs as potential biomarkers for Pompe disease (PD). We analyzed microRNA expression by small RNA-seq in tissues from the PD mouse model at two different ages (3 and 9 months), and in plasma from 6 PD patients.  In the PD mouse we found 211 microRNAs that were differentially expressed in gastrocnemii and 66 in heart, with a different pattern of expression at different ages. In a preliminary analysis in plasma from 6 PD patients 55 microRNAs were differentially expressed.

overall_design: Plasma miRNA profiles of 6 PD patients and 6 controls were generated by next generation sequencing (NGS).  3 and 9 months-old wild-type (WT) and PD mice were generated in triplicate by NGS

first: Antonietta

last: Tarallo

first: Giancarlo

last: Parenti


title: Differential Effect of Surgical Manipulation on Gene Expression in Normal Breast Tissue and Breast Tumour Tissue

city: odense

first: mads

last: thomassen

address: soender boulevard 29

country: Denmark

institute: odense university hospital

summary: Gene expression profiling is a promising diagnostic and prognostic tool. Expression profiles are snap-shots of mRNA levels at time of extraction and they have been shown to be affected by tissue handling during sample collection. The effect of cold (room temperature) ischemia in the time interval between surgical removal of the specimen and freezing has been described in a number of studies. However, not much is known about the effect of warm (body temperature) ischemia during surgery.

overall_design: Biopsies from normal and tumour tissue were taken in situ immediately after induction of anaesthesia prior to radical mastectomy. All tumours in this study were well defined and easily palpable. Biopsies from normal tissue were taken as far from the tumour as possible.  After surgical excision 4 biopsies were taken ex vivo, 3 from normal and 1 from tumour tissue.

first: Mads

last: Thomassen


title: SNP-ChIP: a versatile and tag-free method to quantify changes in protein binding across the genome

city: New York

first: Andreas

last: Hochwagen

state: New York

address: 100 Washington Square East, 1009 Silver Center

department: Biology

institute: New York University

summary:
SNP-ChIP is a novel method leveraging small-scale intra-species genetic polymorphisms, mainly SNPs, to allow quantitative spike-in normalization of ChIP-seq results. SNP-ChIP uses a different strain of the same organism as the spike-in material and can be applied to any organism for which genome assemblies are available for two different strains or individuals with sufficient genetic diversity. This ensures antibody cross-reactivity and thus extends the applicability of the method beyond the small number of highly conserved proteins. It also ensures complete physiological coherence between the test and the spike-in cells. In this work we develop and validate the method using test cases from budding yeast meiosis. We use strains with ~0.7% genomic sequence divergence as test strain background and the spike-in strain, respectively. Sequencing reads are mapped to a hybrid genome, with naturally occurring sequence polymorphisms allowing assignment of most reads to one of the two genomes. By targeting the yeast chromosomal protein Red1, we show that SNP-ChIP reliably identifies previously reported changes in overall protein levels, irrespective of changes in binding distribution. We also show that SNP-ChIP is robust to wide changes in sequencing depth, as well as the amount of spike-in material. SNP-ChIP allowed discovery of novel regulators of global Red1 protein accumulation and is also shown to allow quantitative analysis of the DNA-damage associated histone modification gamma-H2AX. SNP-ChIP is a robust and versatile spike-in normalization method that can be used with any target against which a ChIP-grade antibody is available and for any organisms with sufficient intra-species diversity, including most model organisms as well as human cells.

Grant ID: FY16-208
Grant title: Meiotic segregation of small chromosomes
Funding source: March of Dimes
Grantee name: Andreas Hochwagen, New York University, New York, NY, United States

overall_design: ChIP-seq analysis of budding yeast strain SK1 spiked with strain S288C 3 hrs after induction of synchronous meiosis.

first: Luis

last: Vale-Silva


title: RNA-seq approach to study the specific effects of SREBF1-depleting antisense oligonucleotide (ASO) reagent in human melanoma cells.

status: Public on Nov 20 2018

city: Charlestown

first: Su

last: Wu

state: MA

address: Building 149 7-330, 13th Street

department: Cancer Center

institute: Mass General Hospital

summary: Purpose: Detailed exploration of de novo Fatty Acid Synthesis (DNFA) transcription regulation and clinical relevance in melanomas. This study was designed to achieve the following goals: 1) determine the impact of SREBP1 depletion on gene expression in metastatic melanoma cells; 2) determine the specificity of ASO and other reagents inhibiting SREBF1 mRNA.  Method: RNA-Seq was performed after culture with control and various SREBF1-depleting agents, including pooled siRNAs and individual ASOs, in HT-144 cells.  Results: using STAR, we mapped about 2 X 4 million pair-end sequence reads per sample to the human genome (build GRCh38.94) and identified around 2 million annotated transcripts per sample.

overall_design: 6 RNA samples (4 technical replicates for each biological sample) were sequenced (paired-end) on a NextSeq® 500 sequencer (Illumina). RNA sequence alignment was performed on the 24 pairs of FASTQ files from the sequence results.


title: GLIS3 Transcriptionally Activates WNT Genes to Promote Differentiation of Human Embryonic Stem Cells to Posterior Neural Progenitors

city: RTP

first: Raja

last: Jothi

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

summary: Anterior-posterior (A-P) specification of the neural tube involves initial acquisition of anterior fate followed by the induction of posterior characteristics in the primitive anterior neuroectoderm. Several morphogens have been implicated in the regulation of A-P neural patterning; however, our understanding of factors regulating these morphogens remains incomplete. Here we show that the Krüppel-like zinc finger transcription factor GLI-Similar 3 (GLIS3) directs differentiation of human embryonic stem cells into posterior neural progenitor cells in lieu of the default anterior pathway. Transcriptomic analyses reveal that this switch in cell fate is due to rapid activation of an autocrine WNT signaling pathway. Mechanistically, through genome-wide RNA-Seq, ChIP-Seq and functional analyses, we show that GLIS3 binds to and directly regulates the transcription of several WNT genes, including the strong posteriorizing factor WNT3A. Inhibition of WNT signaling is sufficient to abrogate GLIS3-induced posterior specification. Altogether, our findings suggest a critical role for GLIS3 in A-P specification through the direct transcriptional activation of WNT genes.

overall_design: We performed ChIP-Seq analysis to map genome-wide occupancy of exogenous, HA-tagged GLIS3 in G3-hESCs(+) after 12 h of NPC induction and employed RNA-Seq to profile global gene expression changes at various time points during G3-hESC to NPC differentiation (0 h, 12 h, 1, 2, 3, and 7 days), in the presence or absence of DOX.

first: Kilsoo

last: Jeon

first: Dhirendra

last: Kumar

first: Amanda

last: Conway

first: Kyeyoon

last: Park

first: Anton

last: Jetten


title: The gene expression profiles of EGFR-mutant SCLC cell lines derived from lung adenocarcinoma patients after failed EGFR-TKI treatment.

city: Taipei

first: CHIH-AN

last: LIN

address: 7F, No. 2, Xuzhou Road

department: Clinical Laboratory Science and Medical Biotechnology

institute: National Taiwan University

summary:
In this study, we established 2 EGFR-mutant SCLC cell lines from lung adenocarcinoma patients after failed EGFR-TKI treatment. These 2 EGFR-mutant SCLC cell lines displayed 2 different phenotypes: suspensive and adherent.
We used microarrays to identify the global gene alterations and molecular basis of  EGFR-mutant SCLC cell lines.

overall_design: The patient-derived EGFR-mutant SCLC cell lines CLH and CLH5 were established   in F medium, and after several passages were adapted to RPMI medium. Both CLH and CLH5 cell lines different phenotypes: suspensive cells (CLH-S and CLH5-S) and adherent cells (CLH-A and CLH5-A). The gene expression profiling of these 4 cell lines were performed by microarray analysis. We tried to compare the gene expression profiles of adherent cells with suspensive cells to identify the specific pathways include tumor growth, metastasis and drug resistance.

first: Chih-An

last: Lin

first: Sung-Liang

last: Yu

first: Chao-Chi

last: Ho


title: scRNA-seq, bulk RNA-seq, and ATAC-seq data from progenitor exhausted and terminally exhausted CD8+ T cells from tumors and chronic viral infection

first: Kevin

last: Bi

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

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


title: 10X single-cell RNASeq profiling of GP33-tetramer+ CD8+ T-cells from mice chronically infected with LCMV Clone 13

summary: Four distinct populations of exhausted CD8+ T-cells occur in chronic LCMV Clone 13 infection

overall_design: Profiling of CD8+ T-cells from mice chronically infected with LCMV Clone 13 (day 28 post-infection)

first: Bi

last: Kevin

first: Miller

last: Brian

first: Al

last: Rose


title: 10X single-cell RNASeq profiling of tumor-infiltrating CD8+ T-cells from B16-OVA mouse melanoma tumors

summary: Distinct populations of progenitor exhausted (Tcf1+Tim-3-) and terminally exhausted (Tcf1-Tim-3+) CD8+ T-cells occur in B16-OVA tumors

overall_design: Profiling of CD8+ T-cells from day 10 and day 20 B16-OVA mouse melanoma tumors


title: A genetic murine model of CLL based on B cell-restricted expression of Sf3b1 mutation and Atm deletion

first: Catherine

address: 450 Brookline Avenue

summary: The RNA splicing factor SF3B1 is recurrently mutated in chronic lymphocytic leukemia (CLL), but its functional role in the pathogenesis of this disease has not been firmly established. Here, we show that conditional expression of heterozygous Sf3b1-K700E mutation in mouse B lineage cells disrupts pre-mRNA splicing, alters B-cell development and function, and induces a state of cellular senescence. B-cell restricted expression of this mutation combined with Atm deletion led to the overcoming of cellular senescence, together with enhanced genome instability and the development of clonal B220+CD5+ CLL cells in elderly mice at low penetrance. Mice with CLL-like disease were found to have amplifications of chromosomes 15 and 17. Integrated transcriptome and proteome analysis of the CLL-like cells revealed coordinated dysregulation of multiple CLL-associated cellular processes. This included an unexpected signature of deregulated B-cell receptor (BCR) signaling, which we could also identify in SF3B1-mutated CLL samples from two independent patient cohorts. Notably, human CLLs harboring SF3B1 mutations exhibited greater sensitivity and altered response kinetics to BTK kinase ibrutinib. Our genetically faithful murine model of CLL thus reveals fresh insights regarding the impact of SF3B1 mutation on CLL pathogenesis and suggests a system for identifying vulnerabilities related to this mutation that can be further exploited for the treatment of CLLs with this common mutation.

overall_design: RNA-seq of B cells from WT, Sf3b1 MT, Atm MT, DM and DM-CLL mice

first: Lili

last: Wang

first: Shanye

last: Yin


title: Telomere-Dependent and Telomere-Independent Roles of RAP1 in Regulating Human Stem Cell Homeostasis

city: Beijing

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

country: China

institute: State Key Laboratory of Stem Cell and Reproductive Biology

summary: RAP1 is well known as a telomere-binding protein; yet its functions in human stem cells remain unclear. Here we generated RAP1-deficient human embryonic stem cells (hESCs) by CRISPR/Cas9 and obtained RAP1-deficient human mesenchymal stem cells (hMSCs) and neural stem cells (hNSCs) via directed differentiation. In both hMSCs and hNSCs, RAP1 negatively regulated telomere length. In addition, RAP1 acted as a transcriptional regulator of RLEN by tuning the methylation status of its promoter region. Phenotypically, RAP1 deficiency resulted in enhanced self-renewal and delayed senescence in hMSCs rather than in hNSCs, suggesting a complex role of RAP1 in regulating lineage specific stem cell homeostasis. Altogether, these results indicate that RAP1 plays both telomeric and non-telomeric roles in regulating the homeostasis of human stem cells.

overall_design: Transcriptomic and WGS analyses of WT and Rap1 deficiency mesenchymal stem cell or neural stem cells.

first: Guanghui


title: A whole lifespan mouse multi-tissue DNA methylation clock

first: Vadim

last: Gladyshev

address: 77 avenue louis pasteur

country: USA

institute: BWH

summary: Age predictors based on DNA methylation levels at a small set of CpG sites, DNAm clocks, have been developed for humans and extended to several other species. Three currently available versions of mouse DNAm clocks were either created for individual tissues or tuned towards young ages. Here, we constructed a robust multi-tissue age predictor based on 435 CpG sites, which covers the entire mouse lifespan and remains unbiased with respect to any particular age group. It can successfully detect the effects of several lifespan-modulating interventions on biological age as well as the rejuvenation effect related to the transition from fibroblasts to iPSCs. We have carried out comparative analyses of available mouse DNAm clocks, which revealed their broad applicability, but also certain limitations to the use of tissue-specific and multi-tissue age predictors. Together, these tools should help address diverse questions in aging research.

overall_design: Examination of DNA methylation (RRBS) in liver, heart, lung and cortex in age groups ranging from 6 months to 30 months

first: Margarita

middle: V

last: Meer

middle: N


title: Heat Shock Factor 1 drives intergenic association of its target gene loci during heat shock

city: Chicago

first: David

last: Pincus

state: IL

institute: University of Chicago

summary:
Transcriptional induction of Heat Shock Protein (HSP) genes in yeast is accompanied by dynamic changes in their 3D structure and spatial organization, yet the molecular basis for these phenomena remains unknown. Using chromosome conformation capture and single cell imaging, we show that genes transcriptionally activated by Heat Shock Factor 1 (Hsf1) specifically interact across chromosomes and coalesce into diffraction-limited intranuclear foci. Genes activated by the alternative stress regulators Msn2 and Msn4, in contrast, do not interact among themselves nor with Hsf1 targets.
Likewise, constitutively expressed genes, even those interposed between HSP genes, show no detectable interaction. Hsf1 forms discrete subnuclear puncta when stressactivated, and these puncta dissolve in concert with transcriptional attenuation, paralleling the kinetics of HSP gene coalescence and dissolution. Nuclear Hsf1 and RNA Pol II are both necessary for intergenic HSP gene interactions, while DNA-bound Hsf1 is necessary and sufficient to drive coalescence of a heterologous gene. Our findings demonstrate that Hsf1 can dynamically restructure the yeast genome.

overall_design:
4 yeast RNA seq samples;
We performed RNA seq coupled Hsf1-AA at 30ºC and following 10' heat shock at 39ºC.  1 µM rapamycin was added for 45 minutes to anchor away Hsf1.


title: TRES2015

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

summary:
Analysis of difference in RNA expression in embryonic striata in two Ebf1 cKO models and littermate controls
The striatum controls behaviors via the activity of direct and indirect pathway projection neurons (dSPN and iSPN) that are intermingled in all compartments. While such cellular mosaic ensures the balanced activity of the two pathways, its origin and pattern of development remains largely unknown. Here, we show that both SPN populations are specified embryonically and intermix progressively through multidirectional iSPN migration. Using conditional mutant mice, we found that inactivation of the dSPN-specific transcription factor Ebf1 impairs selective dSPN properties, including axon pathfinding while molecular and functional features of iSPN were preserved. Ebf1 mutation disrupted iSPN/dSPN intermixing, resulting in an uneven distribution. Such architectural defect was selective of the matrix compartment, highlighting that intermixing is a parallel process to compartment formation. Our study reveals while iSPN/dSPN specification is largely independent, their intermingling emerges from an active migration of iSPN, thereby providing a novel framework for the building of striatal architecture.

overall_design: 3 biological samples (dissected striata obtained from different brains) for each of three experimental conditions (Control, Dlx5/6::Cre;Ebf1fl/-; Islet1Cre;Ebf1fl/-)

first: Andrea

last: Tinterri

first: Sophie

last: Lemoine

first: Fanny

last: Coulpier


title: RNA sequencing with KSHV infection and enrichment for circular RNAs

city: Bethesda

first: Joseph

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

summary: The purpose was to measure expression changes in human and viral circular RNAs.

overall_design: Total RNA was harvested from KSHV-infected HUVEC and MC116 cells. A portion of the RNA was digested with RNase R to enrich for circular RNAs.

first: Shaojian

last: Gao


title: Single-Cell Transcriptome Analysis Reveals Estrogen Signaling Coordinately Augments One-Carbon, Polyamine, and Purine Synthesis in Breast Cancer [II]

city: Macau

first: Edwin

last: Cheung

address: Avenida da Universidade,Taipa

department: faculty of health sciences

institute: University of Macau

summary: Estrogen regulates diverse physiological effects and drives breast tumor progression by directly activating the estrogen receptor α (ERα). However, due to the stochastic nature of gene transcription and the resulting heterogeneous cellular responses, it is important to investigate estrogen-stimulated gene expression profiles at the single-cell level in order to fully understand how ERα regulates transcription in breast cancer cells. In this study, we performed single-cell transcriptome analysis on ERα-positive breast cancer cell lines following 17β-estradiol stimulation. We sequenced a total of 177 single-cell transcriptomes and observed robust gene expression diversity between individual cells.

overall_design: High throughput single-cell RNA sequencing of ER-positive breast cancer cell line MCF7 (SRP159204,PRJNA488528) at 0 or 12 hr following 17β-estradiol stimulation

first: Detu

last: Zhu

first: Zuxianglan

last: Zhao


title: Effects of rFVIIIFc on human macrophages

city: Waltham

first: Katalin

last: Kis-Toth

address: 225 Second Avenue

institute: Bioverativ

summary: Immune responses in hemophilia A patients to replacement factor VIII can be either tolerogenic or immunogenic, the latter resulting in induction of non-neutralizing anti-factor VIII antibodies or neutralizing antibodies called inhibitors. Since these inhibitors render replacement FVIII treatment essentially ineffective, preventing or eliminating them are of top priority in disease management. The extended half-life recombinant factor VIII Fc fusion protein (rFVIIIFc) is an approved therapy for hemophilia A patients. In addition, it has been reported that rFVIIIFc can induce tolerance to FVIII in hemophilia A patients that have developed inhibitors. Given that the IgG1 Fc region has the potential to interact with immune cells expressing Fc receptors and thereby affect the immune response to rFVIII, we investigated how human macrophages, expressing both Fc receptors and receptors reported to bind FVIII, respond to rFVIIIFc. We show herein that rFVIIIFc, but not rFVIII, uniquely skews macrophages towards an alternatively activated regulatory phenotype. rFVIIIFc initiates signaling events that result in morphological changes, as well as a specific gene expression and metabolic profile that is characteristic of the regulatory type Mox/M2-like macrophages. Further, these changes are dependent on rFVIIIFc-Fc receptor interactions. Our findings elucidate mechanisms of potential immunomodulatory properties of rFVIIIFc.

overall_design: Human monocyte-derived macrophages (n=3) were treated with hIgG1, rFVIII or rFVIIIFc for 6h


title: Enhanced PAT-ChIP (EPAT-ChIP), a new procedure for reliable genome-wide studies in clinical FFPE tissues

city: Fano (PU)

first: Stefano

last: Amatori

state: PU

address: Via Arco d'Augusto, 2

department: Biomolecular Sciences

institute: University of Urbino

summary: Chromatin immunoprecipitation (ChIP) has allowed the study of protein-DNA interactions in chromatin, bringing new insights into the role of histone post-translational modifications (HPTMs) in cancer and other diseases. The coupling of ChIP with next-generation sequencing (NGS) techniques has revealed the distribution of HPTMs over the entire genome allowing the identification of altered epigenetic profiles in pathological conditions. However, until recently, these studies have been limited to cultured cells or fresh/frozen tissues. The development of a new technique named PAT-ChIP has enabled chromatin studies in formalin-fixed paraffin-embedded (FFPE) tissues, opening the doors to a huge number of samples stored in pathology archives and related clinical information.  However, chromatin studies in FFPE archival samples can be hindered by the extensive formalin fixation to which these tissues are routinely subjected. Here, we describe enhanced PAT-ChIP (EPAT-ChIP), a new ChIP procedure that facilitates epigenomic studies in archival FFPE tissues. EPAT-ChIP improves the extraction of soluble chromatin, allowing the study of multiple histone marks from limited amounts of starting material. In addition, EPAT-ChIP assures higher yields of final immunoselected DNA, especially when poorly represented histone marks (e.g. narrow peaks of H3K4me3) are investigated, and the consequent production of reliable NGS libraries. In this procedure, FFPE samples are subjected to heat-mediated limited reversal of crosslinking (LRC) which predisposes the tissue to better release soluble chromatin after sonication without altering the antigenic potential of its biomolecules.  After investigating differentially-fixed normal colon specimens specifically produced for this study, ePAT-ChIP was successfully used to study three different HPTMs (H3K4me3, K3K27me3, H3K27ac) at genome-wide level in an archival invasive breast carcinoma (IBC) sample.

overall_design: Our newly designed method EPAT-ChIP was compared with standard PAT-ChIP for validation. Both methods were applied in parallel to the genome-wide study of the low abundant histone mark H3K4me3, known to be associated with active gene promoters, in an archival IBC sample. Then, the comparison between standard PAT-ChIP and EPAT-ChIP was extended to other functionally different histone marks, such as H3K27ac, known to be associated with active promoters and enhancers, and H3K27me3, which characterizes silenced genomic regions.

first: Giuseppe

last: Persico

first: Claudio

last: Paolicelli

first: Roman

last: Hillje

first: Nora

last: Sahnane

first: Francesco

last: Corini

first: Daniela

last: Furlan

first: Lucilla

last: Luzi

first: Saverio

last: Minucci

first: Marco

last: Giorgio

first: Pier Giuseppe

last: Pelicci

first: Mirco

last: Fanelli


title: Activation of a novel ULK1-MLK3-ERK5 pathway by the IFNg receptor is required for IFNg-inducible antiviral responses

first: Diana

last: Saleiro

state: Illinois

address: 303 E. Superior St.

department: Hematology-Oncology

institute: Robert H. Lurie Comprehensive Cancer Center

summary: Although well established that signal transducer and activator of transcription 1 (STAT1) activation is required for an interferon (IFN)-mediated antiviral response, the potential roles of other IFNg-activated cellular pathways in the process are unknown. We provide evidence that Unc-51-like kinase 1 (ULK1) is activated during engagement of the Type II IFN receptor and is required for IFNg-mediated transcription of key interferon stimulated genes involved in anti-viral and innate immune responses.

overall_design: Ulk1/2+/+ and Ulk1/2-/- mouse embryonic fibroblasts (MEFs) were plated as four biological replicates and were either left untreated or were treated for 6 hours with 2.5x103 IU/ml of mouse IFNg, followed by total RNA isolation. Total mRNA profiles of untreated versus IFNg-treated Ulk1/2+/+ and Ulk1/2-/- MEFs were then generated by deep sequencing, using Illumina NextSeq 500.

first: Patrick

last: Ozark

first: Leonidas

last: Platanias


title: Effect of chromatin accessibility due to loss of PIN1

city: PORTLAND

first: Yulong

last: Su

state: OR

address: Oregon Health & Science University CLSB, 4N082, 2730 SW Moody Ave

department: MMG

institute: Oregon Health & Science Univeristy

summary: The goal of this study was to determine the chromatin accessibility difference between WT and PIN1 knockout mouse embryonic fibroblasts.

overall_design: Wildtype and PIN1 knockout MEFs were serum starved for 48 hours, and stimulated 4hrs to induce MYC expression. ATAC-seq were performed on three biological replicates for each condition.

first: Andrew

last: Adey

first: Rosalie

last: Sears


title: Targets and genomic constraints of ectopic Dnmt3b expression

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

summary: DNA methylation plays an essential role in mammalian genomes, hence DNA methyltransferase expression is tightly controlled. Deregulation of the de novo enzyme DNMT3B is frequently observed in many diseases, yet little is known about its ectopic genomic targets. Here we used an inducible transgenic mouse model to identify rules delineating abnormal DNMT3B targeting and explore the constraints of its activity across different cell types. Our results explain the preferential susceptibility of certain CpGs to aberrant methylation and point to transcriptional state and the associated chromatin landscape as the strongest predictors. Although DNA methylation and H3K27me3 are usually antagonistic at CpG islands, H3K27me3 can transiently co-occur with DNMT3B-induced DNA methylation and its depletion has minimal affect on ectopic methylation targets or levels in mouse embryonic fibroblasts. Our multilayered genome-wide data combined with ultra-deep locus-specific bisulfite sequencing suggest a hit-and-run model that induces hypermethylation and provides insights for interpreting the cancer methylome.

overall_design:
To systematically study the impact of Dnmt3b deregulation, we generated ESCs containing a heterozygous inducible Dnmt3b1 construct and derived transgenic mice. We induced ectopic expression of Dnmt3b through doxycycline supplied in drinking water for 1.5 or 3 months and harvested six different tissues (liver, lung, muscle, intestine, kidney, heart) and several blood cell types (B cells, helper T cells, cytotoxic T cells, monocytes, granulocytes) from both induced and control (Dnmt3b1 construct, non-induced) mice.
We also performed ChIP for H3K27me3 and H3K4me3 on control and induced liver tissue from mice treated for 3 months after birth.
To compare our in vivo findings to an in vitro system, we isolated MEFs from E13.5 embryos and performed RNAseq, H3K27me3 ChIP, H3K4me3 ChIP and H3K27me3-ChIP-BS on control and induced MEFs at 1 and 7 days.

Please note that the following processed data files were generated by merging two sample raw (bam) data for CpG calling or peak data;
mouse_mef_control_noshRNA_RRBS.bed (mouse_mef_7day_control_RRBS_r1 and r2)
mouse_mef_dox_noshRNA_RRBS.bed
(mouse_mef_7day_dox_RRBS_r1 and r2)

mouse_mef_7day_control_H3K27me3_ChIP_peaks.txt peak file
(mouse_mef_7day_control_H3K27me3_ChIP_1.bam and _2.bam)
and are linked to the corresponding *_r1 or *_ChIP_1 sample records.

first: Yingying

last: Zhang

first: Rahul

last: Karnik

first: Isabel

last: Beerman

first: Zachary

middle: D

last: Smith

first: Hongcang

last: Gu

last: Boyle

first: Kendell

last: Clement

first: Ramona

last: Pop

first: Andreas

last: Gnirke

first: Derrick

last: Rossi

first: Alexander

last: Meissner


title: Requirement for NF-kB in maintenance of molecular and behavioral circadian rhythms in mice.

first: Heekyung

last: Hong

address: 303 E Superior Street

department: Medicine

institute: Northwestern University

summary:
Purpose: In this study we employed unbiased, genome-wide techniques to investigate how inflammation-induced NF-kB activation by acute (LPS vs. saline) and chronic (high-fat diet vs. regular chow) environmental stimuli leads to circadian disruption.
Methods: We performed ChIP-seq with antibodies directed against the p65 subunit of NF-kB, CLOCK, BMAL1, H3K27Ac and RNA Poll II in livers from mice treated with LPS or saline.  ChIP-seq analysis was also performed in livers from mice that were fed high-fat diet for 4 weeks or regular chow. In addition, we performed ChIP-seq with BMAL1 in mouse embryonic fibroblast deficient in p65.
Results: Induction of NF-kB reconfigures the genome-wide position of core clock transcription factors. Acute (i.e. LPS) and chronic (e.g. high-fat diet) inflammation-induced NF-kB re-localizes components of the forward limb of clock (CLOCK/BMAL1) to sites convergent with NF-kB and acetylated H3K27 and enriched in RNA POL II in liver. In addition, NF-kB activation leads to higher p65 binding specific to E-box elements within the negative limb of the clock with both acute and chronic stimuli.
Conclusions: Our findings cast new light on NF-kB as a pivotal genomic control node integrating metabolic inflammation and circadian systems at both the cellular and organismal levels. In particular, NF-kB directly regulates the expression of the negative limb of the clock while at the same time the clock activator TFs CLOCK/BMAL1 co-localize with NF-kB at new sites to regulate transcription following inflammatory stimuli. In addition, our data indicate significant overlap between NF-kB activation following both acute and chronic inflammatory challenges in liver.

first: Hee-Kyung


title: Loss of the Chr16p11.2 candidate gene QPRT leads to aberrant neuronal differentiation

city: Frankfurt am Main

first: Denise

last: Haslinger

address: Theodor-Stern-Kai 7

institute: University Hospital Frankfurt

summary:
Background: Altered neuronal development is discussed as underlying pathogenic mechanism of Autism Spectrum Disorders (ASD). Copy number variations of 16p11.2 have recurrently been identified in individuals with ASD. Of the 29 genes within this region quinolinate phosphoribosyltransferase (QPRT) showed the strongest regulation during in-vitro neuronal differentiation. We hypothesized a causal relation between this tryptophan related enzyme and neuronal differentiation. We thus analyzed the effect of QPRT on differentiation of a neuronal cell line and specifically focused on neuronal morphology, metabolites of the tryptophan pathway and the neurodevelopmental transcriptome.

Methods: The gene dosage dependent change of QPRT expression following Chr16p11.2 deletion was investigated in a lymphoblastoid cell line (LCL) of a deletion carrier and compared to his non-carrier parents. Expression of QPRT was tested for correlation with neuromorphology in SH-SY5Y cells. QPRT function was inhibited in SH-SY5Y neuroblastoma cells using (i) siRNA knockdown (KD), (ii) chemical inhibition, and (iii) complete CRISPR/Cas9 induced knockout (KO). QPRT-KD cells underwent morphological analysis. Chemically inhibited and QPRT-KO cells were characterized using viability assays. Additionally, QPRT-KO cells underwent metabolite and whole transcriptome analyses. Genes differentially expressed upon KO of QPRT were tested for enrichment in biological processes and co-regulated gene-networks of the human brain.

Results: QPRT expression was reduced in the LCL of the deletion carrier and significantly correlated with neurite maturation in SH-SY5Y cells. The reduction of QPRT altered neuronal morphology of differentiated SH-SY5Y cells. Chemical inhibition as well as complete KO of the gene were lethal upon induction of neuronal differentiation, but not proliferation. The QPRT associated tryptophan pathway was not affected by KO. At the transcriptome level neuronal processes like “synapse organization” were affected. Differentially regulated genes were enriched for ASD-candidates and co-regulated gene networks were implicated in the development of the dorsolateral prefrontal cortex, the hippocampus, and the amygdala.

Conclusions: In this study QPRT was causally related to in vitro neuronal differentiation and affected the regulation of genes and gene-networks that were previously implicated in ASD. Thus, our data suggest that QPRT may play an important role in the pathogenesis of ASD in Chr16p11.2 deletion carriers.

overall_design: MACE (massive analysis of cDNA ends) analysis of 12 samples, consisting of 3 replicates each for SH-SY5Y wild type (WT) cells, 2 different CRISPR/Cas9 induced QPRT knockout cell lines (del268T, ins395A) and cells harbouring the empty control vector (eCtrl) after 3 days of BDNF-RA induced neuronal differentiation.

first: Regina

last: Waltes

first: Afsheen

last: Yousaf

first: Silvia

last: Lindlar

first: Ines

last: Schneider

first: Edwin

last: Lim

first: Meng-Miao

last: Tsai

first: Boyan

last: Garvalov

first: Amparo

last: Acker-Palmer

first: Till

last: Acker

first: Gilles

last: Guillemin

first: Simone

last: Fulda

first: Christine

last: Freitag

last: Chiocchetti


title: Impaired immune surveillance accelerates accumulation of senescent cells and aging [RNA-seq]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science

summary: Cellular senescence is a stress response that imposes stable cell-cycle arrest in damaged cells, preventing their propagation in tissues. However, long-term presence of senescent cells might promote tissue degeneration and malignant transformation via secreted pro-inflammatory and matrix-remodeling factors. These factors lead to immune-cell recruitment and senescent-cell clearance. Senescent cells accumulate in tissues in advanced age. The extent of immune-system involvement in regulating age-related accumulation of senescent cells, and its consequences, are unknown. Here we show that mice with impaired cell cytotoxicity exhibit both higher senescent-cell tissue burden and chronic inflammation. They suffer from multiple age-related disorders and significantly lower survival. Strikingly, pharmacological elimination of senescent-cells by ABT-737 partially alleviates accelerated aging phenotype in these mice. In progeroid mice, impaired cell cytotoxicity further promotes senescent-cell accumulation and shortens lifespan. ABT-737 administration during the second half of life of these progeroid mice abrogates senescence signature and increases median survival. Our findings shed new light on mechanisms governing senescent-cell presence in aging, and could motivate new strategies for regenerative medicine.

overall_design: The experiment focused on 4 tissues: kidney, liver, lung and skin. For each tissue, we had 3 experimental groups: ABT-737 treated, Vehicle treated and Young, with at least 3 biological replicates in each.

first: Yossi

last: Ovadya

first: Tomer

last: Landsberger

first: Hanna

last: Leins

first: Ezra

last: Vadai

first: Hilah

last: Gal

first: Anat

last: Biran

first: Reut

last: Yosef

first: Adi

last: Sagiv

first: Amit

last: Agrawal

first: Alon

last: Shapira

first: Joseph

last: Windheim

first: Michael

last: Tsoory

first: Reinhold

last: Schirmbeck

last: Ido

first: Hartmut

last: Geiger

first: Valery

last: Krizhanovsky


title: Distinct constitutive and pathogen-induced transcriptional programs in dendritic cells derived from CD16- versus CD16+ monocytes

city: Montréal

first: Jean-Philippe

last: Goulet

address: C.P. 6128, succursale Centre-ville

institute: Université de Montréal

summary:
Classical CD16- versus intermediate/non-classical CD16+ monocytes differ in their homing potential and immunological functions; but whether they differentiate into dendritic cells (DC) with distinct contributions to immunity against bacterial/viral pathogens remains poorly investigated. Here, we employed a systems biology approach to identify differences between CD16+ and CD16- monocyte-derived DC (MDDC) with potential clinical relevance
Although both CD16+ and CD16- MDDC acquire classical DC markers in vitro, genome-wide transcriptional profiling revealed unique molecular signatures for CD16+ MDDC, including adhesion molecules (CD103), transcription factors (TCF4), enzymes (ALDH1L2), and chemokines (CCL22).

overall_design: 30 samples. 5 donors x 2 cell populations (CD16+/CD16-) x 3 conditions (media, HIV, LPS)

first: Vanessa

last: Wacleche

first: Amélie

last: Cattin

first: Dominique

last: Gauchat

first: Annie

last: Gosselin

first: Aurélie

last: Cleret-Buhot

first: Yuwei

last: Zhang

first: Cécile

last: Tremblay

first: Jean-Pierre

last: Routy

first: Petronela

last: Ancuta


title: Homolog-selective degradation as a strategy to probe the function of CDK6 in AML

city: Wien

first: Georg

middle: E

last: Winter

state: Austria

address: Lazarettgasse 14, AKH BT25.3

country: Austria

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

summary: The design of selective small-molecules is often stymied by similar ligand binding pockets. Here we report the first cyclin-dependent kinase 6 (CDK6) degrader, BSJ-03-123, that uses phthalimide-conjugation to exploit protein-interface determinants to achieve proteome-wide degradation selectivity.  Pharmacologic CDK6 degradation targets a selective dependency of acute myeloid leukemia cells, and coupling acute degradation with transcriptomics and phosphoproteomics enabled dynamic mapping of the immediate role of CDK6 in coordinating signaling and transcription.

overall_design: RNA-seq of MV4-11 cells treated for 6h with the CDK4/6 inhibitor palbociclib or the CDK6-specific phthalimide conjugates BSJ-03-123 and YKL-06-102

first: Matthias

last: Brand


title: Effect of global MYC DNA binding due to loss of PIN1

first: Yulong

last: Su

summary: The goal of this study was to determine the MYC binding difference between WT and PIN1 knockout mouse embryonic fibroblasts.

overall_design: Wildtype and PIN1 knockout MEFs were serum starved for 48 hours, and stimulated 4hrs to induce MYC expression. DNA IPed from N262 antibody was harvested from 2 independent experimental replicates per genotype.

first: Rosalie

last: Sears


title: Post-translational modification of MYC localizes MYC to the nuclear pore basket to regulate local histone acetylation and gene expression

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

overall_design: Refer to individual Series


title: Genome-wide expression profiling in bladder cancer cells

city: LOS ANGELES

first: MARINA

last: KOUTSIOUMPA

state: CA

address: 650 Charles E. Young Dr South, CHS 33-315

department: MEDICINE

institute: UCLA

summary: Differential gene expression profiling in PPP2R2A depleted RT-112 cells was performed using Human Genome U133 Plus 2.0 Array

overall_design: Expression profiles of RT-112 cells from technical duplicates of control and PPP2R2A-transiently silenced cells by siRNA.

first: Dimitrios

last: Iliopoulos

first: Marina

last: Koutsioumpa


title: Pathway analysis of RNA sequencing of various stages of myodifferentiation identifies conditions favoring type I and type II fibers, and highlights increased efficiency of combined differentiation

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

summary: RNA-Seq of C2C12 cells differentiated for 0, 2, or 7 days using classic myogenic (DM1), adipogenic (DM2), or mixed (DM3) stimulation.

overall_design: Fourteen samples were sequenced: two control samples at day 0 before differentiation was initiated, and 2 at each differentiation condition (DM1/DM2/DM3) at day 2 and day 7. cDNA libraries were constructed using stranded protocol from New England Biolabs. Poly-A selection was used to remove the majority of rRNA from samples. Each library was sequenced with single-end 50 bp reads on HiSeq 2500 sequencer, generating between 25 and 40 million raw reads. Reads were aligned to primary assembly of mouse genome GRCm38 using Gencode vM12 annotation, using STAR v.2.5.1b. Overall alignment rate for each sample was in 95-99% range, with 74-83% of original reads aligning uniquely, and less than 5.5% rRNA contamination. Aligned reads were then quantified using RSEM (v.1.2.31) and analyzed using DESeq2 and fGSEA R packages, as well as MsigDB and Morpheus online tools.

first: Oksana

last: Ivanova

first: Natalia

last: Khromova

first: Artem

last: Kiselev

first: Dmitry

last: Polev

last: Smolina

first: Anna

last: Kostareva

first: Renata

middle: I

last: Dmitrieva


title: Regulatory Discrimination of mRNAs by FMRP Controls Adult Neural Stem Cell Differentiation

city: Worcester

first: Botao

last: Liu

state: Massachusetts

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

summary: Fragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), a translation-inhibitor RNA binding protein. The impact of FMRP-deficiency on neural function is widespread, including its regulation of adult neural stem cell (aNSC) differentiation. To assess FMRP activity, we performed ribosome profiling of aNSCs from normal and Fmr1 knockout mice, which revealed diverse gene expression changes at the mRNA and translation levels. Many mitosis and neurogenesis genes were dysregulated primarily at the mRNA level, while numerous synaptic genes were mostly dysregulated at the translation level. Translational “buffering” was also evident, whereby changes in ribosome association with mRNA is compensated by alterations in RNA abundance. Our data revealed that FMRP-regulated neurogenesis is mediated by the transcriptional factor necdin and that FMRP determines mitochondrial mRNA expression and energy homeostasis. Thus, FMRP controls diverse transcriptional and post-transcriptional gene expression programs critical for the adult neural stem cell differentiation.

overall_design: Ribosome profiling and RNA-seq of wild type (WT) and Fmr1 -/y mouse adult neural stem cells were generated from four biological replicates using Illumina Nextseq.

first: Yue

last: Li

first: Emily

last: Stackpole

first: Xinyu

last: Zhao

first: Joel

last: Richter


title: Transcriptional changes of serum stimulation in mouse embryonic fibroblasts due to loss of PIN1

first: Yulong

last: Su

summary: The goal of this study was to determine the transcriptional difference between WT and PIN1 knockout mouse embryonic fibroblasts.

overall_design: Wildtype and PIN1 knockout MEFs were serum starved for 48 hours, and stimulated 4hrs to induce MYC expression. RNA was harvested from 2 independent experimental replicates per genotype.

last: Sears


title: Functional and transcriptomic basis of enhanced muscle function after denervation-induced paralysis of the mouse whisker pad

status: Public on Nov 19 2018

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: The functional state of denervated muscle is a critical factor in the ability to restore movement after injury- or disease-related paralysis. Here we used peripheral optogenetic stimulation in the mouse whisker system to investigate the time course of changes in nerve and muscle function following facial nerve transection. While most skeletal muscles atrophy after lower motor neuron denervation, optogenetic muscle stimulation of the paralyzed whisker pad revealed sustained increases in the sensitivity, velocity, and amplitude of whisker movements, and reduced fatigability, starting 48 h after denervation. Transcriptome profiling showed distinct regulation of multiple gene families in denervated whisker pad muscles compared to the atrophy-prone soleus, including prominent changes in ion channels and contractile fibers. Together, our results define the functional and transcriptomic landscape of muscle denervation supersensensitivty, and have implications for restoring movement after neuromuscular injury or disease.

overall_design: RNA-seq of intact or lesioned skin and muscle from rostral whisker pad.

first: Thomas

last: Vajtay

first: Akhil

last: Bandi

first: Aman

last: Upadhyay

first: Mavis

middle: R

last: Swerdel

middle: P

first: Christian

last: Lee

first: David

last: Margolis


title: Single cell transcriptomes of replicatively cellular senescenct cells and ionizing radiation induced senescent cells

city: Shanghai

first: Zhiyong

last: Mao

address: 1239 Siping Road

institute: Tongji University

summary: In order to identify the transcriptome change and heterogeneity in replicative senescent cells and stress-induced senescent cells, =we measured 1600 single cell transcriptomes of young quiescent cells at a population doubling (PD) number of 38, middle age quiescent cells (PD = 48), replicative senescent (PD = 71) cells and 50Gy X-ray induced senescent cells of PD38 control cells by Drop-seq.

overall_design: Drop-seq of RS and SIPS cells.

first: Huanyin

last: Tang


title: JunB modulates an IRF4-dependent transcriptional program to regulate homeostasis and suppressive functions of effector regulatory T cells [RNA-Seq]

city: Onna-son,Kunigami-gun

first: Hiroki

last: Ishikawa

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology Graduate University

summary: To understand molecular mechanisms by which JunB regulates Treg function, we performed RNA-seq analysis of JunB-deficient and control Treg cells (CD4+ CD25hi).

overall_design: Gene expresson profiles in WT and JunB-deficient Treg cells.

first: Shin-ichi

last: Koizumi

first: Daiki

last: Sasaki

first: Nana

last: Arakaki

last: Yamasaki


title: JunB modulates an IRF4-dependent transcriptional program to regulate homeostasis and suppressive functions of effector regulatory T cells [ChIP-Seq]

summary: To understand molecular mechanisms by which JunB regulates Treg function, we performed ChIP-seq analysis of JunB-deficient and control Treg cells (CD4+ CD25hi).

overall_design: ChIP-seq analysis of JunB,BATF,IRF4 in in vitro-activated Treg cells.

last: Koziumi


title: JunB modulates an IRF4-dependent transcriptional program to regulate homeostasis and suppressive functions of effector regulatory T cells

summary:
To understand molecular mechanisms by which JunB regulates Treg function, we performed RNA-seq and ChIP-seq analyses of JunB-deficient and control Treg cells (CD4+ CD25hi).

This SuperSeries is composed of the SubSeries listed below.

overall_design:
RNA-seq analysis of WT and JunB-deficient Treg cells.
ChIP-seq analysis of JunB,BATF and IRF4 in in vitro-activated Treg cells.

Refer to individual Series


title: Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations [cHi-C]

city: Berlin

first: Andreas

last: Magg

state: Berlin

address: Ihnestraße 63-73

department: Development and Disease

institute: Max-Planck-Institute for Molecular Genetics

summary: Here we study the effect of balanced chromosomal rearrangements (BCRs) on gene expression in vivo in mouse embryos by generating a series of genomic inversions that place an active enhancer cluster located in the Epha4 regulatory domain at different positions within a neighboring gene dense region. Expression studies in embryonic limb buds show that the inverted enhancer cluster was able to activate several genes downstream of its new position, resulting in gene misexpression and limb phenotypes. Capture Hi-C from mutant limb buds showed that the activated genes were located within a region of asymmetric three-dimensional contacts, so called architectural stripes. Deletion of the CTCF binding site at that position of the stripe anchor resulted in a collapse of the stripes, down regulation of ectopic gene expression, and a rescue of the skeletal phenotype. In cells in which the enhancers are not active, such as mouse embryonic stem cells (mESCs), stripes do not form, indicating that their formation is also dependent on enhancer activity. Based on HiC from limb buds we show that architectural stripes are a frequent feature in the genome often associated with developmentally active enhancers. Thus, BCRs can induce ectopic gene expression via the formation of asymmetric chromatin contacts. The formation of these stripes is dependent on CTCF anchors and enhancer activity.

overall_design: We used Capture Hi-C enriching a 10 Mb region at the Epha4 locus in Mus musculus to study the effects of CRISPR/Cas9-induced inversions on the genomic landscape. We analysed wild type limb buds, mutant limb buds (from five mutants) and one mutant ESC line as singleton (limb buds of 10 embryos for each condition), as it was done in similar studies (See Franke et la., Nature, 2016 or Bianco et al., Nat. Gen. 2018). Embryonic E11.5 forelimb tissue and hindlimb tissue or ESCs were used, respectively.

first: Katerina

last: Kraft

first: Verena

last: Heinrich


title: Serial Inversions Induce Tissue-specific Architectural Stripes, Gene Misexpression and Congenital Malformations [ChIP-seq]

overall_design: We used ChIP-seq to identify the binding profiles of key players for genomic architecture (CTCF and Rad21/cohesin) in Inv1 and Inv1DelCTCF mutants which were used for detailed analysis of architectural stripes. Moreover, in wild type limb buds ChIP-seq for H3K9me3 was performed in order to locate marks for heterochromatin which was later implemented into the EpiCSeg algorhithm (Mammana and Chung, 2015). For each condition (WT, Inv1, Inv1DelCTCF), limb buds of 10 embryos (Embryonic stage E11.5) or 10 million cells (Inv1) were used, respectively.