title: CXCR5+PD-1+CD8+ T cells are a distinct sublineage of CD8+ Tfh cells and Stat5 suppresses the expression of the Tfh-specific genes in CXCR5+PD-1+CD8+  T cells  [RNA-Seq]

first: Robert

last: Burns

summary: Many autoimmune diseases are characterized by the production of autoantibodies. The current view is that CD4+ Tfh cells are the main subset regulating autoreactive B cells. Here, we discover a novel CXCR5+PD1+ Tfh subset of CD8+ T cells whose development and function are negatively regulated by Stat5. These CD8+ Tfh cells regulate the GC B cell response and control autoantibody production. Deficiency of Stat5 in CD8+ T cells leads to an increase of CD8+ Tfh cells, resulting in the breakdown of B cell tolerance and autoantibody production. CD8+ Tfh cells share similar gene signatures with CD4+ Tfh cells and require CD40L/CD40 and TCR/MHCI interactions to deliver help to B cells. Our study highlights the diversity of follicular T cell subsets that contribute to the breakdown of B-cell tolerance

overall_design: Splenic CXCR5-PD-1-CD8+, CXCR5+PD-1-CD8+, CXCR5+PD-1+CD8+ T cells were sorted from LCMV-infected  Stat5+/+CD8Cre and Stat5fl/-CD8Cre mice (Armstrong, day8)  or from Stat5fl/-CD8CreIgHELsHEL mice, and subjected to RNA-seq analysis. Each genotype had 3 mice.

first: Yuhong

last: Chen

first: Mei

first: Yongwei

last: Zheng

first: Renren

last: Wen

first: Demin

last: Wang


title: Expression profile (nanoCAGE-seq), chromatin accessibility (ATAC-seq) profile, and histone modification profile (ChIP-seq for H3K4me3, H3K9me3, and H3K27me3) during the course of mouse gonocyte development

status: Public on Aug 29 2019

city: Shinjuku-ku

first: Haruhiko

last: Siomi

state: Tokyo

address: Shinanomachi 35

department: Department of Molecular Biology

country: Japan

institute: Keio University, School of Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

summary: How de novo DNA methylation over heterochromatin is introduced in mouse gonocyte remains obscure. We performed nanoCAGE-seq, ChIP-seq for three major histone marks (H3K4me3, H3K9me3, H3K27me3), ATAC-seq, Hi-C during the course of mouse gonocyte development (E13.5, E17.5, E19.5, P2)

overall_design: The FACS-sorted Mvh-Venus cells from E13.5, E17.5, E19.5, or P2, are used as starting material. Using each sample, ATAC-seq, ChIP-seq, and Hi-C library preparation was performed in duplicate. For nanoCAGE-seq analysis, the experiments were done in triplicate. All DNA libraries were sequenced by Illumina MiSeq or HiSeq.

first: Soichiro

last: Yamanaka


title: Targets mediated microRNA arm-imbalance promotes gastric cancer progression [lncRNA]

status: Public on Aug 25 2019

city: Beijing

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

country: China

institute: Peking Union Medical College

summary: Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression.   Conclusion: Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy.  Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression.   Conclusion: Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy.  Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression. Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy.

overall_design: IBA57-AS1, KLRC2 were overexpressed in MGC-803 cells, S100A1 and TMEM54 were knocked down in MGC-803 cells using siRNAs, and then lncRNA sequencing was conducted

first: Zhengyi

last: Zhang

first: Jingnan

last: Pi

first: Dongling

last: Zou

first: Xiaoshuang

first: Jiayue

last: Xu

first: Yanni

last: Ma

first: Dong

first: Jia

last: Yu


title: A Novel PI3K Regulator, ARID4B, Presents Synthetic Essentiality in PTEN-deficient Prostate Cancer [RNA-seq]

status: Public on Aug 23 2019

city: Miami

first: Karoline

last: Briegel

state: FL

address: 1600 NW 10th Ave

department: Surgery

country: USA

institute: University of Miami

summary: Phosphatase and tensin homologue (PTEN) is the most frequently mutated tumor suppressor gene in human prostate cancer. Synthetic essentiality is defined as cancer that harbors a specific tumor suppressor deficiency is dependent on synthetic-essential genes for the malignant phenotypes. Recently, targeting such synthetic-essential genes has become an attractive treatment approach for cancers that acquire loss-of-function mutations in tumor suppressor genes. Here, we show that AT-rich interaction domain 4B (ARID4B) functions as a synthetic-essential gene in prostate tumorigenesis driven by PTEN deficiency. This functional interaction between ARID4B and PTEN is recapitulated in the mouse model carrying prostate-specific deletions of Pten and Arid4b in which ablation of ARID4B attenuated prostate cancer progression elicited by loss of PTEN. Although the tumor suppressor function of PTEN is most attributed to its lipid phosphatase activity that counters the PI3K action in cytoplasm, we identified the PTEN-ARID4B-PI3K axis in which nuclear PTEN inhibits expression of ARID4B, while ARID4B serves as a transcriptional activator of the PI3K subunits PIK3CA and PIK3R2 to trigger the PI3K/AKT pathway. Our study further demonstrated that the reciprocal binding of ARID4B and histone H1 to the PIK3CA and PIK3R2 promoters modulates chromatin condensation, indicating a mechanism by which ARID4B activates these promoters. Finally, a three-gene signature consisting of PTEN, ARID4B, and PI3K substantially improves the predictive power for tumor recurrence in human prostate cancer patients, underscoring the clinical significance of this newly identified PTEN-ARID4B-PI3K axis. These findings reveal a novel synthetic-essential relationship between ARID4B and PTEN, thus exposing a previously unidentified cancer-specific vulnerability, and supporting ARID4B as a potential therapeutic target for prostate cancer patients with PTEN mutations.

overall_design: mRNA profiles of  control and ARID4B siRNA knockdown PC3 cells were generated by RNA sequencing

first: Ray

last: -Chang Wu

first: In-Chi

last: Young

first: Yu-Fang

last: Chang

first: Sung-Ting

last: Chuang

first: Antoun

last: Tougaji

first: Mei-Yi

last: Wu


title: Deconvolution of melanoma transcriptomes and miRNomes by independent component analysis

city: Luxembourg

first: Arnaud

last: Muller

address: 84 Val Fleuri

department: DONC

country: Luxembourg

institute: LIH

summary: The repositories for various “omics” data collected from different cancer types are constantly growing. However, robust diagnostic and/or prognostic conclusions can often not be extracted from mixed transcriptomes or other heterogenous datasets obtained from large cohorts as important signals or single features can be masked. Here, computational microdissection of bulk transcriptome data was applied to gain insights into patient prognosis and to investigate important processes and cell subtypes within new samples in silico. We developed parallel consensus ICA that decomposes many whole transcriptomes into independent signals (components), some of which originated from distinct cell subtypes while others accounted for technical biases. We show that the weight of components allows for prediction of clinically relevant patient characteristics, which was further validated on an independent patient cohort. Moreover, ICA components can be linked to biological functions, thus new samples could be classified by presence of respective biological properties such as immune signals, angiogenic activity and proliferation. Finally, through integration of different data types (transcriptomes and miRNomes) by ICA, biological functions of miRNAs were deduced, which would otherwise not be possible. Taken together, ICA represents a versatile tool to dissect complex data cohorts into individual components allowing for better use of such datasets.

overall_design: 1 cell line (NHEM) and 4 biopsies have been submitted for RNA-Seq. Biopsies correspond to 3 different patients caraterized as primary melanoma tumor. Additionally, one matched normal skin has been used as control.

first: Petr

middle: V

last: Nazarov

first: Anke

middle: K

last: Wienecke-Baldacchino

first: Andrei

last: Zinovyev

first: Urszula

last: Czerwińska

first: Dorothée

last: Nashan

first: Gunnar

last: Dittmar

first: Francisco

last: Azuaje

first: Stephanie

last: Kreis


title: Gene expression profiling of wing imaginal disc upon caspase activity inhibition

status: Public on Aug 22 2019

city: Bunkyo-ku

first: Natsuki

last: Shinoda

address: 7-3-1 Hongo

department: Department of Genetics, Faculty of Pharmaceutical Sciences

institute: The University of Tokyo

summary: Caspase is best known as an enzyme involved in programmed cell death that is conserved in multicellular organisms. In addition to its role in cell death, caspase is emerging as an indispensable enzyme for a wide range of cellular functions, which have recently been termed as Caspase-Dependent non-lethal cellular Processes. We carefully examined the involvement of cell death signaling in tissue size determination using Drosophila wing as a model. We found that executioner caspase activity promoted wing growth independent of apoptosis. To identify the gene expression changes which account for the observed phenomena, we performed microarray analysis of wing imaginal disc upon caspase activity-inhibition by overexpressing p35. The analysis revealed the change in overall transcriptome, but not in the major tissue growth promoting signaling pathways.

overall_design: We collected total RNA from wing imaginal discs of wandering 3rd larvae. We used C10 > p35 larvae for caspase activity-inhibited group and C10 > GFP and C10 >LacZ larvae for control groups. N = 5 for each group.

first: Masayuki

last: Miura


title: Targets mediated microRNA arm-imbalance promotes gastric cancer progression [miRNA]

first: Xu

last: yue

type: Non-coding RNA profiling by high throughput sequencing

summary: Two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, were reversely expressed and played exact opposite role in gastric cancer progression. miR-574-5p/-3p ratio was also strongly correlated with higher TNM stages and shorter survival of patients. The increase of miR-574-5p/-3p ratio, or the arm-imbalance of miR-574 was due to the dynamic expression of their highly complementary targets in gastric carcinogenesis. The arm imbalance of miR-574 in turn strongly contributed to and further promoted gastric cancer progression.   Conclusion: Our findings indicated that targets mediated miR-574 arm-imbalance contributed to gastric cancer progression. Re-modification of the miR-574-targets homeostasis may represent a realistic approach for gastric cancer prevention and therapy.

overall_design: The four highly complementary targets of miR-574-5p/3p, including IBA57-AS1, KLRC2, S100A1 and TMEM54, were overexpressed in MGC-803 cells and then small RNA sequencing was conducted

first: Zhengyi

last: Zhang

first: Jingnan

last: Pi

first: Dongling

last: Zou

first: Xiaoshuang

last: Wang

first: Jiayue

last: Xu

first: Yanni

last: Ma

first: Dong

first: Jia

last: Yu


title: Comprehensive landscape of active deubiquitinating enzymes profiled by advanced chemoproteomics

status: Public on Aug 31 2019

city: Oxford

first: Ping

address: Roosevelt Drive

department: Ludwig Institute for Cancer Research

country: United Kingdom

institute: University of Oxford

summary: Enzymes that bind and process ubiquitin, a small 76 amino acid protein, have been recognized as pharmacological targets in oncology, immunological disorders and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition of the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation and more potent/selective ubiquitin active-site probes with propargyl based electrophiles to profile 74 DUBs including distinguishable isoforms for five DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents, pan-DUB inhibitors ubiquitin combined with probe labelling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry, demonstrating that USP13, 39 and USP40 are non-reactive to probe, reflecting no, low or restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small molecule DUB selectivity profiling.

overall_design: Transcriptome profiling in MCF7 cells

first: Adán

last: Pinto-Fernández

first: Simo

last: Davis

first: Abigail

middle: B

last: Schofield

first: Hannah

middle: C

last: Scott

first: Eidarus

last: Salah

first: Sebastian

last: Mathea

first: Philip

middle: D

last: Charles

first: Andreas

last: Damianou

first: Gareth

middle: L

last: Bond

first: Roman

last: Fischer

first: Benedikt

middle: M

last: Kessler


title: A Novel PI3K Regulator, ARID4B, Presents Synthetic Essentiality in PTEN-deficient Prostate Cancer

first: Karoline

last: Briegel

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

overall_design: Refer to individual Series


title: Mitochondrial Calcium Exchange links Metabolism with the Epigenome to Control Cellular Differentiation

city: Philadelphia

first: Andrew

last: Gibb

state: PA

address: 3500 N. Broad St.

institute: Temple University


title: Genome wide maps of ELK1 bingding sites in HDFs control and mechanic loading groups.

status: Public on Aug 27 2019

city: Shanghai

first: Gao

last: Ya

state: Shanghai

address: Zhizaoju road No.639

department: School of medicine

institute: Shanghai Jiao Tong University

summary: HDFs  were cultured for 24 hrs for adhesion and to reach 50-70% confluence before mechanical tension was applied. Cyclic mechanical stretch (CMS) with a 0.5-Hz sinusoidal curve at 10-20% elongation was applied using a Flexcell○RFX-5000TM Tension System  during the stretching. Cells were harvested immediately after the application of CMS stimulation was completed. Control cells were cultured on the same plates in the same incubator with no stretching.

overall_design: Examination of ELK1's different bind motifs of HDFs in the control condition and mechanic loading condition.

first: Ya

last: Gao

first: Yifang

last: Zhang

first: Qingfeng

last: Li


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

status: Public on Aug 21 2019

city: Strasbourg

first: Isabelle

last: Caldelari

address: rue René Descartes

country: France

institute: CNRS

summary: The human opportunistic pathogen Staphylococcus aureus produces numerous small regulatory RNAs (sRNAs) for which functions are still poorly understood. Here, we focused on an atypical and large sRNA called RsaC. Its length varies between different isolates due to the presence of repeated sequences at the 5’ end while its 3’ part is structurally independent and highly conserved. Using MS2-affinity purification coupled with RNA sequencing (MAPS) and quantitative differential proteomics, we identified sodA mRNA as a main target of RsaC sRNA. SodA is a Mn-dependent superoxide dismutase involved in oxidative stress response. We demonstrated that in presence of RsaC, S. aureus cells were less resistant to oxidative stress, in relation with lower activity of SodA enzyme. Remarkably, rsaC gene is co-transcribed with the major manganese ABC transporter MntABC and, consequently, RsaC is mainly produced in response to Mn starvation. This 3’UTR-derived sRNA is released from mntABC-RsaC precursor after cleavage by RNase III. By blocking the Mn-containing enzyme SodA synthesis, RsaC favors oxidative stress response mediated by SodM, an alternative SOD enzyme using either Mn or Fe as co-factor. Thus, RsaC may balance two interconnected defensive responses (i.e. against oxidative stress and manganese starvation) when S. aureus faces host immune cells.

overall_design: Affinity purification of in vivo regulatory complexes coupled with high throughput RNA sequencing methodology or MAPS, standing for “MS2 affinity purification coupled with RNA"

first: Arnaud

last: Tomasini

first: Stefano

last: Marzi

first: David

last: Lalaouna

first: Pascale

last: Romby


title: A Novel PI3K Regulator, ARID4B, Presents Synthetic Essentiality in PTEN-deficient Prostate Cancer [ChIP-seq]

overall_design: PC3 cells were used for ChIP, library preparation, sequencing, and initial data analysis. ChIP assays were performed using the anti-ARID4B antibody. Input DNA was used for control.

first: Ray-Chang

last: Wu

first: In-Chi

last: Young

first: Yu-Fang

last: Chang

first: Sung-Ting

last: Chuang

first: Antoun

last: Tougaji

first: Mei-Yi


title: Transcriptional Regulation and Mechanism of SigN (ZpdN), a pBS32 encoded Sigma Factor

city: Bloomington

first: Daniel

last: Kearns

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

summary: Laboratory strains of Bacillus subtilis encodes as many as 16 alternative sigma factors, each dedicated to expressing a unique regulon such as those involved in stress resistance, sporulation, and motility. The ancestral strain of B. subtilis also encodes an additional sigma factor homolog, ZpdN, not found in lab strains due to it being encoded on the large, low copy number plasmid pBS32 that was lost during domestication. DNA damage triggers pBS32 hyper-replication and cell death in a manner that depends on ZpdN but how ZpdN mediates these effects was unknown. Here we show that ZpdN is a bona fide sigma factor that can direct RNA polymerase to transcribe ZpdN-dependent genes and we rename ZpdN to SigN accordingly. Rend-seq analysis was used to determine the SigN regulon on pBS32, and the 5’ ends of transcripts were used to predict the SigN consensus sequence. Finally, we characterize the regulation of SigN itself, and show that it is transcribed by at least three promoters: PsigN1, a strong SigA-dependent LexA-repressed promoter, PsigN2, a weak SigA-dependent constitutive promoter, and PsigN3, a SigN-dependent promoter. Thus, in response to DNA damage LexA is derepressed, SigN is expressed and then experiences positive feedback. How cells die in a pBS32-dependent manner remains unknown, but we predict that death is the product of expressing one or more genes in the SigN regulon.

sample_organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

overall_design: RNA-seq of WT with and without 2hMMC, ZpdN mutant with 2hrMMC and zpdN overexpression

first: Aisha

last: Burton

first: Aaron

last: DeLoughery

first: Gene-Wei


title: Mitochondrial Calcium Exchange links Metabolism with the Epigenome to Control Cellular Differentiation (RNA-seq)

first: Andrew

last: Gibb

summary: Fibroblast to myofibroblast differentiation is crucial for the initial healing response but excessive myofibroblast activation leads to pathological fibrosis. Therefore, it is imperative to understand the mechanisms underlying myofibroblast formation. Here we report that mitochondrial calcium (mCa2+) signaling is a regulatory mechanism in myofibroblast differentiation and fibrosis. We demonstrate that inhibition of mCa2+ uptake in fibroblasts enhances myofibroblast formation and this translates to increased fibrosis following injury. Fibrotic signaling alters the gating of the mitochondrial calcium uniporter (mtCU) to reduce mCa2+ uptake and induce specific changes in metabolism. mCa2+-dependent metabolic reprogramming leads to the activation of αKG-dependent demethylases which epigenetically modify promoter regions specific to the myofibroblast gene program resulting in differentiation. Our results uncover an important role for mCa2+ uptake beyond metabolic regulation and cell death and demonstrate that mCa2+ signaling regulates the epigenome to influence cellular differentiation.

overall_design: Examination of transcriptional changes associated with myofibroblast differentiation

first: Alyssa

middle: A

last: Lombardi

first: John

middle: W

last: Elrod


title: Mitochondrial Calcium Exchange links Metabolism with the Epigenome to Control Cellular Differentiation (ATAC-seq)

overall_design: Examination of changes in chromatin accessibliity associated with myofibroblast differentiation


title: Discrete WT1-positive hepatic fibrogenic cell lineages of distinct developmental mesothelial origin are paradoxically inhibited by WT1

city: Edinburgh

first: Timothy

middle: James

last: Kendall

address: Crewe Road

department: MRC Human Genetics Unit

institute: University of Edinburgh

summary: Activated hepatic stellate cells orchestrate scar formation during fibrotic liver injury. Recent evidence has shown limited quiescent precursor derivation from the mesoderm during development. Here, we use lineage-tracing from development, through adult homeostasis, to adult fibrotic injury, to show that discreet subpopulations of activated hepatic stellate cells are defined by expression of WT1, a transcription factor controlling morphological transitions in organogenesis and adult homeostasis. Morphologically and transcriptionally distinct subpopulations are evident in fibrotic human disease and animal models. Populations defined by WT1 expression after injury derive from a discreet population of quiescent adult precursors originating from the embryonic mesothelium. WT1-deletion permits morphological transition to an enhanced fibrotic myofibroblast phenotype. Our findings demonstrate functional heterogeneity of adult scar-forming cells that can be whole-life traced back through specific quiescent precursors in adult homeostasis to differential origin in development, and defines WT1 as a paradoxical anti-fibrotic regulator during adult injury.

overall_design: RNA profiles of hepatic stellate cells, quiescent after embryological lineage labelling or activated by in vivo carbon tetrachloride injury under condition of WT1 deletion using PDGFRbCre, were generated by deep sequencing

middle: J

first: Stuart

last: Aitken


title: High-fat diet fuels prostate cancer progression by rewiring the metabolome and amplifying the MYC program

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Systemic metabolic alterations associated with increased consumption of saturated fat and obesity are linked with increased risk of prostate cancer progression and mortality but the molecular underpinnings of this association are poorly understood. Furthermore, the mechanisms by which metabolic rewiring alters the prostate cancer epigenome, the effector arm of intra- and extra-cellular signals, is equally nebulous. Here, we demonstrate, in a murine prostate cancer model, that high-fat diet (HFD) enhances the MYC transcriptional program through metabolic alterations that favour histone H4K20 hypomethylation at the promoter regions of MYC regulated genes, leading to a HFD-dependent phenotype characterized by increased cellular proliferation and tumour burden. Importantly, these results are recapitulated in prostate cancer patients, where increased saturated fat intake (SFI), but not monounsaturated or polyunsaturated fat intake, is also associated with an enhanced MYC transcriptional signature. Additionally, the SFI-induced MYC signature independently predicts prostate cancer progression and death. Finally, a dietary intervention consisting of switching from a high-fat to control diet, greatly attenuates the MYC transcriptional program. Our findings suggest that in primary prostate cancer, dietary saturated fat intake contributes to tumour progression by mimicking MYC over expression, setting the stage for therapeutic approaches involving changes to the diet.

overall_design: RNA-Seq for WT and MYC mice fed CTD or HFD

first: David

middle: P

last: Labbé

first: Giorgia

last: Zadra

first: Massimo

last: Loda

first: Myles

last: Brown


title: Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

type: Methylation profiling by high throughput sequencing


overall_design: ChIP-Seq for H4K20me1 and PHF8 of WT and MYC mice fed CTD or HFD


title: MET regulates expression of co-stimulatory and co-inhibitory molecules in tumor cells and contributes to suppression of immune cell function

status: Public on Aug 20 2019

city: Seoul

first: Sehui

last: Kim

address: 101, Daehak-ro Jongno-gu

department: Pathology

country: South Korea

institute: Seoul National University

summary: MET-altered human cancer cell lines including Hs746T (MET-mutated/amplified), H596 (MET-mutated) and H1993 (MET-amplified) cells were used. In microarray analysis, MET suppression using MET inhibitor or siRNAs up-regulated variable co-stimulatory molecules, including 4-1BBL, OX40L and CD70, and down-regulated variable co-inhibitory molecules. Among co-inhibitory molecules, PD-L1 was one of the most markedly down-regulated genes by MET suppression, which was validated at the mRNA and total/surface protein levels in Hs746T and H1993 cells. Consistently, MET activation by HGF treatment increased PD-L1 expression in H596 cells. Co-culture of human peripheral blood mononuclear cells (PBMC) with Hs746T cells suppressed IFNg production from PBMC, which was restored by an MET inhibitor or PD-L1 blockade. A significant positive correlation between MET and PD-L1 expression was observed in The Cancer Genome Atlas (TCGA) analysis for variable cancer types and immunohistochemistry for lung cancer. MET overexpression in PD-L1-high tumor exhibited decreased expressions of T-cell effector molecules in TCGA analysis for lung cancer. In summary, MET overexpression/activation is related to immunosuppressive phenotype and is involved in immune escape of tumor by PD-L1 up-regulation. MET-targeted therapy combined with immunotherapy could be a potential therapeutic strategy in MET-dependent cancer.

overall_design: Gene expression of Hs746T cell line: DMSO (control) versus PHA665752 (MET inhibitor), scramble siRNA (control) versus MET siRNA (MET knockdown), total 4 samples

first: Hyun

last: Ahn

first: Dohee

last: Kwon

first: Jaemoon

last: Koh

first: Young

first: Kwangsoo

first: Doo

last: Chung

first: Yoon

last: Jeon


title: mouse normal lung epithelial cell single cell RNA-seq

city: los angeles

first: Changfu

last: Yao

state: Ca

address: 8700 Beverly Blvd. AHSP Room A9401

department: Lung and Regenerative Medicine Institutes

institute: cedars-sinai medical center

summary: Single cell RNA-seq profiling adult mouse lung epithelial cells reveals the heterogeneity of mouse lung epithelium.

overall_design: Single cell RNA-seq using 10x chromium system on two batches adult mouse lung epithlial cells isolated from 2 female and 2 male each batch

first: Barry

last: Stripp


title: Rhythmic chromatin interactions with lamin B1 in liver reflect stochasticity in variable lamina-associated domains during the circadian cycle

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

summary:
Purpose: Many mammalian genes exhibit circadian expression patterns concordant with periodic binding of transcription factors, chromatin modifications and chromosomal interactions. We determined whether lamina-associated domains (LADs) display oscillatory circadian patterns of interaction with nuclear lamin B1 during hte circadian cycle, and identified any relationship to changes in gene expression patterns in oscillatory LADs or in their vinicity.
Methods: To this end, we mapped LADs by  chromatin immunoprecipitation-sequencing (ChIP-seq) of lamin B1 (LMNB1) (antibody ab16048, Abcam) from mouse livers colected every 6 h, for 30 h, after entrainment of the circadian clock by 24-h fasting and refeeding.  Gene expression profiles were also analyzed by RNA-sequencing (RNA-seq) at the same time points.
Results and Conclusions: We report periodic interactions of chromatin domains with nuclear lamin B1, suggesting rhythmic associations of fractions of the genome with the nuclear lamina. Entrainment of the circadian clock by fasting and refeeding is accompanied in mouse liver by a gain of lamin-chromatin interactions followed by oscillations in these interactions at hundreds of lamina-associated domains (LADs). A subset of these oscillations exhibit periodicity and affect one or both LAD borders or entire stand-alone LADs. Periodic LADs are however not a dominant feature of these variable LADs, as most LADs are conserved during the circadian cycle. LAD oscillations are for the most part asynchronous between the 5’ and 3’ ends of LADs. Periodic LADs also uncoupled from gene expression patterns, periodic or not, within or in vicinity of these LADs. Accordingly, periodic genes, including central clock-control genes, are located megabases away from LADs, suggesting their residence in a transcriptionally permissive environment throughout the circadian cycle. Our data suggest autonomous oscillatory associations of fractions of the genome with the nuclear lamina, providing new evidence for rhythmic spatial configurations of chromatin. However, our data also argue that periodic LADs constitute a minor fraction of variable LADs, and reflect stochasticity in variable lamin-chromatin interactions during the circadian cycle.

overall_design: Lamin B1 ChIP-seq analysis (2 biological replicates, i.e. 2 mice) and RNA-seq analysis (3 biological replicates; 3 mice) of the livers collected from wild-type C57Bl/6 male mice as follows: non-synchronized (NS) mice,  18 h before entrainment of the circadian clock, and mice at the following time points after entrainment of the clock by 24-h fasting and refeeding ad lib: circadian time zero (CT0), CT12, CT18, CT24 and CT30. Seven mice were sacrified aat each time point, livers were collected, partitioned and snap-frozen in liquid nitrogen. For LMNB1 ChIL-seq, ChIP DNA was purified by phenolchloroform extraction and ethanol precipitation, before Illumina library preparation at our sequencing facility on an Illumina HiSeq2500. For RNA-seq, total RNA was isolated from 3 replicates using the RNeasy Mini Kit (Qiagen). DNase treatment was done with RQ1 RNase-Free DNase (M101, Promega) and libraries were prepared and sequenced on an Illumina HiSeq2500.

first: Annaël

last: Brunet

first: Frida

last: Forsberg


title: Transcriptomic-based functional characterization of adverse events following lymphatic filariasis treatment

city: St. Louis

first: Britt

middle: Juul

last: Andersen

state: MO

address: 4444 Forest Park Blvd.

institute: Washington University

summary:
Intro: Lymphatic filariasis (LF) is a neglected tropical disease caused by the nematode parasite Wuchereria bancrofti. The primary tool used by the Global Program to Eliminate LF is mass drug administration (MDA), and some 500 million people take the medications each year. Mild to moderate adverse events (AEs) are common after LF treatment, and these pose a challenge for the LF elimination program. To better understand the pathogenesis of AEs, we studied patients from a LF treatment trial in Côte d’Ivoire.
Method: Total RNA was extracted from peripheral blood leukocytes collected before and 24h after treatment (when AEs peak). Global RNA sequencing was performed for 9 individuals with systemic moderate AEs and for 9 matched controls without AEs. Differential gene expression analysis (DESeq) identified transcriptional signatures (TS) associated with post-treatment AEs.
Results: Out of the 36 sequenced samples, the 9 post-treatment samples from subjects with AEs had a distinct TS (P=0.006 by clustering analysis); 744 genes were significantly upregulated in this group (post vs pre-treatment, paired). These genes were enriched for many biological pathways that included pro-inflammatory pathways such as TLR and NF-kappa B signaling. Genes upregulated in AEs were also significantly enriched for having STAT1/2/3 transcription factor binding sites indicating the importance for interferons in the AEs pathogenesis.

overall_design: A total of 38 samples were sequenced (pre and post-treatment samples from 19 individuals. Ten of the individuals had adverse events (Aes) (9 with moderate Aes and 1 with mild Aes), and 9 individuals had no Aes. 16 samples were sequenced on HiSeq2000, and 22 samples were sequenced on HiSeq4000 (Illumina TruSeq Stranded Total RNA)

first: Bruce

last: Rosa


title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [GRO-Seq]

status: Public on Aug 19 2019

first: Frederick

last: Alt

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

summary: RAG endonuclease initiates IgH locus (Igh) V(D)J assembly in progenitor (pro)-B cells by joining Ds to JHs, before joining upstream VHs to DJH intermediates.  In mouse pro-B cells, the CTCF-binding element (CBE)-anchored chromatin loop domain at the 3’end of Igh contains an internal sub-domain spanning the 5’CBE anchor (IGCR1), the DHs, and a RAG-bound recombination center (RC).  The RC comprises JH-proximal D (DQ52), 4 JHs, and the intronic enhancer (“iEmu”).  Robust RAG cleavage is restricted to paired V(D)J segments flanked by complementary recombination signal sequences (12RSSs and 23RSSs). Ds are flanked downstream and upstream by 12RSSs that, respectively, mediate deletional joining with convergently-oriented JH-23RSSs and VH-23RSSs. Despite 12/23 compatibility, inversional D to JH joining via upstream D-12RSSs is rare.  Plasmid-based assays attributed lack of inversional D to JH joining to sequence-based preference for downstream D-12RSSs, as opposed to putative linear scanning mechanisms.  Given recent findings that RAG linearly scans convergent CBE-anchored chromatin loops, potentially formed by cohesin-mediated loop extrusion, we revisited a scanning role.  Here, we report that JH-23RSS chromosomal orientation programs RC-bound RAG to linearly scan upstream chromatin in the 3’Igh sub-domain for convergently-oriented D-12RSSs and, thereby, to mediate deletional joining of all Ds, except RC-based DQ52 that joins by a diffusion-related mechanism.  In a DQ52-based RC, formed in the absence of JHs, RAG bound by the downstream DQ52-RSS scans the downstream constant region exon-containing 3’Igh sub-domain in which scanning can be impeded by targeted nuclease-dead Cas9 (dCas9) binding, by transcription through repetitive Igh switch sequences, and by the 3’Igh CBE-based loop anchor. Notably, each scanning impediment focally increases RAG activity on potential substrate sequences within the impeded region.  High resolution mapping of RC chromatin interactions reveals that such focal RAG targeting is associated with corresponding impediments to the loop extrusion process that drives chromatin past RC-bound RAG.

overall_design: We performed GRO-Seq in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion-mediated RAG scanning in IgH V(D)J recombination.

first: Yu

last: Zhang

first: Xuefei


title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination

type: Genome variation profiling by high throughput sequencing

overall_design: We performed HTGTS V(D)J-seq, 3C-HTGTS, GRO-Seq, ChIP-Seq and Hi-C in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion-mediated RAG scanning in IgH V(D)J recombination.


title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [3C-HTGTS]

overall_design: We performed 3C-HTGTS using IgH intronic enhancer as bait in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion-mediated RAG scanning in IgH V(D)J recombination.


title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [HTGTS V(D)J-seq]

overall_design: We performed HTGTS V(D)J-seq in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion-mediated RAG scanning in IgH V(D)J recombination.


title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [ChIP-Seq]

overall_design: We performed RAD21 and NIPBL ChIP-Seq in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion mediated-RAG scanning in IgH V(D)J recombination.

first: Zhuoyi

last: Liang


title: The Fundamental Role of Chromatin Loop Extrusion in Physiological V(D)J Recombination [Hi-C]

overall_design: We performed Hi-C in v-Abl transformed pro-B cells to study roles of chromatin loop extrusion-mediated RAG scanning in IgH V(D)J recombination.

first: Muhammad

middle: S

last: Shamim

first: Aviva

last: Presser Aiden

first: Erez

last: Lieberman Aiden


title: The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A)-translation

city: Mainz

first: Petra

last: Beli

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology (IMB)

summary: Human cells have evolved quality control mechanisms to ensure protein homeostasis by detecting and degrading aberrant mRNAs and protein products. A common source of aberrant mRNAs is premature polyadenylation, which can result in non-functional protein products. Translating ribosomes that encounter poly(A) sequences are terminally stalled, followed by ribosome recycling and rapid decay of the truncated nascent polypeptide via the ribosome-associated quality control (RQC). Here, we demonstrate that the conserved RNA-binding E3 ubiquitin ligase Makorin Ring Finger Protein 1 (MKRN1) promotes ribosome stalling at continuous A-tracts during RQC. Using individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP), we show that MKRN1 is positioned upstream of A-rich stretches and poly(A) tails in mRNAs through an interaction with the cytoplasmic poly(A)-binding protein (PABP). Ubiquitin remnant profiling uncovered PABP and ribosomal protein RPS10 as well as additional translational regulators as main substrates of MRKN1. We propose that MKRN1 serves as a first line of poly(A) recognition at the mRNA level to prevent production of erroneous proteins, thus maintaining proteome integrity.

overall_design: iCLIP experiments for GFP-MKRN1 with crosslinking at 254 nm and with 4SU and crosslinking at 365 nm

first: Andrea

last: Hildebrandt


title: Unified Feature Association Networks through Integration of Transcriptomic and Proteomic Data

status: Public on Aug 18 2019

city: Richland

first: Ryan

last: McClure

state: Washington

address: 11829272 Battelle for the US DOE, 790 6th Street

department: Microbiology

institute: Pacific Northwest National Laboratory

summary: Transcriptomic and proteomic data from human cells infected with Dengue virus was used to infer a number of networks to determine which network inference methods were best for linking protiens and transcripts in the same network.  GENIE3, a random forest method, was found to be the best and once inferred with this method networks were interrogated to gain knowledge regarding host pathogen interactions surrounding Dengue infection.

overall_design: Human U-937 cells were incubated with Dengue viral strains for varying amounts of time before both transcriptomic and proteomic data was collected.  Networks were inferred with 10 methods and methods were ranked by their ability to link proteins and transcripts as well as their accuracy in grouping transcripts and proteins of similar functions together.

first: Brooke

last: Kaiser

first: Ralph

last: Baric

first: Joshua

last: Adkins

first: Katrina

last: Waters

first: Jason

last: McDermott


title: JC Polyomavirus Infection of Primary Human Renal Epithelial Cells Is Controlled by a Type I IFN-Induced Response

status: Public on Aug 15 2019

city: Providence

first: Walter

last: Atwood

address: 70 Ship Street

institute: Brown University

summary: JC polyomavirus (JCPyV) established a persistent infection, but BK polyomavirus (BKPyV) killed the cells in 15 days. To identify the cellular factors responsible for controlling JCPyV infection and promoting viral persistence, we profiled the transcriptomes of JCPyV- and BKPyV-infected cells at several time points postinfection. We found that  interferon-stimulated genes (ISGs) were only activated in the JCPyV and not in the BKPyV-infected cells.

overall_design: Primary Human Renal Epithelial cells were either not infected or infected with JC polyomavirus or BK polyomavirus. Three time points were tested: 3 days, 6 days and 9 days post infection. Three independent replicates were analyzed per condition. Total RNA was harvested, and a stranded RNAseq 2x50 bp was performed using Illumina techonology by Beckman Coulter Genomics

first: Benedetta

last: Assetta


title: Small non-coding RNA transcriptome of four high-altitude vertebrates and their low-altitude relatives

city: Chengdu

first: Yao

last: Ma

state: Sichuan

address: Huiming road #211

institute: Sichuan Agricultural University

summary:
Purpose:  The goal of this study was to compare the microRNA transcriptomes of four high-altitude vertebrates and their low-altitude relatives for six organs (heart,liver,spleen,lung,kidney and muscle).
Methods: Three adult females for each population of the five species from distinct altitudes (600 m, 2000 m, and 3000 m) were  humanely killed to ameliorate suffering. A piece of tissue fragments from six organs including heart, liver, spleen, lung, kidney and skeletal muscle(longissimus muscle for pig, cattle, yak and sheep, and pectoral muscle for chicken) were used to extract total RNA. Small RNA libraries were constructed using the Illumina TruSeq Small RNA Sample Prep kit and sequenced on the Illumina HiSeq 2500. The raw data were submitted to miRDeep2.0 to detect miRNAs for each species with default parameters.
Results: we detected 2,036 mature miRNAs in five species and identified 49 orthologues among vertebrate, 111 orthologues in artiodactyla and 171 orthologues in ruminant .
Conclusions:  We identified comparable numbers of miRNAs in each species.

sample_organism:
Gallus gallus
Sus scrofa
Bos taurus
Ovis aries
Bos grunniens

overall_design: Six organs (heart,liver,spleen,lung,kidney and muscle) miRNA profiles of four high-altitude vertebrates and their low-altitude relatives were generated by deep sequencing, in triplicate using Illumina Hiseq2500 .


title: Expression of miRNAs in ovarian cancer recurrence

city: Tainan

first: Chia-Hao

last: Tung

address: 138 Shengli Road

country: Taiwan

institute: National Cheng Kung University

summary: Recurrence is the major cause of treatment failure in patients with ovarian cancer. The purpose of this study is to identify novel miRNAs contributing to ovarian cancer recurrence.

platform_organism:
Primates
Homo sapiens

overall_design: The total RNA extracted from three pairs of primary and recurrent tumor tissues from two patients were used for miRNA microarray analysis.

first: Yuh-Ling

last: Chen

first: Tse-Ming

last: Hong


title: Transcriptomic analysis of Brassica oleracea challenged with Xanthomonas campestris pv. campestris

city: Pontevedra

first: Maria

last: Tortosa

state: Galicia

address: Pazo de Salcedo nº8

country: Spain

institute: Mision Biologica de Galicia (MBG-CSIC)

summary: We investigated  the transcriptome dynamics of Brassica oleracea in response to Xcc race 1 infection at 3 and 12 days after inoculation by using Massive Analysis of 3′-cDNA Ends (MACE) technology

overall_design: Three biological replicates of leaves from control and inoculated plants were analysed 3 and 12 days after the inoculation with Xantomonas campestris pv. Campestris (Xcc) race 1 (a total of 12 samples).

first: María

first: Víctor

last: Rodríguez


title: The nuclear receptor REV-ERBa modulates Th17 cell differentiation and function by competing with RORgt

status: Public on Aug 16 2019

city: La Jolla

first: Ruth

middle: T

last: Yu

state: CA

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

summary: T helper 17 (Th17) cells produce interleukin-17 (IL-17) cytokines and drive inflammatory responses in autoimmune diseases such as multiple sclerosis and rheumatoid arthritis. The differentiation of Th17 cells is dependent on the retinoic acid receptor-related orphan nuclear receptor RORgt. Here we identify REV-ERBa (encoded by Nr1d1), a member of the nuclear hormone receptor family (NHR), as a transcriptional repressor that antagonizes RORgt function in Th17 cells. REV-ERBa binds to ROR response elements (RORE) in Th17 cells and inhibits the expression of RORgt-dependent genes such as Il17a and Il17f. Furthermore, elevated REV-ERBa expression or treatment with a synthetic REV-ERB agonist significantly delays the onset and impedes the progression of experimental autoimmune encephalomyelitis (EAE), a Th17 cell-mediated autoimmune disease. These results suggest that modulating REV-ERB activity may hold therapeutic potential for treatment of Th17 cell-mediated autoimmune diseases.

overall_design: Identification of REVERBalpha binding sites in mouse Th17 cells.

first: Ye

last: Zheng


title: Maternal obesity alters neurotrophin-associated MAPK ignaling in the hypothalamus of male mouse offspring

city: Cologne

first: Eva

last: Hucklenbruch-Rother

state: North rhine Westphalia

address: Robert Straße 14, Gebäude 44a

department: Department of Pediatric and Adolescent Medicine

institute: University Hospital of Cologne

summary: In the present project we examined the effects of maternal obesity to offspring hypothalamic tissue at postnatal day (P) 21. Maternal obesity has emerged as an important risk factor for the development of metabolic disorders in the offspring.To obtain an overview of affected genes in the offsprings hypothalamus, the center of hunger and satiety in the brain, we performed whole genome microarray expression profiling. Female mice were fed either a control diet (SD) or a high fat diet (HFD) after weaning until mating and during pregnancy and gestation. On P21, male pups were sacrificed and blood samples were collected for further analyses. The hypothalamus was cut immediately caudal to the optic chiasm. The dissection was limited laterally by the hypothalamic sulci and dorsally by the mammillothalamic tract. Hypothalamic tissue was immediately frozen at −80° C. A maximum of two offspring per dam were analysed to minimize litter-dependent bias. All studies were performed using male offspring.

overall_design: Microarray experiments of mice hypothalamic RNA were performed as single-color experiments using 4_44K Mouse (v2) Whole Genome Arrays from Agilent Technologies (Santa Clara, CA). First, differentially expressed genes between the CO group and HFD group, were identified using the Rank Product test. Genes were called significant with a percentage false positive below 0.001. All statistical calculations were performed using R version 3.1.2 and Bioconductor. Functional Annotation Clustering was performed by DAVID Bioinformatics Resources (http://david 6.7.abcc.ncifcrf.gov/home.jsp).

first: Andre

last: Oberthuer

first: Inga

last: Bae-Gartz


title: RNASeq of bone lining niche cell components from myeloma-bearing mice treated daily with small molecule LDN193189 (LDN) or vehicle control

status: Public on Aug 14 2019

city: Oxford

first: Sarah

last: Gooding

state: Oxon

address: John Radcliffe Site, Headley Way

department: Weatherall Institute of Molecular Medicine

institute: Oxford University

summary: We compare gene expression in FACS-sorted bone lining cell components (stromal progenitors, osteoprogenitors, endothelial cells) from LDN193189 vs. vehicle-treated myeloma-bearing mice, and in myeloma cells flushed from the central marrow vs. myeloma cells digested from the bone-lining niche. The myeloma model used is the murine 5TGM1 cell line injected into immunocompetent KaLwRij mice. LDN193189 is a type 1 BMP receptor inhibitor.

overall_design: Comparative gene expression differences in 100-cell aliquots of sorted bone marrow niche or myeloma cell types. N = 4 - 8 biological replicates per cell type (from different mice) per condition (LDN or vehicle treated).

first: S

first: E

last: Repapi


title: DC3: Deconvolution and coupled clustering from bulk and single cell genomics data

city: Stanford

first: Zhana

last: Duren

address: 318 Campus Drive

institute: Stanford university

summary: HiChIP data generated for the retinoic acid-induced mESC differentiation at day 4.

overall_design: We introduce DC3 (for De-Convolution and Coupled-Clustering) as a method for the joint analysis of bulk HiChIP, scRNA-seq and scATAC-seq data from the same heterogeneous cell population.

first: Wanwen

last: Zeng

first: Xi

first: Yong

last: Wang

first: Rui

last: Jiang

first: Wing

last: Wong


title: Transcriptomic analysis of Clec12A-deficient BMDCs stimulated with RIG-I agonist

city: Los Angeles

first: Kai

last: Li

address: 8700 Beverly Boulevard

institute: Cedar-Sinai Medical Center

summary: Innate  immune receptors rely on the detection of diverse immunological cues and intensive crosstalk to generate context-dependent responses. The inhibitory C-type lectin receptor Clec12A has been shown to sense dead cells and danger-associated molecule uric acid crystal, and to subsequently limit inflammation. However, whether Clec12A plays additional roles in innate immunity has not yet been determined. Here we demonstrate that the activation of Clec12A enhances the induction of type I interferon (IFN-I) response. Through integrating data from RNA-seq, gene set enrichment analysis, and biochemical studies, we show that Clec12A is required for optimal transcription of interferon-stimulated genes in response to pattern recognition receptors (e.g. RIG-I) activation.

overall_design: BMDCs generated from 4 WT and 4 Clec12A deficient mice were untreated, or stimualted with 3pRNA alone, or costimulated with 3pRNA and MSU crystals. The RNA were extracted from those cells and  analysed by RNA-sequencing.

first: Jürgen

last: Ruland


title: RNASeq of bone lining niche cell components from healthy vs. myeloma-bearing mice

summary: We compare gene expression in FACS-sorted bone-lining cell components: stromal progenitors, osteoprogenitors and endothelial cells, from myeloma-bearing vs. from healthy mice, and also between myeloma cells flushed from the central bone marrow vs. myeloma cells digested from the bone surface (myeloma-bearing mice only). The myeloma model used is the 5TGM1 murine myeloma cell line, injected into immunocompetent KaLwRij mice.

overall_design: Comparative gene expression differences in 100-cell aliquots of sorted bone marrow niche cell types. N = 4 or 5 biological replicates per cell type (from different mice) per condition (healthy or myeloma-bearing).


title: Transcriptomic profiling of the myeloma bone-lining niche identifies BMP signalling as a target for bone disease

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

overall_design: Refer to individual Series


title: RNA degradomes reveal substrates and importance for dark and nitrogen stress responses of Arabidopsis XRN4

status: Public on Aug 13 2019

city: Newark

first: Pamela

last: Green

state: DE

address: 15 Innovation Way

department: Plant and Soil Sciences

institute: Delaware Biotechnology Institute

summary:
Application of Parallel Analysis of RNA Ends (PARE), an RNA degradome approach to identify substrates of Arabidopsis XRN4. The xrn4 mutants overaccumulate decay intermediates from multiple mRNA turnover pathways.
This material is based on work supported by the National Science Foundation [under Grant Numbers MCB1021636 and MCB1817764 to P.J.G.]

overall_design: Examination of polyA+ and polyA- profiles in WT and xrn4 mutants of Arabidopsis, using PARE and RNA-seq

first: Vinay

last: Nagarajan


title: Discovery and Characterization of a Cellular Potent Positive Allosteric Modulator of the Polycomb Repressive Complex 1 Chromodomain, CBX7

first: Oliver

last: Bell

state: CALIFORNIA

address: 1450 Biggy Street

department: Biochemistry and Molecular Medicine

institute: Keck School of Medicine of the University of Southern California

summary: Polycomb-directed repression of gene expression is frequently misregulated in human diseases. A quantitative and target-specific cellular assay was utilized to discover the first potent positive allosteric modulator (PAM) peptidomimetic, UNC4976, of nucleic acid binding by CBX7, a chromodomain methyl-lysine reader of Polycomb repressive complex 1. The PAM activity of UNC4976 resulted in enhanced efficacy across three orthogonal cellular assays by simultaneously antagonizing H3K27me3-specific recruitment of CBX7 to target genes while increasing non-specific binding to DNA and RNA. PAM activity thereby reequilibrates PRC1 away from H3K27me3 target regions. Together, our discovery and characterization of UNC4976 not only revealed the most cellularly potent PRC1-specific chemical probe to date, but also uncovers a potential mechanism of Polycomb regulation with implications for non-histone lysine methylated interaction partners.

overall_design: Mouse embryonic stem cells (mESCs) were treated with peptidomimetic CBX7 antagonists or control compound for 4 hours and the impact on genomic PRC1 binding and histone modification was analysed by ChIP-seq.

first: Daniel

last: Bsteh


title: Epigenome analysis of pediatric glioma

status: Public on Aug 12 2019

city: Toronto

first: Cynthia

last: Hawkins

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

summary: Genome wide methylation profiling of pediatric low-grade glioma samples (n=151). The Illumina Infinium HumanMethylation850 BeadChip was used (under manufacturer guidelines) to obtain DNA methylation signatures. Samples were exclusively tumors specimen and no normal tissue was included in this analysis.

overall_design: DNA was  bisulphite converted and hybridized to the Illumina Infinium HumanMethylation850 BeadChip.

first: Uri

last: Tabori

first: Ana

last: Stucklin

first: Scott

last: Ryall


title: Extracellular RNA in a single droplet of human serum reflects physiologic and disease states

first: Sheng

last: Zhong

address: 9500 Gilman Dr

institute: UCSD

summary: We developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to efficiently sequence both integral and fragmented cfRNAs from a small droplet (5-7 microliters) of liquid biopsy. We carried out SILVER-seq on more than 150 serum droplets from male and female donors ranging from 19 to 48 years of age. SILVER-seq detected cfRNAs from more than a quarter of the human genes, including small RNAs and fragments of mRNAs and long non-coding RNAs (lincRNAs).

overall_design: 128 different samples, consisting of 32 samples from self-reported non-breast-cancer donors, 28 samples from cancer recurrence donors and 68 samples from cancer non-recurrence donors, were constructed to mols-seq libraries for cancer-normal and recurrence-nonrecurrence study.

first: Zixu

last: Zhou


title: Ageing affects DNA methylation and transcriptional cell-to-cell variability in muscle stem cells [scRNA-seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

summary: Age-related tissue alterations have been associated with a decline in stem cell number and function. Increased cell-to-cell variability in transcription or epigenetic marks has been proposed to be a major hallmark of ageing. Here, using parallel single-cell transcriptome and DNA methylome profiling, we find a global increase of uncoordinated transcriptional heterogeneity and context-dependent alterations of DNA methylation heterogeneity in ageing mouse muscle stem cells. Importantly, promoters with increased methylation heterogeneity are associated with increased transcriptional heterogeneity of the genes they drive. Notably, old cells diverging from young cells revealed alterations in the transcription of multiple extracellular matrix related genes. These findings show linked increases in heterogeneity between the epigenome and the transcriptome, with attendant degradation of coherent transcriptional networks and stem cell functional decline during ageing.

overall_design: 5 young and 3 old mice.

first: Irene

last: Hernando-Herraez

first: Brendan

last: Evano

first: Thomas

last: Stubbs

first: Pierre

middle: H

last: Commere

first: Stephen

last: Clark

first: Shahragim

last: Tajbakhsh

first: Wolf

last: Reik


title: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [CUT&RUN]

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

summary: Many of the regulatory features governing erythrocyte specification, maturation, and associated disorders remain enigmatic. To identify new regulators of erythropoiesis, we performed a functional genomic screen for genes affecting expression of the erythroid marker CD235a/GYPA. Among validating hits were genes coding for the N6-methyladenosine (m6A) mRNA methyltransferase (MTase) complex, including, METTL14, METTL3, and WTAP.  We found that m6A MTase activity promotes erythroid gene expression programs through selective translation of ~300 m6A marked mRNAs, including those coding for SETD histone methyltransferases, ribosomal components, and polyA RNA binding proteins, and novel genes. Remarkably, loss of m6A marks resulted in dramatic loss of H3K4me3 marks across key erythroid-specific KLF1 transcriptional targets (e.g., Heme biosynthesis genes). Further, each m6A MTase subunit and a subset of their mRNAs targets are required for human erythroid specification in primary bone-marrow derived progenitors. Thus, m6A mRNA marks promote the translation of a network of genes required for human erythropoiesis.

overall_design: Contains 3 NTC control HEL CUT&RUN samples and 2 METTL3, METTL14, and WTAP CRISPR KO HEL CUT&RUN samples.

last: Kuppers

first: Yiting

last: Lim

first: Andrea

first: Lucas

last: Carter

first: Philip

last: Corrin

first: Christopher

last: Plaisier

first: Ryan

last: Basom

first: Jeffrey

last: Delrow

first: Shiyan

last: Wang

first: Housheng

last: He

first: Beverly

last: Torok-Storb

first: Andrew

last: Hsieh

first: Patrick

last: Paddison


title: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [crispr]

overall_design: Contains 3 Day0 samples representing the initial representation of the ZhangV2 whole genome CRISPR library, 7 Day 12 endpoint samples with all surviving cells, 7 Day 12 endpoint samples enriched for CD235a low or negative cells

first: Daniel


title: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [RNA-Seq]

overall_design: series of gene KOs


title: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [MeRIP-seq]

overall_design: Contains  input control poly-A RNAseq samples and  m6A IP poly-A RNA samples

first: D

first: S

first: Y

first: A

first: L

first: P

first: C

first: R

first: J

first: H

first: B

first: AC


title: Human induced pluripotent stem cell-derived vocal fold mucosa mimics development and responses to smoke exposure

status: Public on Aug 09 2019

city: Madison

first: Ziyue

state: WI

address: 425 Henry Mall

institute: UW Madison

summary: Development of treatments for vocal dysphonia has been inhibited by lack of human vocal fold (VF) mucosa models because of difficulty in procuring VF epithelial cells, epithelial cells’ limited proliferative capacity and absence of cell lines. We report development of engineered VF mucosae from hiPSC, transfected via TALEN constructs for green fluorescent protein, that mimic development of VF epithelial cells in utero. Modulation of FGF signaling achieves stratified squamous epithelium from definitive and anterior foregut derived cultures. Robust culturing of these cells on collagen-fibroblast constructs produces three-dimensional models comparable to in vivo VF mucosa. Second, we demonstrate mucosal inflammation upon exposure of these constructs to 5% cigarette smoke extract. Upregulation of pro-inflammatory genes in epithelium and fibroblasts leads to aberrant VF mucosa remodeling. Collectively, our results demonstrate that hiPSC-derived VF mucosa is a versatile tool for future investigation of genetic and molecular mechanisms underlying epithelium-fibroblasts interactions in health and disease.

overall_design: Comppared mRNA profiles of 4 samples from human primary vocal fold (VF) epithelial cell with 4 samples from human induced pluripotent stem cell derived vocal fold basal progenitors (iPScell-derived VBPs)

first: Vlasta

last: Lungova


title: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis

first: Sonali


title: A Pandas complex adapted for piRNA-guided transposon silencing (CLIP-seq)

city: Beijing

first: Ming

state: Beijing

address: #15 Datun Road, Chaoyang, Beijing 100101, China

department: Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: The repression of transposons by the Piwi-interacting RNA (piRNA) pathway is essential to protect animal germ cells. In Drosophila ovaries, Panoramix (Panx) enforces transcriptional silencing by binding to the target-engaged Piwi-piRNA complex, although the precise mechanisms by which this occur remain elusive. Here, we show that Panx functions together with a germline specific paralogue of a nuclear export factor, dNxf2, and its cofactor dNxt1 (p15) as a ternary complex to suppress transposon expression. Structural and functional analysis demonstrate that dNxf2 binds Panx via its UBA domain and play an important role in transposon silencing through binding to transposon transcripts directly. Unexpectedly, dNxf2 interacts directly with dNxf1 (TAP), which is also essential for transposon silencing. Transient tethering of dNxf2 to nascent transcripts leads to their nuclear retention. Therefore, we propose that dNxf2 may function as a Pandas (Panoramix dNxf2 dependent TAP/p15 silencing) complex, which counteracts the canonical RNA exporting machinery (TAP/p15) and restricts transposons to nuclear peripheries. Our finding may have broader implications for understanding how RNA metabolism modulates epigenetic gene silencing and heterochromatin formation.

overall_design: GoldCLIP applied to characterize the dNxf2 binding RNAs from OSC cell line knockdown of mael (comparing to LacZ knockdown).

first: Kang

last: Zhao

first: Sha

last: Cheng

last: Miao

first: Ping

last: Xu

first: Xiaohua

last: Lu

first: Yuhan

last: Zhang

first: Xuan

last: Ouyang

first: Xun

last: Yuan

first: Weiwei

last: Liu

first: Xin

first: Peng

last: Zhou

first: Jiaqi

last: Gu

first: Yiqun

first: Ding

last: Qiu

first: Zhaohui

last: Jin

first: Chen

last: Su

first: Chao

last: Peng

first: Jian-Hua

first: Meng-Qiu

last: Dong

first: Youzhong

last: Wan

first: Jinbiao

last: Ma

first: Hong

first: Ying

last: Huang

first: Yang

last: Yu


title: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis[Ribosome Profiling]

first: Sonali

last: Arora

overall_design: Contains three replicates of ribosome protected RNA samples and total input RNA from non-targeting control sgRNA HEL cells and WTAP sgRNA KO HEL cells

first: Daniel

last: Kuppers

first: Yiting

last: Lim

first: Andrea

first: Lucas

last: Carter

first: Philip

last: Corrin

first: Christopher

last: Plaisier

first: Ryan

last: Basom

first: Jeffrey

last: Delrow

first: Shiyan

last: Wang

first: Housheng

last: He

first: Beverly

last: Torok-Storb

first: Andrew

last: Hsieh

first: Patrick

last: Paddison


title: Precise temporal regulation of Dux is important for embryo development

status: Public on Aug 07 2019

city: Shanghai

first: Mingyue

last: Guo

address: Siping

department: School of Life science and technology

institute: Tongji University


title: Tet inactivation disrupts YY1 binding and long-range chromatin interactions to cause developmental defects in embryonic heart

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: Tet-mediated DNA methylation oxidation plays an important role in shaping the epigenetic landscapes and chromatin accessibility during gene expression. While several studies demonstrated pivotal roles of Tet proteins in regulating embryonic development, little is known about their functions in heart development. Here we systemetically analyzed DNA methylation and hydroxymethylation dynamics during early cardiac development in both human and mice. We discovered that cardiac-specific deletion of Tet2 and Tet3 in mice (Tet2/3-DKO) led to ventricular non-compaction cardiomyopathy (NCC) with embryonic lethality. Single-cell and bulk RNA-seq analyses revealed dramatic decrease of cardiomyocytes in Tet2/3-DKO heart tissues. Impaired DNA demethylation and chromatin accessibility in Tet2/3-DKO mice further compromised chromatin association of a key transcription factor, Ying-yang1 (YY1), and reduced long-range promoter-enhancer interactions at key genes involved in cardiac development. Taken together, our studies establish the physiological role of Tet proteins in the regulation of DNA methylation dynamics and chromatin configuration during embryonic heart development in mammals.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: In this study, we systematically investigated the DNA methylation and hydroxymethylation dynamics during early cardiac development in both human and mice. Furthermore, we generated a cardiac specific Tet2 and Tet3 double deficient mouse model to investigate the function of Tet-mediated DNA modifications during early cardiac development. These mice developed severe developmental defects in the ventricular wall reminiscent of non-compaction cardiomyopathy (NCC). With this disease-relevant in vivo model, we further unveiled previously-unrecognized roles of Tet-mediated DNA hydroxymethylation in regulating chromatin accessibility to facilitate the genomic recruitment of one key transcription factor, Ying-Yang 1 (YY1). More excitingly, our study uncovered a crucial role of Tet/5hmC in modulating chromatin long-range interactions to coordinate higher-order chromatin organization during embryonic heart development.

first: Yun

first: Deqiang

last: Sun

first: James

middle: F

last: Martin


title: RNAseq analysis of dormant cells

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

summary:
We report the application of ssequencing technology for high-throughput profiling of hypoxia cell in the yeast Cryptococcus neoformans.
Our study represents the first detailed analysis of yeast transcriptomes in hypoxia 8 d compated with normoxia 8 d, stationnary phase and logarithmic phase, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA profiles in hypoxia.

sample_organism:
Saccharomyces cerevisiae
Cryptococcus neoformans

overall_design: Examination of hypoxia condition in one cell type and 4 different experimental conditions

first: Aude

last: Leclère

first: Alexandre

last: Alanio


title: A Pandas complex adapted for piRNA-guided transposon silencing (RNA-seq)

first: Ming

overall_design: Examination of transcriptome from dNxf2 mutant comparing to dNxf2 heterogygous with panx tethered to FL10B tethered, and Panx mutant comparing to Panx heterogygous with dNxf2 tethered to FL10B from Drosophila ovaries.

first: Kang

last: Zhao

first: Sha

last: Cheng

last: Miao

first: Ping

last: Xu

first: Xiaohua

last: Lu

first: Yuhan

last: Zhang

first: Xuan

last: Ouyang

first: Xun

last: Yuan

first: Weiwei

last: Liu

first: Xin

first: Peng

last: Zhou

first: Jiaqi

last: Gu

first: Yiqun

first: Ding

last: Qiu

first: Zhaohui

last: Jin

first: Chen

last: Su

first: Chao

last: Peng

first: Jian-Hua

first: Meng-Qiu

last: Dong

first: Youzhong

last: Wan

first: Jinbiao

last: Ma

first: Hong

first: Ying

last: Huang

first: Yang

last: Yu


title: Single cell RNA-Seq of Proliferative (NMU-O-P) and Differentiated (NMU-O-D) Normal Mouse Urothelium Organoids

status: Public on Aug 06 2019

city: Madrid

first: Jaime

last: Martinez de Villarreal

state: Madrid

address: Melchor Fernández Almagro, 3

department: Molecular Oncology Programme

institute: CNIO

summary: Single cell RNA-seq was performed in Proliferative (n = 6826) and Differentiated (n = 4896) Normal Mouse Urothelium  Organoids to get insight into the differentiation program activated in both conditions.

overall_design: scRNA-Seq of NMU-O-P and NMU-O-D organoids.

first: Catarina

last: Pereira Santos

last: Martinez Villarreal

first: FX

last: Real


title: Calcineurin promotes myogenic gene expression

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: We identified four major temporal patterns of Calcineurin (Cn)-dependent gene expression in differentiating myoblasts and determined that Cn is broadly required for the activation of the myogenic gene expression program. Cn promotes gene expression through direct binding to myogenic promoter sequences and facilitating the binding of BRG1 and other SWI/SNF subunit proteins as well as the binding of MyoD, a critical lineage determinant for skeletal muscle differentiation. We conclude that the Cn phosphatase directly impacts the expression of myogenic genes by promoting ATP-dependent chromatin remodeling and formation of transcription-competent promoters.

overall_design: Gene expression profiles of C2C12 cells treated with DMSO or FK506 at four time points growth, 0h, 24h, 72h in differentiation.

first: Jumpei

last: Nogami

first: Kazumitsu

last: Maehara

first: Anthony

middle: N

last: Imbalzano


title: Nuclear receptor RORγ is a targetable master regulator of cholesterol in a subtype of breast cancer

status: Public on Aug 04 2019

city: Sacramento

first: Demin

last: Cai

institute: UC Davis

overall_design: Refer to individual Series


title: A Pandas complex adapted for piRNA-guided transposon silencing and heterochromatin formation

first: Ming

last: Wang


title: The intestinal microbiota regulate neuronal function and fear extinction learning

status: Public on Aug 05 2019

first: Hattie

last: Chung

address: 415 Main St

institute: Broad Institute

summary: Assessing gene expression changes in the medial prefrontal cortex of adult mice associated with antibiotic treatment

overall_design: Single nucleus RNA sequencing of medial prefrontal cortex isolated from 4 adult mice (two treated with antibiotics, two control)

first: Aviv

last: Regev

first: Coco

last: Chu

first: David

last: Artis


title: Metabolic regulation of gene expression by histone lactylation

city: Chicago

first: Di

last: Zhang

state: IL

address: 929 E 57th GCIS, W403R

institute: the University of Chicago

summary: Cancer-augmented lactogenesis has been described by the Warburg effect, and is associated with several major hallmarks of neoplasia. However, the non-metabolic functions of elevated lactate in physiology and disease remain unknown. Here we report histone lysine lactylation as a new type of epigenetic mechanism and as a functional destination for lactate. Histone lactylation is induced under glycolytic conditions such as hypoxia and M1 macrophage polarization. In the late phase of M1 macrophage polarization, increases in histone lactylation but not acetylation mark M2-like genes for activation. Our findings suggest a feedback mechanism of the innate immune system to switch from proinflammation to resolution through histone Kla-associated gene expression. This mechanism is implemented by the coopted function of lactate and histone lactylation in metabolism and epigenetics. Together, our study opens a new avenue for understanding function of lactate and glycolysis underlined diverse pathophysiological conditions.

overall_design: LPS and IFNg were used to induce M1 polarization of bone marrow-derived macrophage. After 24 hours of M1 polarization, ChIP-seq with spiked-in was carried out to study the genome-wide distribution and comparing H3K18la and H3K18ac marks in M0 and M1 macrophages. To study the correlation between histone marks and gene expression, mRNA dynamics at 0h, 4h, 8h, 16h, 24h after M1 polarization, and 8h, 16h, 24h after lactic acid treatment during the M1 polarization were measured by RNA-seq.

first: He


title: Nuclear receptor RORγ is a targetable master regulator of cholesterol in a subtype of breast cancer [RNA-Seq]

summary: We show that triple-negative breast cancer (TNBC) exhibits a hyper-activated MVA-CB program that is strongly linked to nuclear receptor RORγ, compared to estrogen receptor-positive breast cancer. Genetic and pharmacological inhibition of RORγ reduces tumor cholesterol contents and synthesis rate while preserving host cholesterol homeostasis. We demonstrate, for the first time, that RORγ functions as a master activator of the entire MVA-CB program, dominantly over SREBP2, through its own direct binding and facilitating the recruitment of SREBP2. RORγ inhibition disrupts its association with SREBP2 and reduces MVA-CB chromatin acetylation. RORγ antagonists cause sustained TNBC tumor regression in patient-derived and immune-intact models. Their combination with cholesterol-lowering statins elicits superior anti-tumor synergy selectively in TNBC. Together, our studies uncover a previously unsuspected master regulator of MVA-CB and an attractive target for TNBC.

overall_design: A total of 12 samples were analyzed in this study. The study included two cell lines HCC70 and MDA-MB468. Both Cells were cultured in medium containing vehicle control, XY018 (1.25 or 2.5 µM), atorvastatin (ATV, 1.25 µM) or the combination of XY018 (1.25 µM) and ATV for 24 hours. For MDA-MB468, cells were cultured in growth medium containing vehicle control or GSK805 (2.5 µM) for 24 hours. After treatment, all cells were collected for RNA-Seq assay.

first: Hong-wu

last: Chen


title: Light-entrained and brain-tuned circadian circuits regulate ILC3 and gut homeostasis

status: Public on Aug 02 2019

city: Lisboa

first: Miguel

middle: Alves

last: Rendas

state: Lisbon

address: Av. Brasília, 1400-038 Lisboa

country: Portugal

institute: Champalimaud Foundation

summary: Group 3 innate lymphoid cells (ILC3) are major regulators of inflammation, infection, microbiota composition and metabolism. ILC3 and neuronal cells were shown to interact at discrete mucosal locations to steer mucosal defence. Nevertheless, whether neuroimmune circuits operate at an organismal level, integrating extrinsic environmental signals to orchestrate ILC3 responses remains elusive. Here we show that light-entrained and brain-tuned circadian circuits regulate enteric ILC3, intestinal homeostasis and the host lipid metabolism. We found that enteric ILC3 display circadian expression of clock genes and ILC3-related transcription factors. ILC3-autonomous ablation of the circadian regulator Arntl led to disrupted gut ILC3 homeostasis, impaired epithelial reactivity, deregulated microbiome, increased susceptibility to bowel infection and disrupted lipid metabolism. Loss of ILC3-intrinsic Arntl shaped the gut postcode receptors of ILC3. Strikingly, light-dark cycles, feeding rhythms and microbial cues differentially regulated ILC3 clocks, with light signals as major entraining cues of ILC3. Accordingly, surgical- and genetically-induced deregulation of brain rhythmicity led to disrupted circadian ILC3 oscillations, deregulated microbiome and altered lipid metabolism. Our work reveals a circadian circuitry that translates environmental light cues into enteric ILC3, shaping intestinal health and organismal homeostasis.

overall_design: Small intestine lamina propria ILC3 (CD45.2+ Lin- Thy1.2hi KLRG1-) were sort-purified from the small intestine of 8-14 weeks old WT (Arntlwt/fl) and KO (Rorc-Cre.Arntlfl/fl) mice at two different timepoints: ZT05 (WT n=3; KO n=3) and ZT23 (WT n=3; KO n=3). Total RNA was extracted (Qiagen Micro Kit) and quality was assessed using an Agilent 2100 Bioanalyzer. SMART-SeqII (ultra-low input RNA) libraries were prepared using Nextera XT DNA sample preparation kit (Illumina). Sequencing was performed on an Illumina HiSeq4000 platform, PE100.

first: Cristina

last: Godinho-Silva

first: Rita

middle: G

last: Domingues

first: Bruno

last: Raposo

first: Hélder

last: Ribeiro

first: Joaquim

last: Silva

first: Ana

last: Vieira

first: Rui

last: Costa

first: Nuno

last: Barbosa-Morais

first: Tânia

last: Carvalho

first: Henrique

last: Veiga-Fernandes


title: Nuclear receptor RORγ is a targetable master regulator of cholesterol in a subtype of breast cancer [ChIP-Seq]

first: Demin

last: Cai

overall_design: A total of 12 samples were analyzed in this study. The study included one cell line HCC70. Cells were cultured in medium containing vehicle control or XY018 (5 µM) for 24 hours, cells then were collected for ChIP seq assay.

first: Feng

last: Wu


title: Differential transcriptome dynamics during the onset of conceptus elongation and between female and male porcine embryos

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

summary: this study was designed to analyze global gene expression in porcine embryos during the preimplantation period (Day 8, 10, and 12 of pregnancy) with the aims of (i) characterizing the dynamics of gene expression profiles and the involved functions and thereby (ii) identifying the chromosome X inactivation profile between female and male

overall_design: Female and male embryos were isolated from three stages (Day 8, 10, and 12) (each group n=5), respectively, and then subjected to RNA-sequencing (RNA-Seq).

first: Shuqin

last: Zeng

first: Jochen

last: Bick

first: Susanne

middle: E

last: Ulbrich


title: mRNA profiles of nxf-1 (t2160) and wild type C. elegans in adult stage

city: Logrono

first: María

last: de Toro

state: La Rioja

address: C/Piqueras 98

department: Genomics & Bioinformatics Core Facility

institute: Centro de Investigación Biomédica de La Rioja

summary: Synchronized wild type and nxf-1(t2160) worms were grown at 15˚C. One-day old adult-stage worms were shifted to 25˚C for 16 hours, because t2160 is a ts allele. RNA was isolated using an RNeasy Mini kit (Qiagen,).

overall_design: C. elegans mRNA profiles of worms of nxf-1 (t2160)  or wild type (Control). Three replicates per sample grownd at 15 C and shifted to 25˚C for 12-16 hours. Deep sequencing in Illumina Genome Analyzer IIx and MiSeq. Two samples, three replicates per sample

first: Angelina

last: Zheleva

first: Eva

last: Gómez-Orte

first: Beatriz

last: Sáenz-Narciso

first: Begoña

last: Ezcurra

first: Henok

last: Kassahun

first: Antonio

last: Miranda-Vizuete

first: Ralf

last: Schnabel

first: Hilde

last: Nilsen

first: Juan

last: Cabello


title: RNA Sequencing of CTRL and Heat Stressed C. elegans

city: San Deigo

first: Amy

last: Pasquinelli

address: 9500 Gilman Drive

department: Biological Sciences

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


title: Alterations in Wnt- and/or STAT3 signaling pathways and the immune microenvironment during metastatic progression

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Metastatic breast cancer is an extremely complex disease with limited treatment options due to the lack of information about the major characteristics of metastatic disease. There is an urgent need, therefore, to understand the changes in cellular complexity and dynamics that occur during metastatic progression. In the current study, we analyzed the cellular and molecular differences between primary tumors and paired lung metastases using a syngeneic p53-null mammary tumor model of basal-like breast cancer. Distinct subpopulations driven by the Wnt- and/or STAT3 signaling pathways were detected in vivo using a lentiviral Wnt- and STAT3 signaling reporter system. A significant increase in the overlapping populations driven by both the Wnt- and STAT3 signaling pathways was observed in the lung metastases as compared to the primary tumors. Furthermore, STAT3 signaling activity was markedly enhanced in the metastatic lesions relative to the primary tumors with minimal changes observed in Wnt reporter activity. An analysis of the unique molecular features of the lung metastases revealed a significant association with immune response signatures. Specifically, Foxp3 gene expression was markedly increased and elevated levels of Foxp3+ Treg cells were detected in close proximity to lung metastases. Collectively, these studies illustrate the importance of analyzing intratumoral heterogeneity, changes in population dynamics and the immune microenvironment during metastatic progression.

overall_design:
The breast tumor cells are transplanted into the mammary fat pad to establish primary tumor nodules. The primary tumor can then be surgically removed as in human breast cancer patient
Comment: There are 8 additional samples in the processed file which have already been uploaded in the study GSE124821 (see below relations).

first: Se-Jin

last: Kim

first: Susana

last: Garcia Recio

first: C

last: Creighton

first: Jeff

last: Rosen


title: Epigenome editing strategies for the functional annotation of topological insulators

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

summary: The human genome is folded into regulatory units termed ‘topologically-associated domains’ (TADs), within which the majority of gene-enhancer interactions occur. Genome-wide studies support a global role for the insulator protein CTCF in mediating chromosomal looping and the topological constraint of TAD boundaries3,4. However, the impact of individual insulators on enhancer-gene interactions and transcription remains poorly understood. Here, we investigate epigenome editing strategies for perturbing individual CTCF insulators and evaluating consequent effects on genome topology and transcription. We show that fusions of catalytically-inactive Cas9 (dCas9) to transcriptional repressors (dCas9-KRAB) and DNA methyltransferases (dCas9-DNMT3A, dCas9-DNMT3A3L) can selectively displace CTCF from specific insulators, but only when precisely targeted to the cognate motif. We further demonstrate that stable, mitotically-heritable insulator disruption can be achieved through combinatorial hit-and-run epigenome editing with dCas9-KRAB and dCas9-DNMT3A3L. Finally, we apply these strategies to activate PDGFRA expression in glioblastoma stem cells, thus simulating an insulator loss mechanism implicated in brain tumorigenesis. Our study provides strategies for stably modifying genome organization and gene activity without altering the underlying DNA sequence.

overall_design:
ChIP-seq, BS-seq, and 4C-seq experiments from HEK293 and GSC6 cells following targeted epigenome editing

*** The raw sequencing/alignment data for cell line GSC6 [GSM3937048-GSM3937067] are not provided due to patient confidentiality.

first: Daniel

middle: R

last: Tarjan

first: William

last: Flavahan

first: Bradley

last: Bernstein


title: Transcriptome of adult rat hepatocytes with different ploidy statuses

status: Public on Aug 01 2019

city: Philadelphia

first: Takeshi

last: Katsuda

state: PA

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

summary: To investigate whether rat adult hepatocytes would exhibit different characteristics dependent on their ploidy statuses, we compared the transcriptome profile of 2c, 4c and 8c hepatocytes by mRNA microarray.

overall_design: Rat hepatocytes were isolated from adult female rats (5-14 weeks old). Hepatocytes were stained with Hoechst33342, and then 2c, 4c and 8c hepatocytes were sorted by FACS Aria II or FACS Aria III. Five independent experiments were performed.

first: Kazunori

last: Hosaka

first: Takahiro

last: Ochiya


title: Transcriptomic analysis of PPBL and marginal zone like B cells

city: Basel-Sadt

first: Jordan

middle: Gabriel

last: Loeliger

address: Hebelstrasse 20

department: Department of Biomedicine

institute: University of Basel

summary: We report whole transcriptomic differences between B cells from PPBL patients and marginal zone like B cells from healthy donors using next generation RNA-sequencing

overall_design: Examination of trancriptomes in B cells from two cohorts

first: Christoph

last: Hess

first: Anne

middle: V

last: Burgener


title: Genome-wide maps of chromatin state in PC3 cells

first: Filippo

last: Giancotti

address: 1881 East Road

department: Cancer Biology

institute: UT MD Anderson Cancer Center

summary: To integrate genome-wide occupancy of canonical and ncPRC1 with control of gene expression, we performed ChIPseq analysis for RNF2 (cPRC1 and ncPRC1), BMI1 and PHC2 (cPRC1), and KDM2B  (ncPRC1.1) and integrated the results with the known occupancy data for the transcriptional repression mark H3K27me3 and the activation mark H3K4me3 in PC3 cells. Finally, we show that the capacity of PRC1 is to positively control the gene expression associated with the acquisition of mesenchymal and stem-like traits and progression to metastasis in PC3.

overall_design: Examination of 5 PRC1 subunits with histone H2AK119Ub modifications in PC3 cells. BioProject accession - PRJNA535445. SRA Study accession are as follows: 1_Bmi1  SRR8955278 ; 2_Rnf2 SRR8955279 ; 3_Input SRR8955280 ; 4_Pcgf1 SRR8955281 ; 5_Phc2 SRR8955282 ; 6_Kdm2b SRR8955283 ; 1_ubH2A SRR8980091 ; 2_ubH2A SRR8980090

first: Alekya

last: Rumandla

first: Yan

last: Wang


title: Single cell qRT-PCR (scPCR) for rat hepatocytes and biliary epithelial cell (BEC)-enriched non-parenchymal cells (NPCs).

summary: Using FACS-sorted adult rat hepatocytes with distinct DNA contents (2c and 4c), we compared the expression levels of a 47 gene panel. As non-hepatic control samples, BEC-enriched NPCs were also used for the same scPCR experiment.

overall_design: 92 2c hepatocytes and 245 4c hepatocytes were prpared by C1 single cell capture system.

first: Takesh


title: Transcriptomic data and Genome-wide maps of chromatin state in prostate cancer


title: Single-Cell Transcriptomes and Whole-Brain Projections of Serotonin Neurons in the Mouse Dorsal and Median Raphe Nuclei

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

summary: We performed a comprehensive survey of DR and MR serotonin neurons in the adult mouse brain by scRNA-seq. To specifically label serotonin neurons, we crossed Sert-Cre mice (Gong et al., 2007) with the tdTomato Cre reporter mouse, Ai14 (Madisen et al., 2010). (Serotonin transporter, or Sert, is a marker for serotonin neurons; see more details below.) We collected serotonin neurons acutely dissociated from brain slices by fluorescence-activated cell sorting (FACS) and used Smart-seq2 (Picelli et al., 2013) to generate scRNA-seq libraries.

overall_design: We used both male and female adult mice (postnatal day 40-45) and applied two dissection strategies to separate the serotonin neurons originating from anatomically-distinct brain regions: 1) in the first set of experiments, we dissected the brainstem region that contain the entire MR and DR; 2) in the second set of experiments, we focused on the principal DR (pDR, corresponding to the traditional B7 group) region by dissecting specifically the DR but excluding its caudal extension (cDR, corresponding to the traditional group B6). After quality control, we determined the transcriptomes of 709 cells from eight samples that include MR, pDR, and cDR, and 290 cells from six pDR-only samples (999 cells passing quality threshold out of 1536 total cells). We sequenced to a depth of  ~1 million reads per cell and detected ~10,000 genes per cell.


title: SIRT1 regulates enhanced mitochondrial respiration and leukemogenicity in CML stem cells

city: Birmingham

first: Ravi

last: Bhatia

state: Alabama

address: 1720 2nd Avenue South, NP2540

department: Hematology/Oncology

institute: University of Alabama at Birmingham

summary: Chronic myeloid leukemia (CML) results from hematopoietic stem cell transformation by the BCR-ABL tyrosine kinase. We have shown that the SIRT1 deacetylase is overexpressed in CML LSC, and may contribute to their maintenance. Here, using genetic deletion of SIRT1 in transgenic CML mice, we definitively demonstrate that SIRT1 is required for leukemia development, and reveal its critical role in mediating increased mitochondrial respiration in CML LSC.

overall_design: Bone marrow LSK cells were sorted from SIRT1 deleted (cre+) and control (cre-) CML mice and resuspended into RLT buffer and RNA is extracted. Four biological replicates were used from each genetic group. RNA samples were quality checked and proceeded to library preparation.

first: Ajay

last: Abraham


title: Paxillin regulates genomic networks in prostate cancer [LNCaP]

city: Rochester

first: Stephen

last: Hammes

state: NY

address: 601 Elmwood Ave, Box 693

department: Medicine

institute: University of Rochester

summary: We report that the adaptor protein, paxillin, regulates some androgen responsive genes in the castration sensitive prostate cancer cell line, LNCaP.

overall_design: LNCaP cells were transfected with either Non-specific siRNA or Paxillin-targeted siRNA for 48 hours, followed by serums starvation of 12 hours, cells are then treated with either 2.5nM dihydrotestosterone (DHT) or vehicle (ethanol), and RNA from these groups were isolated and proceeded to RNA sequecning.

first: Xiaoting

last: Ma

first: Anindita

last: Biswas


title: Paxillin regulates genomic networks in prostate cancer

overall_design: Refer to individual Series


title: Transcriptomic data of established mouse prostate cancer cell lines like RM1 and Pten Smad4

city: Houston

summary: RM1 and Pten Smad4 are two mouse models with mesenchymal and stem like features. We applied the RNA Seq to provide the transcriptomic profiling of these two cell lines.

overall_design: RNA Seq of  RM1 and Pten Smad4 cell lines have 3 replicates each. BioProject accession - PRJNA535445. SRA Study accession are as follows: 1_Pten_Smad4 SRR9110007 ; 2_Pten_Smad4 SRR9110006 ; 3_Pten_Smad4 SRR9110005 ; 4_RM1 SRR9110004 ; 5_RM1 SRR9110003 ; 6_RM1 SRR9110002


title: Small RNA profiling in mouse alcohol-induced liver injury and steatosis model.

city: Guangxi

first: Songqing

last: He

address: No.22 Shuangyong road

institute: Guangxi Medical University

summary: Complement is known to play a role in alcoholic fatty liver disease (AFLD), but the underlying mechanisms are poorly understood, thereby constraining the development of a rational approach for therapeutic intervention in the complement system.here we demonstrate protection in wild type mice by treatment with CR2-Crry, a C3 inhibitor that specifically targets sites of complement activation. We found that the expression of glycine transfer (t) RNA-derived fragments (Gly-tRFs) is upregulated in ethanol-fed mice, and that inhibition of Gly-tRFs in vivo decreases chronic ethanol-feeding-induced hepatosteatosis without affecting inflammation

overall_design: small RNAs expression profiling of liver tissues obtained after 16 days EtOH feed.

first: Fudi

last: Zhong


title: Alcohol metabolism directly fuels histone acetylation in the brain [RNA-Seq II]

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

summary: In the adult brain, epigenetic control of gene expression has important roles in the processing of neural activity. Emerging evidence suggests that epigenetic regulation is dependent on metabolic state, implicating specific metabolic factors in neural functions that drive behavior. In neurons, histone acetylation is dependent on the metabolite acetyl-CoA that is produced from acetate by chromatin-bound ACSS21. Here, using in vivo stable isotope labeling in mouse, we show that alcohol metabolism rapidly fuels histone acetylation in the brain by direct deposition of alcohol-derived acetyl groups onto histones in an ACSS2-dependent manner. A similar induction was observed with heavy labeled acetate injection in vivo. Injection of labeled alcohol into a pregnant mouse results in incorporation of labeled acetyl groups into gestating fetal brains, indicating that the acetate passes through the placenta. In isolated primary hippocampal neurons ex vivo, extracellular acetate induced learning and memory-related transcriptional programs that were sensitive to ACSS2 inhibition. Strikingly, alcohol-related associative learning requires ACSS2 in vivo. These findings establish a novel and direct link between alcohol metabolism and neuronal ACSS2-dependent histone acetylation in the brain, providing evidence that dynamic acetate release from liver metabolism may travel to the brain for direct epigenetic regulation in neurons.

overall_design: This experiment assesses the gene expression response to EtOH in mouse hippocampus by RNA-seq, in the presence or absence of enzyme ACSS2. EtOH was injected systemically via intraperitoneal injection, as was an ACSS2 shRNA knockdown. Controls for EtOH treatment (two replicates each of ACSS2- or control) were previously published under GEO series GSE90855 and are re-uploaded here. Three and four replicates (dorsal and ventral) of EtOH treated ACSS2+ samples are included here, as are five and four replicates (dorsal and ventral) of EtOH treated ACSS2- samples. An additional total hippocampus ACSS2- EtOH+ sample is also included.

first: Philipp

last: Mews

first: Gabor

last: Egervari

first: Raffaella

last: Nativio

first: Simone

last: Sidoli

first: Greg

first: Sonia

middle: I

last: Lombroso

first: Desi

middle: C

last: Alexander

first: S

middle: L

last: Riesche

first: Elizabeth

middle: A

last: Heller

first: Eric

last: Nestler

first: Benjamin

last: Garcia

first: Shelley

last: Berger


title: Alcohol metabolism directly fuels histone acetylation in the brain

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

Reviewers: for a UCSC Genome Browser session of the chIP-seq and the ex vivo RNA-seq, please see:

https://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Gdonahue&hgS_otherUserSessionName=Alcohol%20Metabolism%20Publication


title: Alcohol metabolism directly fuels histone acetylation in the brain [RNA-Seq]

overall_design: This study examines gene expression in mouse hippocampal cells (ex vivo) subjected to (i) ACSS2 inhibition and (ii) acetate treatment to simulate the effects of heavy drinking. RNA-seq was performed on cells treated with an ACSS2 inhibitor or DMSO; those cells were in turn split into two groups and treated with acetate or not. Each of the four experimental groups had four replicates each, except for cells treated with ACSS2 inhibitor and no acetate, which had three.

middle: J