title: The genetic landscape for amyloid beta nucleation accurately discriminates familial Alzheimer’s disease mutations

status: Public on Feb 02 2021

city: barcelona

first: benedetta

last: bolognesi

state: Barcelona

address: c comte borrell 232 5a-1a

country: Spain

institute: IBEC

summary: Alzheimer’s Disease (AD) is the most common form of dementia and a leading global cause of human mortality and morbidity.  Amyloid plaques of the amyloid beta (Aß) peptide are a universal pathological hallmark of AD and rare mutations in Aß can cause familial forms of AD (fAD).  However, hundreds of additional mutations in Aß of uncertain significance are likely to exist in the human population, making clinical interpretation of genetic variation a difficult challenge even in this short peptide.  Here, we use deep mutagenesis to quantify the effects of all possible single nucleotide variants and thousands of double mutations on the ability of Aß to nucleate amyloid fibrils in vivo. This data provides the first comprehensive view of how mutations alter the nucleation of an amyloid, reveals  a modular organisation of mutational effects in Aß, and demonstrates the importance of charge in preventing nucleation.  Moreover, the in vivo nucleation data, unlike computational predictors, accurately discriminates the known dominant fAD mutations.  These results illustrate how deep mutagenesis can be used to genetically validate assays as discovery platforms.  They also further prioritize nucleation as the critical biochemical event to target in order to prevent and treat AD.

overall_design: Systematic measurement of the amyloid nucleation of 15,000 mutations of Aβ42

first: Benedetta

last: Bolognesi

first: Ben

last: Lehner


title: A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression [ChIP-seq]

status: Public on Feb 23 2021

city: Chapel Hill

first: Zachary

last: Carico

state: NC

address: 250 Bell Tower Dr, CB7100

department: Integrative Biological and Genome Sciences program

country: USA

institute: University of North Carolina

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Purpose: Chromatin loop formation and maintenance is regulated by the cohesin complex. Here, we investigate whether a cancer mutation to a cohesin complex subunit, SMC1A-R586W, alters genome architecture and gene expression.
Method: Genome wide binding patterns of known architectural proteins and histone PTMs were assessed in WT and SMC1A-R586W mESCs by ChIP-seq.

overall_design: ChIP-seq was performed in wild type and mutant mESCs in a minimum of two biological replicates for all factors studied.

first: Jill

middle: M

last: Dowen

first: Megan

middle: N

last: Justice

first: Holden

middle: C

last: Stefan


title: A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expression

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Sp8 regulatory function in the limb bud ectoderm

status: Public on Feb 01 2021

city: Santander

first: Marian

last: Ros

address: Albert Einstein, 22 (PCTCAN)

institute: Consejo Superior de Investigaciones Cientificas (CSIC) with Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC)


title: ChIP-Seq H3K4me3 in Jurkat treated with either OICR-9429, PBIT or DMSO

status: Public on Apr 16 2021

city: Marseille

first: Salvatore

last: Spicuglia

state: France

address: Luminy

country: France

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

summary: To assess whether BH4Ds are more or less sensitive than sharp H3K4me3 peaks to perturbation of H3K4me3 levels, we performed H3K4me3 ChIP-seq experiments from Jurkat cells treated with DMSO or with either 2-(4-methylphenyl)-1,2-benzisothiazol-3(2H)-one (PBIT), a specific inhibitor of JARID1 family of H3K4me3 demethylases, also known as KDM5, or OICR-9429, an inhibitor of the MLL-WDR5, previously shown to decrease cellular levels of H3K4me3.

overall_design: 4 samples in singlicate: 3 ChIP-Seq with spike-in and their input control. The DMSO-treated ChIP sample is used as reference to compare signal variation induced by each inhibitor treatment.

first: Mohamed

last: Belhocine

first: Mathieu

last: Simonin

first: Agata

last: Cieslak

first: Lydie

last: Pradel

first: Charlotte

last: Smith

first: Eve-Lyne

last: Mathieu

first: Guillaume

last: Charbonnier

first: José-David

middle: A

last: Flores

first: Iris

last: Manosalva

first: Joost

middle: H

last: Martens

first: Hendrik

middle: G

last: Stunnenberg

first: Denis

last: Puthier

first: Pierre

last: Ferrier

first: Vahid

last: Asnafi


title: Integration of high-throughput reporter assays identify a critical enhancer of the Ikzf1 gene

status: Public on Mar 31 2021

summary: The Ikzf1 locus encodes the lymphoid specific transcription factors Ikaros, which play an essential role in both T and B cell differentiation, while deregulation or mutation of IKZF1/Ikzf1 is involved in leukemia. Tissue-specific and cell identity genes are usually associated with clusters of enhancers, also called super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. Several potential regulatory regions have been identified in close proximity of Ikzf1, however, the full extent of the regulatory landscape of the Ikzf1 locus is not yet established. In this study, we combined epigenomics and transcription factor binding along with high-throughput enhancer assay and 4C-seq to prioritize an enhancer element located 120 kb upstream of the Ikzf1 gene. We found that the deletion of the E120 enhancer resulted in a significant reduction of Ikzf1 mRNA. However, the epigenetic landscape and 3D topology of the locus were only slightly affected, highlighting the complexity of the regulatory landscape regulating the Ikzf1 locus

overall_design: We used CRISPR/Cas9 technology to delete the IkE120 enhancer in the P5424 cell line. ChIP-seq was used to assess H3K27ac enrichment in wild-type and knock-out cells; 4C was used to interrogate chromatin interactions with the Ikzf1 promoter.

first: Jaafar

last: Aliomari

first: Anne

last: Molitor

first: Nori

last: Sadouni

first: Magali

last: Torres

first: Wiam

last: Saadi

first: Lan

middle: T

last: Dao

first: David

last: Santiago-Algarra

first: Jean

last: Andrau

first: Tom

last: Sexton


title: Induction and expansion of human PRRX1+ limb-bud-like mesenchymal cells from pluripotent stem cells

status: Public on Jul 08 2021

city: okayama

first: Takeshi

last: Takarada

state: okayama

address: 2-5-1 Shikata-cho

department: Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

country: Japan

institute: Okayama university

summary: Comparison of gene expression profiles during differentiation from pluripotent state to limb bud state.

overall_design: RNA samples extracted from hiPSC or its-derived cells: LPM, LBM, ExpLBM PRRX1 high, ExpLBM PRRX1 low, ExpLBM PRRX1 high after chondrogenic induction

first: Daisuke

last: Yamada

first: Masahiro

last: Nakamura


title: m6A-meRIP sequencing

status: Public on Apr 09 2021

city: Chengdu

first: Yanyun

last: Wang

address: No. 20 Ren Min Nan Lu

country: China

institute: West China Second University Hospital, Sichuan University

summary:
Background: Abdominal aortic aneurysm (AAA) is a vascular disease with indeterminate prevalence but high mortality rates when complicated with rupture. The pathogenesis of AAA has not been fully elucidated. N6-methyladenosine (m6A) modification is likely important in the development of AAA. In the present study, m6A-MeRIP sequencing and RNA sequencing were performed to identify the m6A sites. Bioinformatics analysis was used to evaluate the m6A patterns of the aorta walls of AngII-induced abdominal aortic aneurysm (AAA) model and normal mice.
Results: There were 2039 differentially methylated m6A peaks involving 1865 mRNAs in the AAA group relative to the control, of which 1610 peaks in 1466 mRNAs were hypermethylated and 429 peaks in 410 mRNAs were hypomethylated. The hypermethylated mRNAs in AAA group were mostly enriched in transcription regulation and intercellular signaling, especially the Wnt signaling-associated processes. Hypomethylated m6A sites were mainly enriched in G protein-coupled receptor activity and ion channel activity.
Conclusion: Our study suggested an original viewpoint that AAA might mainly be relevant to combined effect of m6A methylation modification in Wnt pathway, G protein-coupled receptor and ion channel- associated genes, which were worthy of further investigation.

overall_design: Examing 2 conditions, each with 3 replicates

first: Tianyu

last: Miao


title: Differential DNA methylome between low and high-grade gliomas

status: Public on Dec 31 2020

city: Alicante

first: Luis

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

institute: ISABIAL

summary: Glioblastoma (GB) is the most aggressive form of glioma and is characterized by a poor prognosis and high recurrence, despite intensive clinical interventions. To retrieve the key factors underlying the high malignancy of GB, we performed differential methylation analysis between low and high-grade gliomas by using Infinium MethylationEPIC beadchips.

overall_design: We inspected 6 II-grade, 2 III-grade and 8 IV-grade gliomas from individual surgical resections.


title: Sp8 regulatory function in the limb bud ectoderm [RNA-seq]

first: Marian

last: Ros

summary: Sp8 and Sp6, members of the Sp family of transcription factors, are required in a dose-dependent manner to induce Fgf8 and En1 in the limb bud ectoderm, therefore controlling proximo-distal and dorso-ventral limb development. Mouse genetics revealed that Sp8 makes a much greater contribution than Sp6 but the nature of its regulatory mechanism was unknown. Here, by combining ChIP-seq and RNA-seq genome-wide analyses we show that Sp8 predominantly functions as an activator from putative distal enhancers regulating crucial limb patterning genes and underscoring its master role in limb development. We also provide compelling evidence for Sp8 cooperating with Dlx5 for the regulation of a considerable set of its target genes. Our work supports a model in which Sp8, Sp6 and Dlx5 act conjointly to regulate target genes with a final functional outcome that depends on their relative availability. This should be considered when interpreting Sp and Dlx mutant phenotypes.

overall_design: Transcriptional profiles in mouse E10.5 forelimb ectoderms isolated from WT and Sp8-/- embryos using RNA-seq.

first: Rocío

last: Pérez-Gómez

first: Álvaro

last: Rada-Iglesias


title: Characterizing cis-regulatory elements associated with mammary gland function

status: Public on Apr 06 2021

city: College Station

first: Monique

last: Rijnkels

state: Texas

address: 660 Raymond Stotzer Pkway

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

summary: The goal of this study is to improve the quality, efficiency, and sustainability of milk production by improving the understanding of the function of cis-regulatory elements in regulating the bovine mammary gland. To this end, we have characterized the non-lactating and lactating mammary gland transcriptomes by whole transcriptome shotgun sequencing (RNA-seq). We will identify cis-regulatory elements in the non-lactating and lactating bovine mammary gland genome-wide. Finally, we will annotate and characterize mammary gland cis-regulatory elements by computational analysis and identify high-resolution genome-wide in vivo footprints of diverse trans-acting-factors (TF), over-represented TF bindings sites and overlapping SNPs.

overall_design: RNA-Seq analysis of 31 samples of mammary epithelial organoids isolated from mammary gland biopsies taken from 16 dairy cows at two time points. 15 samples are derived from biopsies performed at 14 months of age on virgin animals, and 16 samples are derived from biopsies of the same animals at mid-lactation (40-60 days lactation). For one animal, only the lactating sample was suitable for RNA-Seq.

first: Hannah

middle: S

last: Lyman

first: Christa

last: Kuhn

first: Adrian

last: Molenaar

first: Kuljeet

last: Singh

first: Ian

last: Korf

first: Danielle

last: Lemay


title: Cross species transcriptomic signatures predict response to MK2 inhibition in mouse models of chronic inflammation

status: Public on Jan 08 2021

city: Boston

first: Bing

last: Shui

state: MA

address: 360 Longwood Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

summary: Translating observations from preclinical models to patients is one of the most pressing challenges in biomedical research. Part of the challenge derives from the necessity of studying preclinical therapeutic responses in genetically and environmentally homogenous mouse models, which exhibit less variability than genetically and environmentally heterogeneous humans. This problem is especially relevant for inflammatory bowel diseases (IBD), which are genetically complex and exhibit significant inter-patient heterogeneity in disease presentation and therapeutic response. Here, we show that mouse models of IBD exhibit variable responses to inhibition a MK2, a pro-inflammatory serine/threonine kinase, and that MK2 inhibition suppresses inflammation by targeting inflammatory monocytes and neutrophils. Using a computational approach (TransComp-R) that allows for cross-species comparison of transcriptomic features, we identified an IBD patient subgroup that is predicted to respond to MK2 inhibition and an independent preclinical model of chronic intestinal inflammation predicted to be non-responsive, which we validated experimentally. Thus, cross-species mouse-human translation approaches can help to identify patient subpopulations in which to deploy new therapies.

overall_design: RNA-Seq of two mouse models of Inflammatory Bowel Disease (IBD): T Cell Transfer (TCT) and TNF∆ARE. Non-inflamed control and inflamed animals from both models were treated with vehicle or MK2 inhibitor for 24 hours. Mouse intestines were harvested and subjected to RNA-Seq.

first: Shui

last: Bing

first: Haigis

last: Kevin


title: Expression of immune-related genes in peripheral blood mononuclear cells of HBV infected patients prior to and at 6 hours after the first PegIFNα injection

status: Public on Nov 01 2020

city: Bethesda

first: Barbara

last: Rehermann

state: Maryland

address: 10 Center Drive

department: Liver Diseases Branch

institute: National Institutes of Health

summary: This study was conducted to assess how treatment with PEG-IFNα affects the expression of interferon-stimulated genes in peripheral blood mononuclear cells from nucleot/side analogue-treated virally suppressed patients with chronic HBV infection

overall_design: Cryopreserved, subsequently thawed peripheral blood mononuclear cells were subjected to NanoString nCounter expression analysis of immune-related genes

first: Akira

last: Nishio


title: Diurnal rhythms across the human dorsal and ventral striatum

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

institute: UNIVERSITY OF PITTSBURGH

summary: The human striatum can be subdivided into the caudate, putamen, and nucleus accumbens (NAc). Each of these structures have some overlapping and some distinct functions related to motor control, cognitive processing, motivation, and reward. Previously, we used a “time of death” approach to identify diurnal rhythms in RNA transcripts in human cortical regions. Here, we identify molecular rhythms across the three striatal subregions collected from postmortem human brain tissue in subjects without psychiatric or neurological disorders. Core circadian clock genes are rhythmic across all three regions and show strong phase concordance across regions. However, the putamen contains a much larger number of significantly rhythmic transcripts than the other two regions. Moreover, there are many differences in pathways that are rhythmic across regions. Strikingly, the top rhythmic transcripts in NAc (but not the other regions) are predominantly snoRNAs and lncRNAs, suggesting that a completely different mechanism might be used for the regulation of diurnal rhythms in translation and/or RNA processing in the NAc versus the other regions. Further, although the NAc and putamen are generally in phase with regards to timing of expression rhythms, the NAc and caudate, and caudate and putamen, have several clusters of discordant rhythmic transcripts, suggesting a temporal wave of specific cellular processes with the caudate preceding the other regions. Taken together, these studies reveal distinct transcriptome rhythms across the human striatum and are an important step in helping to understand the normal function of diurnal rhythms in these  regions and how disruption could lead to pathology.

overall_design:
NAc, caudate, and putamen tissue samples were obtained through the University of Pittsburgh Brain Tissue Donation Program and the NIH NeuroBioBank. Brain tissue was obtained, following consent from the next of kin, during autopsies conducted at the Allegheny County (Pittsburgh, PA) or Davidson County (Nashville, TN) Medical Examiner’s Office. All procedures were approved by the University of Pittsburgh Institutional Review Board for Biomedical Research and Committee for Oversight of Research and Clinical Training Involving Decedents. The absence of lifetime psychiatric disorders was determined by an independent committee of experienced clinicians using information from clinical records, toxicology results, and standardized psychological autopsy. Subjects were included based on three criteria: 1)  known time of death (TOD) within a 4-hour window and meeting the criteria of rapid death; 2) age less than 65 years; 3) postmortem interval (PMI) less than 30 hours. A total of 60 subjects  met these criteria. One subject (ID: 13250) was excluded from all analyses due to overall low expression levels and low correlation with the other subjects (n=59 for all analyses). The right hemisphere of each brain was blocked coronally, immediately frozen, and stored at -80° C. Tissue blocks containing the body of the caudate, putamen, and NAc were selected for analysis. The medial-lateral border between the caudate and putamen was scored to specifically exclude the internal capsule. The ventral border of the caudate and putamen, and accordingly the dorsal border of the NAc, was defined by the anterior thalamic radiation of the internal capsule or the anterior commissure. Cryostat sections were cut at 40 µm thickness, and each striatal subregion from an individual section was placed into its respective collection tube until a total of volume of 35 mm3 was collected from each region. Total RNA was extracted from the tissue samples using a combination of Trizol (Invitrogen, Carlsbad, CA) and RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany). RNA quantity and quality were assessed using fluorometry (Qubit RNA Broad Range Assay Kit and Fluorometer; Invitrogen, Carlsbad, CA) and chromatography (Bioanalyzer and RNA 6000 Nano Kit; Agilent, Santa Clara, CA), respectively.

Please note that 'Corrected.TOD' is time of death corrected by sunrise and sunset time. 'HU' is sample ID which is one-to-one matched to "pair" numbers. 'PMI' is postmortem interval.

first: Colleen

last: McClung

first: George

last: Tseng

first: Kyle

last: Ketchesin

first: Wei

last: Zong


title: Genomic characterization of cisplatin response uncovers priming of cispla-tin-induced genes in a resistant cell line

status: Public on Jun 07 2021

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem

summary: We conducted a comprehensive genomic characterization of the cisplatin sensitive A2780 ovarian cancer cell line compared to A2780cis, its resistant derivative.   The data includes eXcision Repair-sequencing (XR-seq) to map cisplatin repair,RNA-Seq to characterize gene expression and ATAC-Seq to detect changes in chromatin accessibility.

overall_design:
We performed XR-seq, RNA-Seq, ATAC-Seq in A2780 and A2780cis cells treated with 200μM ciplatin for 3h.
XR-Seq: 3 A2780 replicates, 2 A2780cis replicates
RNA-Seq: 3 replicates for each condition: A2780 control, A2780 + cisplatin, A2780cis control, A2780cis + cisplatin
ATAC- Seq: 3 replicates for control samples, 2 replicates for cisplatin samples

first: H

last: Golan Berman

first: P

last: Chauhan

first: S

last: Shalev

last: Hassanain

first: A

last: Parnas


title: BET inhibition disrupts transcription but retains enhancer-promoter contact [RNA-seq]

status: Public on Oct 26 2020

city: Oxford

first: Thomas

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Enhancers are DNA sequences that enable complex temporal and tissue-specific regulation of genes in higher eukaryotes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Bromodomain and Extra-Terminal domain (BET) and Mediator proteins have been shown capable of forming phase condensates and are thought to be essential for super-enhancer function. Here, we show that targeting of cells with inhibitors of BET proteins or pharmacological degradation of BET protein Bromodomain-containing protein 4 (BRD4) has a strong impact on transcription but very little impact on enhancer-promoter interactions. Dissolving phase condensates reduces BRD4 and Mediator binding at enhancers and can also strongly affect gene transcription, without disrupting enhancer-promoter interactions. These results suggest that activation of transcription and maintenance of enhancer-promoter interactions are separable events. Our findings further indicate that enhancer-promoter interactions are not dependent on high levels of BRD4 and Mediator, and are likely maintained by a complex set of factors including additional activator complexes and, at some sites, CTCF and cohesin.

overall_design: RNA-seq

first: Nicholas

last: Crump

first: Laura

last: Godfrey


title: A computer-guided design tool to increase the efficiency of cellular conversions

first: Evan

middle: Michael

last: Appleton

address: 75 Kneeland St.

institute: Colossal Biosciences

summary: Here we introduce a computer-guided design tool that combines a computational framework for prioritizing more efficient combinations of instructive factors (IFs) of cellular conversions, called IRENE, with a transposon-based genomic integration system for efficient delivery. Particularly, IRENE relies on a stochastic gene regulatory network model that systematically prioritizes more efficient IFs by maximizing the agreement of the transcriptional and epigenetic landscapes between the converted and target cells. Our predictions substantially increased the efficiency of two established iPSC-differentiation protocols (natural killer cells and melanocytes) and established the first protocol for iPSC-derived mammary epithelial cells with high efficiency.

overall_design: Bulk RNA-sequencing of iPS-derived Mammary Epithelial Cells (HMEC), NK-cells, and Melanocytes

last: Church


title: Single-cell RNA sequencing reveals time- and sex-specific responses of spinal cord microglia to peripheral nerve injury and links ApoE to neuropathic pain

status: Public on Dec 07 2020

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

summary: Activation of microglia in the spinal cord following peripheral nerve injury is critical for the development of long-lasting pain hypersensitivity. However, it remains unknown whether distinct microglia subpopulations or states contribute to different stages of pain development and maintenance. Here, we demonstrate, using single-cell RNA-sequencing, that microglia transcriptional states differ at early and late time points following nerve injury. Male microglia show more proliferation and distinct transcriptional changes in response to nerve injury comparing to females. Apolipoprotein E (Apoe) was the top upregulated gene in microglia at chronic time points after nerve injury in mice and polymorphisms in the APOE in humans are associated with chronic pain. Single-cell analysis of human spinal cord microglia reveals a subpopulation with a disease-related transcriptional signature. Our data provide a detailed analysis of transcriptional states of mouse and human spinal cord microglia and identify a previously unrecognized role for ApoE in neuropathic pain.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Single-cell RNA sequencing of male and female mouse microglia, before and after peripheral nerve injury (3 days, 14 days and 5 months)

first: Shannon

last: Tansley

first: Luke

last: Healy

first: Moein

last: Yaquibi

first: Sonali

last: Uttam

first: Alba

last: Ureña Guzmán

first: Arkady

last: Khoutorsky


title: BET inhibition disrupts transcription but retains enhancer-promoter contact [Capture-C]

overall_design: Next generation Capture-C

first: Erica

last: Ballabio


title: The effect of plant extracts on human macrophage activation

status: Public on Oct 20 2020

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary:
Members of the Caryophyllaceae Juss. family possess anabolic, adaptogenic, radioprotective, antitumoral and hemorheological properties and have been used in medical practice for the treatment of various inflammatory disorders. Macrophages are key immune cells that coordinate the inflammatory reaction.
To identify the effects of Silene sendtneri and Silene roemeri on macrophage activation, primary human macrophages were cultured with extracts of these plants .We used microarrays to determine the global expression pattern induced by the extracts in macrophages.

overall_design: PBMC derived monocytes were stimulated either with IFNgamma or left unstimulated and cultured with extracts of Silene sendtneri or Silene roemeri. On the 6th day RNA was isolated and whole transcriptome was analyzed using Affymetrix microarrays

first: Elena

last: Filonenko

first: Alexandru

last: Gudima


title: Sp8 regulatory function in the limb bud ectoderm [ChIP-seq]

first: Marian

last: Ros

overall_design: Genome-wide binding profiles for SP8 and H3K4me2 were investigated in mouse E10.5 forelimb ectoderm using ChIP-seq.

first: Rocío

last: Pérez-Gómez

first: Álvaro

last: Rada-Iglesias


title: High grade glioma methylation analysis using bisulfite and oxidative bisulfite-treatment

status: Public on Oct 06 2020

city: Toronto

first: Paul

last: Kongkham

state: ON

address: 399 Bathurst St, WW4-450

department: Surgery

institute: University of Toronto

summary:
Bisulfite and oxidative bisulfite treated sample methylation analysis of IDH1 mutant and wild-type high grade human gliomas, to profile 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC).
Genomic DNA isolated directly from fresh-frozen human high grade glioma specimens.

overall_design: IDH1 mutant samples n = 12; IDH1 wild-type samples n = 9. No technical replicates performed.


title: Expression data from Saccharomyces cerevisiae

status: Public on Jan 01 2021

city: Gothenborg

first: Xiaowei

last: Li

address: Kemivägen 10

department: Biology and Biological

country: Sweden

institute: Chalmers University of Technology

summary: In response to carbon source switching from glucose to non-glucose, such as ethanol and galactose, yeast cells can directionally preprogram cellular metabolism to efficiently utilize the nutrients. However, the understanding of cellular responsive network to utilize a non-natural carbon source, such as xylose, is limited due to the incomplete knowledge on the xylose response mechanisms. Here, through optimization of the xylose assimilation pathway together with combinational evaluation of reported targets, we generated a series of mutants with varied growth ability. However, understanding how cells respond to xylose and remodel cellular metabolic network is far insufficient based on current information. Therefore, genome-scale transcriptional analysis was performed to unravel the cellular reprograming mechanisms underlying the improved growth phenotype.

overall_design: To gain sufficient xylose-metabolism-related information, we designed a sample pool and divided it into three groups: (1) four constructed strains X029, X058, X109 and X158, with gradually improved cellular growth capacity on xylose; (2) X058 with three different preculture mode, on glucose, ethanol, and xylose, respectively; (3) strains X058 and X158 at different OD600 values, in order to track the cellular metabolism rearrangement on time-course

first: Gang

first: Yanyan

last: Wang

first: Quanli

last: Liu

first: Rui

last: Pereira

first: Yun

last: Chen

first: Jens

last: Nielsen


title: ATAC-Seq of human early thymopoieisis

status: Public on Jul 09 2020

first: Salvatore

last: Spicuglia

summary: Four sorted human thymic subpopulations (CD34+1a-7+, CD34+1a+, EC, LC) from two donors were used for ATAC-Seq. Samples were sequenced in house in single-end 75nt mode using the NextSeq® 500/550 (Illumina) according to manufacturer’s instructions. Reads were trimmed with sickle and aligned with bowtie2 using default settings. Aligned reads from tCD34+1a-7+ and tCD34+1a+ populations from the two donors were merged to generate the tCD34 ATAC sample.

overall_design: Chromatin accessibility using ATAC-Seq was examinated for four human thymic subpopulations  (CD34+1a-7+, CD34+1a+, EC, LC) from two donors.

first: Agata

last: Cieslak

first: Guillaume

last: Charbonnier

first: Melania

last: Tesio

first: Eve-Lyne

last: Mathieu

first: Mohamed

last: Belhocine

first: Aurore

last: Touzart

last: Hypolite

middle: P

last: Andrieu

first: Joost

last: Martens

first: Eva

last: Janssen-Megens

first: Marta

last: Gut

first: Ivo

first: Nicolas

last: Boissel

first: Arnaud

last: Petit

first: Denis

last: Puthier

first: Elizabeth

last: Macintyre

first: Hendrik

last: Stunnenberg

first: Vahid

last: Asnafi


title: RNA-seq profiling of C/EBPβ-overexpressing myoblasts

status: Public on Dec 19 2020

city: Ottawa

first: Nadine

last: Wiper-Bergeron

state: Ontario

address: 451 Smyth Road

department: Cellular and Molecular Medicine

institute: University of Ottawa

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

overall_design: Refer to individual Series


title: Expression data and methylation analysis of IDH1 mutant and wild-type high grade gliomas

first: Paul

last: Kongkham

type:
Expression profiling by array
Methylation profiling by array


title: scRNA-seq of the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion

status: Public on Oct 07 2020

city: Aurora

first: Stephen

middle: William

last: Santoro

state: Colorado

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

summary: The objectives of this study were to use unilateral naris occlusion (UNO) to characterize the effects of olfactory deprivation on 1) gene expression changes within individual cells of the (OE) and 2) changes in the relative abundance of distinct cell types and subtypes.

overall_design: Profiling of the transcriptomes of single cells from the open and closed sides of the olfactory epithelia of PD28 mice following unilateral naris occlusion at PD14

middle: W


title: Epigenomic dynamics of human T-cell precursors reveal TCRA enhancer silencing by HOXA

city: Paris

address: 149 rue de Sèvres

institute: APHP


title: Smoking-induced Reprogramming of Histamine Metabolism Genes in the Human Small Airway Epithelium

status: Public on Aug 03 2020

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Smoking is associated with increased airway histamine responsiveness and elevated histamine levels. Transcript levels of histidine decarboxylase (HDC; histamine synthesis) and histamine N-methyltransferase (HNMT; histamine degradation) were evaluated in small airway epithelial (SAE) cells obtained from smokers or non-smokers. Histamine+ SAE cells increased in smokers compared to nonsmokers (p< 0.03). HDC transcript levels were elevated in smokers compared with non-smokers when comparing both bulk RNA from SAE (p< 0.03) and single cell HDC transcripts in mast cells (p<10-6). Elevated HDC transcript levels in mast cells corre-lated with elevated IL33 transcript levels in smoker SAE basal cells, and elevated transcript levels of the IL33 receptor, IL1RL1, in mast cells. In contrast to HDC, transcript levels of HNMT were decreased (p<10-4) in smoker SAE. Significant decreases in HNMT transcript levels were found broadly across SAE differentiated cell types. An in vitro SAE culture model treated with cigarette smoke extract reduced HNMT transcript levels (p<0.05). Together, the data suggests that smoking results in an accumulation of mast cells, elevated expression of histamine-synthesizing mast cell HDC, and a decrease in histamine-degrading HNMT transcript levels broadly in the epithelium. These smoking induced changes are likely contributors to elevated histamine levels in the airways of smokers.

overall_design: Analysis of bulk RNA-Seq samples obtained from n=20 healthy nonsmokers and n=24 healthy smokers were used for quantification of histamine+ cells. Single cell-RNAseq identified SAE cell-type specific deregulation of histamine metabolism genes by smoking.

first: Gouqing

last: Wang

first: Mahboubeh

middle: R

last: Rostami

last: Strulovici Barel

first: Wu-lin

last: Zuo

first: Fumihiro

last: Ogawa

first: Sarah

middle: L

last: O'Beirne

first: Robert

middle: J

last: Kaner

first: Ronald

last: Crystal

first: Philip

last: Leopold


title: RUNX1 Chip-Seq of human early thymopoieisis

city: Marseille

first: Salvatore

last: Spicuglia

address: Luminy

institute: Aix-Marseille University, INSERM, TAGC, UMR 1090

summary: RUNX1 binding sites in human immature stage of thymic maturation (tCD34+).

overall_design: Chromatin immunoprecipitation of RUNX1 in human thymic CD34+ suppopulation.

first: Agata

last: Cieslak

first: Guillaume

last: Charbonnier

first: Melania

last: Tesio

first: Eve-Lyne

last: Mathieu

first: Mohamed

last: Belhocine

first: Aurore

last: Touzart

last: Hypolite

last: Andrieu

first: Joost

last: Martens

first: Eva

last: Janssen-Megens

first: Marta

last: Gut

first: Ivo

first: Nicolas

last: Boissel

first: Arnaud

last: Petit

last: Puthier


title: Genome-wide maps of chromatin state in major stages of human thymopoieseis

summary: Analysis of histone 3 post-translational modifications in differents stages of human thymopoiesis.

overall_design: Seven ChIP-Seq to complement reference epigenomes produced in the Blueprint project. Inputs for these samples have to be requested to Blueprint DAC.

first: Denis

first: Elizabeth

last: Macintyre

first: Hendrik

last: Stunnenberg

first: Vahid

last: Asnafi


title: Analysis of 1,25-dihydroxyvitamin D3 genomic action reveals calcium regulating and calcium independent effects in mouse intestine and human enteroids

status: Public on Oct 22 2020

city: Houston

first: Noah

last: Shroyer

address: One Baylor Plaza, Room N710

department: Medicine Section of Gastroenterology and Hepatology

institute: Baylor College of Medicine

summary: The objective of this study was to determine how the differentiated and undifferentiated compartments of the human duodenum and colon epithelium respond to 1,25-dihydroxyvitamin D3 via human enteroids

overall_design: mRNA Profiles of human enteroids (differentiated and undifferentiated) treated with Control (Ethanol) or 1,25D3 (Vitamin D) for 24 hours with a total of 48 samples

first: Zachary

middle: K

last: Criss

middle: F


title: DNA methylation signatures reveal the diversity of processes remodeling liver cancer methylomes

status: Public on Sep 03 2020

first: Eric

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

type: Methylation profiling by genome tiling array

summary: Genome-scale DNA methylation was analyzed in a cohort of 239 hepatocellular adenomas and 35 normal liver tissues.

overall_design: Bisulfite converted DNA from 239 hepatocellular adenomas and 35 normal liver samples were hybridized to Illumina HumanMethylation450 BeadChips.

first: Letouzé

last: Eric

first: Meunier

last: Léa

first: Imbeaud

last: Sandrine

first: Zucman-Rossi

last: Jessica


title: Expression Data human IDH1 mutant and wild-type high grade gliomas

first: Paul

last: Kongkham

summary:
Gene expression data generated for the purpose of correlating differentially-expressed genes between IDH1 mutant and IDH1 wild-type high grade gliomas with differential hydroxymethylcytosine profiles as determined using
Illumina EPIC BeadChip platform.

overall_design: RNA isolated directly from fresh-frozen human high grade gliomas.

first: Harshika

last: Jain


title: BET inhibition disrupts transcription but retains enhancer-promoter contact [ChIP-seq]

first: Thomas

last: Milne

overall_design: ChIP-seq

first: Nicholas

last: Crump


title: Design logic of hypothalamus development mapped by single-cell RNA-seq

status: Public on May 06 2020

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

summary:
Purpose: We aimed to reconstruct the development formation of cellular identities' heterogeneity in the hypothalamus with single-cell RNA sequencing. We planned to track branching process of neurogenesis and follow the formation of cell identities.
Results: We integrate single-cell RNA-seq data on 51,199 cells of ectodermal origin, representing critical stages of pre- and postnatal hypothalamus development, supported by anatomical lineage reconstruction to show that bulk neurogenesis in the hypothalamus, dominated by Notch signalling and its interaction with Ascl1, persists until the neonatal period to produce molecularly distinct astrocytes, ependyma, tanycytes and 30 protoclusters of neurons. Alike in adults, the assignment of neurotransmitters and neuropeptides together with transcription factors as positional marks for each neuronal cluster is sufficient to establish the spatially-resolved taxonomy of hypothalamic neurons. By deducing gene regulatory networks, exemplified by hierarchical gene clusters driven by Onecut2/Onecut3 transcription factors for dopamine neurons, we resolve how neuronal lineages diverge into functionally non-overlapping endocrine subtypes. Dopamine neurons are used to illustrate molecular convergence with their shared neurotransmitter identity representing a mismatch to their molecular distances on multidimensional vector spaces. We demonstrate the existence of non-canonical chemotropic axes in the hypothalamus, particularly sequential ligand-receptor switching in the unexpectedly abundant Slit/Robo cassette. Slit2 is identified in ventricular ependymocytes and implicated in repulsing new-born neurons that sequentially express Robo1 and Robo2 receptors for migration and differentiation.
Conclusions: Overall, our unbiased map of hypothalamic cell types and extracellular guidance cues uncovers molecular principles shaping the developmental architecture of the mammalian hypothalamus and rationalise how hypothalamic neuronal heterogeneity is transformed into a multimodal neural unit that retains a virtually infinite adaptive potential throughout life.

overall_design: To follow the developmental progress in the hypothalamus we obtained 10X Genomics single cell samples of the mouse hypothalamus from several developmental timepoints: E15.5 (n=8), E17.5 (n=7), P0 (n=4), P2 (n=4), P10 (n=3), P23 (n=3).

first: Roman

last: Romanov

first: Evgenii

middle: O

last: Tretiakov

first: Maria

middle: E

last: Kastriti

first: Maja

last: Zupancic

first: Martin

last: Häring

first: Solomiia

last: Korchynska

first: Konstantin

last: Popadin

first: Marco

last: Benevento

first: Patrick

last: Rebernik

first: Francois

last: Lallemend

first: Katsuhiko

last: Nishimori

first: Frédéric

last: Clotman

first: William

middle: D

last: Andrews

first: John

last: Parnavelas

first: Matthias

last: Farlik

first: Christoph

last: Bock

first: Igor

last: Adameyko

first: Tomas

last: Hökfelt

first: Erik

last: Keimpema


title: Evidence for additive and synergistic action of mammalian enhancers during cell fate determination [ATAC-seq, CEBPA-ChIP-seq]

status: Public on Jun 03 2020

city: Göttingen

first: Jinmi

last: Choi

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

summary: Enhancer activity is known to drive cell differentiation and cell type determination, but it remains unclear how enhancers cooperate during these processes. Here we investigate enhancer cooperation during transdifferentiation of human B-cells to macrophages using enhancer RNA synthesis from accessible, H3K4-monomethylated chromatin regions as a proxy for enhancer activity. Most enhancers cooperate in an additive way to induce transcription of target genes. However, at ~130 loci, enhancers cooperate synergistically, changing activity of target genes exponentially over time. The latter genes are cell type-specific, indicating that enhancer synergy can drive differentiation and cell type determination. Pioneering factor occupancy, DNA accessibility profiling and eRNA synthesis reveal the temporal order of events that lead to enhancer synergy. Our results are consistent with a condensation model for transcription activation of cell type-specific genes that involves simultaneous contacts of multiple enhancers with their target promoter.

overall_design: ATAC-seq, ChIP-seq of C/EBPa


title: BET inhibition disrupts transcription but retains enhancer-promoter contact

first: Thomas

middle: A

last: Milne


title: Evidence for additive and synergistic action of mammalian enhancers during cell fate determination

first: Kseniia

last: Lysakovskaia

first: Gregoire

last: Stik

first: Carina

last: Demel

first: Johannes

last: Soeding

first: Tian

middle: V

last: Tian

last: Graf

last: Cramer


title: Olfactory stimulation regulates the birth of neurons that express specific odorant receptors

first: Stephen

last: Santoro


title: Identification of GLYMA.08G227700 binding sites in soybean early maturation embryos

status: Public on Jun 20 2020

city: Davis

last: Harada

state: CA

address: One Shields Avenue

department: Plant Biology

institute: University of California

summary: To dissect the gene regulatory networks operating during soybean embryo development, we identified the binding sites genome-wide for transcription factor GLYMA.08G227700  in early maturation embryos using ChIP-seq.

overall_design: Identification of GLYMA.08G227700 binding sites in soybean embryos at the early maturation stage.  ChIP and total chromatin controls (input) were obtained for two biological replicates.  A total of 4 samples were sequenced using the Illumina HiSeq4000 platform.

first: Julie

last: Pelletier

first: Leonardo

last: Jo

first: Rie

last: Uzawa

first: Min

last: Chen

first: Robert

middle: B

last: Golberg


title: Comprehensive RNA-seq transcriptomic profiling in normal thymocytes and adult T lymphoblastic Leukemia

first: Vahid

last: Asnafi


title: Genome-wide analysis of the transcriptional profile of IL1b/TNFa-treated and EAE astrocytes in B6 mice.

status: Public on Feb 12 2020

city: Boston

first: Michael

last: Wheeler

address: 60 Fenwood Rd.

department: Neurology

institute: Brigham and Women's Hospital

summary: We identify pathways regulated by IL1b/TNFa ICV injection and EAE in astrocytes

overall_design: IL1b/TNFa-ICV injected (n=3) and EAE (n=3) mice

first: Emily

middle: C

last: Tjon

first: Veit

last: Rothhammer

first: Francisco

last: Quintana


title: Genome-wide analysis of the transcriptional profile of astrocytes across EAE by CNS region in Gfap-Cre;Ribotag(f/f) mice uisng Ribotag immunoprecipitation.

summary:
We identify pathways regulated in astrocytes across EAE by CNS region.
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: Naïve (n=3 per region); acute (n=3 cerebellum, cranial nerves; n=2 cortex, parenchyma, spinal cord); remitting (n=3 spinal cord, cerebellum, cranial nerves; n=2 cortex, parenchyma)


title: Genome-wide analysis of the transcriptional profile of the CNS in healthy control patients.

summary:
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.
We identify cellular heterogeneity in MS patient samples from the CNS

overall_design: N=5 healthy control patients.

first: Charles

last: Couturier

first: Zhaorong

last: Li


title: Genome-wide analysis of the transcriptional profile of WT and Nfe2l2 KD astrocytes during EAE in B6 mice [Nrf2 RNA-seq]

summary:
We identify pathways regulated by Nfe2l2 in astrocytes during EAE
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: sgScrmbl-targeted (n=3) and sgNfe2l2-targeted (n=3) mice


title: Genome-wide analysis of the transcriptional profile of WT and Mafg KD astrocytes during EAE in B6 mice.

summary: We identify pathways regulated by Mafg in astrocytes during EAE

overall_design: sgScrmbl-targeted (n=3) and sgMafg-targeted (n=3) mice


title: Genome-Wide DNA Methylation Meta-analysis in the Brains of Suicide Completers II

status: Public on Mar 06 2020

city: Exeter

first: Stefania

last: Policicchio

state: Devon

address: RILD building, BARRACK ROAD, Albion Place

institute: University of Exeter, Medical School

summary:
Suicide is the second leading cause of death globally among young people representing a significant global health burden. Although the molecular pathology of suicide remains poorly understood, it has been hypothesised that epigenomic processes may play a role. The objective of this study was to identify suicide-associated DNA methylation changes in the human brain by utilising previously published and unpublished methylomic datasets. We analyzed prefrontal cortex (PFC, n = 211) and cerebellum (CER, n = 114) DNA methylation profiles from suicide completers and non-psychiatric, sudden-death controls, meta-analyzing data from independent cohorts for each brain region separately. We report evidence for altered DNA methylation at several genetic loci in suicide cases compared to controls in both brain regions with suicide-associated differentially methylated positions enriched among functional pathways relevant to neuropsychiatric phenotypes and suicidality, including nervous system development (PFC) and regulation of long-term synaptic depression (CER). In addition, we examined the functional consequences of variable DNA methylation within a PFC suicide-associated differentially methylated region (PSORS1C3 DMR) using a dual luciferase assay and examined expression of nearby genes.  DNA methylation within this region was associated with decreased expression of firefly luciferase but was not associated with expression of nearby genes, PSORS1C3 and POU5F1. Our data suggest that suicide is associated with DNA methylation, offering novel insights into the molecular pathology associated with suicidality.
DNA from bulk post-mortem brain (human cerebellum) from 33 individuals

overall_design: Bisulphite converted DNA from the 33 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Sam

last: Washer

first: Joana

last: Viana

first: Artemis

last: Iatrou

first: Joe

last: Burrage

first: Eilis

last: Hannon

first: Gustavo

last: Turecki

first: Zachary

last: Kaminsky

first: Jonathan

last: Mill

first: Emma

last: Dempster

first: Therese

middle: M

last: Murphy


title: Genome-wide analysis of the transcriptional profile of astrocytes during EAE in Gfap-TdTomato mice by scRNA-seq [scRNA-seq 2]

first: Michael

last: Wheeler

summary:
We identify astrocyte heterogeneity during EAE in B6 mice.
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: Naïve mice (n=4), EAE peak phase (n=4), EAE remission phase (n=4).


title: Genome-wide analysis of chromatin profile in astrocytes isolated from EAE mice transduced with astrocyte-specific Mafg-targeting or non-targeting lentiviruses [ATAC-seq]

summary:
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

We report MAFG regulation of pathogenic activities in astrocytes during EAE.

overall_design: Mice transduced with non-targeting (n=3) or Mafg-targeting (n=3) lentiviruses. EAE induced in mice.

first: Emily

last: Tjon


title: Genome-wide analysis of MAFG binding in astrocytes during EAE [ChIP-seq]

summary:
We report MAFG recruitment to ARE elements in astrocytes during EAE compared to naïve mice

Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: IP of MAFG in astrocytes from EAE mice (n=3) versus naïve mice (n=3); IP samples were normalized to 10% input


title: Genome-wide analysis of the transcriptional profile of WT and CSF2RB astrocyte conditional KO during EAE in B6 mice [Csf2rb RNA-seq]

summary:
We identify pathways regulated by Csf2rb in astrocytes during EAE
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: Littermate controls (n=3) and CSF2RB Aldh1l1-CreERT2-Csf2rb(f/f) (n=3)


title: Single cell RNA sequencing of lung adenocarcinoma

status: Public on Mar 27 2020

city: Seoul

first: Hae-Ock

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Department of Microbiology

country: South Korea

institute: College of Medicine, The Catholic University of Korea

summary: We performed single cell RNA sequencing (scRNA-seq) for 208,506 cells derived from 58 lung adenocarcinomas from 44 patients, which covers primary tumour, lymph node and brain metastases, and pleural effusion in addition to normal lung tissues and lymph nodes. The extensive single cell profiles depicted a complex cellular atlas of lung adenocarcinoma progression which includes cancer, stromal, and immune cells in the surrounding tumor microenvironments.

overall_design:
All single-cell mRNA expression profiles were acquired from forty-four patients pathologically diagnosed with lung adenocarcinoma (LUAD) (58 samples). 11 tumour, 11 distant normal lung, 10 normal lymph node, and 10 metastatic brain tissue samples were obtained from LUAD patients conserving surgery without prior treatment. 7 metastatic lymph node and 4 lung tumour tissue samples from advanced stage LUAD patients were also collected through the endobronchial ultrasound (EBUS) and bronchoscopy (BRONCHO). And 5 pleural fluid samples were obtained from LUAD patients with malignant pleural effusion. We applied the quality measures so as to remove less informative cells and finally obtained 208,506 single cell sequencing data.

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Submitter states that raw data are not availble for open access due to patient privacy concerns. Raw data will be made available under controlled access at EGA: EGAD00001005054 (EGAS00001003680 and EGAS00001003681).
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first: Myung-Ju

last: Ahn


title: MAFG-driven astrocytes promote CNS inflammation

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide analysis of DNA methylation profile in astrocytes isolated from naïve mice or EAE mice transduced with astrocyte-specific Mafg-targeting or non-targeting lentiviruses [WGBS]

summary:
We report MAFG regulation of DNA methylation in astrocytes during EAE.

Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: Naïve mice (n=3). Mice undergoing EAE transduced with non-targeting (n=3) or Mafg-targeting (n=3) lentiviruses. EAE induced in 6 of 9 mice.

first: Francisco

last: Quintana


title: Comprehensive DNA methylation profiling identifies novel diagnostic biomarkers for thyroid cancer

status: Public on Jan 01 2020

city: daejeon

first: Jonglyul

last: Park

address: 52, Eoeun-dong, Yuseong-gu

department: Medical genomics

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
DNA methylation markers in thyroid tumor
We used Illumina HumanMethylation EPIC bead array containing over the 850,000 CpG sites in 34 thyroid normal and tumor samples to identify thyroid subtype-specfic DNA methylation markers.

overall_design: Examination of genome-wide DNA methylation profiling in 34 thyroid normal and tumor samples

first: Yong

middle: S

last: Kim

first: Chan

last: Jung

first: Jong-Lyul


title: DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

status: Public on Mar 18 2020

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

summary: Dysregulation of DNA methylation and mRNA alternative cleavage and polyadenylation (APA) are both prevalent in cancer. Through various mechanisms, these processes promote carcinogenesis by altering the production of oncogenes and tumour suppressors. Although promoter DNA methylation is most studied, the majority of differentially methylated regions occur in non-promoter contexts, including the gene 3′ ends, where APA occurs. Using genome-wide methylation sequencing and poly(A)-sequencing we identified a correlation between DNA methylation and APA. As such, we sought to define the mechanism regulating this relationship. Here, we show that DNA methylation regulates APA using CCCTC binding factor (CTCF) binding and recruitment of the cohesin complex. Using data of cancer subtypes available from The Cancer Genome Atlas we authenticated this correlation in vivo. This mechanism of DNA methylation-regulated APA demonstrates the impact of aberrant DNA methylation on transcriptome diversity in cancer.

overall_design: Cultured cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with G (for Pol2Ser2 and Pol2Ser5) or A (for CTCF, RAD21, SMC1, and H3K27Ac) agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ug of antibody against each protein. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end). Cultured cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (30 ug) was precleared with G (for Pol2Ser2 and Pol2Ser5) or A (for CTCF, RAD21, SMC1, TotalRNAPol2, and H3K27Ac) agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4ug of antibody against each protein. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina's NextSeq 500 (75 nt reads, single end).

first: Vishal

last: Nanavaty

first: Elizabeth

last: Abrash

first: Changjin

last: Hong

first: Thomas

last: Sweet

first: Jeffrey

last: Bhasin

first: Srinidhi

last: Singuri

first: Byron

first: Tae

last: Hwang


title: Skeletal Muscle Fibrosis in Pancreatic Cancer Patients with Respect to Survival

status: Public on Dec 03 2019

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary:
Skeletal muscle wasting is a devastating consequence of cancer that may be responsible for nearly 30% of cancer-related deaths. In addition to muscle atrophy, we have identified significant muscle fiber damage and replacement of muscle with fibrotic tissue in rectus abdominis muscle biopsies from cachectic pancreatic ductal adenocarcinoma (PDAC) patients that associates with poor survival. Transcriptional profiling of muscle harvested from these same patients supported these findings by identifying gene clusters related to wounding, inflammation and cellular response to TGF-B upregulated in cachectic PDAC patients compared with non-cancer controls.
In this dataset, we include the expression data obtained from rectus abdominis muscle biopsies fron non-cancer controls patients undergoing abdominal surgery for benign reasons and from PDAC patients undergoing tumor-resection surgery. PDAC patients were further classified as non-cachectic or cachectic. Cachexia was defined as a body weight loss of >5% during the 6 months prior to surgery. The purpose of this study was to identify the broader transcriptional networks changed in cachectic PDAC patients versus non-cancer controls, that may be associated with the histological changes observed in muscle biopsies harvested from these same patients.

overall_design: For microarray analysis, a total of 46 RNA samples across four groups are included. The groups are as follows: Non-cancer control patients (n = 16); Chronic pancreatitis patients (n = 8); Non-cachectic PDAC patients (n = 5); Cachectic PDAC patients (n = 17). To identify broader gene networks changed in cachectic PDAC patients that may be associated with histological findings of muscle damage and replacement of muscle with fat and fibrotic tissue, we performed differential expression analysis between non-cancer controls and cachectic PDAC patients, and between non-cancer controls and non-cachectic PDAC patients. PDAC patients receiving Stage IV diagnosis were excluded from analyses. Due to the inflammatory nature of chronic pancreatitis, patients diagnosed with chronic pancreatitis were not included in the non-cancer control group and were excluded from analyses.

first: Sarah

last: Judge

first: Rachel

last: Nosacka

first: Daniel

last: Delitto

first: Michael

last: Gerber

first: Miles

last: Cameron

first: Jose

middle: G

last: Trevino

first: Andrew


title: Impact of GNA13 knockdown on gene expression changes in PC3 cells

status: Public on Dec 31 2019

city: SIngapore

first: Suhail Ahmed Kabeer

last: Rasheed

address: 8 College Road

department: Programme in Cancer and Stem Cell Biology

country: Singapore

institute: Duke-NUS Medical School

summary: GNA13 has been shown to have multiple oncogenic roles in many different solid tumors including prostate cancers. However, the molecular mechanisms that drive GNA13-induced oncogenesis and metastasis is not understood completely. To elucidate the mechanisms driven by GNA13 in prostate cancer cells, we performed total RNA sequencing in PC3 cells after knocking down GNA13 expression using two different shRNAs.

overall_design: RNA sequencing of PC3 cells stably expressing GNA13-targeting shRNAs or control shRNA.

first: Suhail

first: Sujoy

last: Ghosh

first: Xiao-ran

last: Chai

first: Veerabrahma

middle: P

last: Seshachalam

first: Patrick

last: Casey


title: The PGR occupancy profiles in nonpregnant and gravid human myometrial tissues

status: Public on Nov 28 2019

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary: Profiles of PGR genome occupancy in human myometrial specimens were documented by ChIP-seq to investigate downstream targets of the progesterone receptor and candidate partner transcription regulators at the nonpregnant and term pregnant stages.

overall_design: Two nonpregnant and two term pregnant myometrial specimens were subject to ChIP-seq analysis. Viable tissue is taken from myometrial margins at the time of hysterotomy performed for clinically indicated cesarean section. After washing each specimen briefly in phosphate buffered saline (PBS), pieces of myometrium are flash frozen. All specimens are stored at <-80°C until use. ChIP-seq was performed by the Active Motif.

first: San-Pin

last: Wu

first: Matthew

last: Anderson

first: Tianyuan

last: Wang

first: Lecong

last: Zhou

first: Olivia

last: Emery

first: Xilong

last: Li

first: Francesco

last: De Mayo


title: A TCR/anti-CD3 bispecific fusion protein targeting gp100 potently activated anti-tumor immune responses in metastatic melanoma

status: Public on Oct 30 2019

city: Rockville

first: Brandon

middle: W

last: Higgs

address: 2273 Research Blvd Suite 220

institute: Immunocore, Ltd

summary: Tumor-specific cytotoxic T cells are required for effective immunotherapy. Here we introduce a bispecific fusion protein (tebentafusp) designed to target gp100 (a melanoma-associated antigen) through a high affinity T cell receptor binding domain, and through an anti-CD3 effector domain re-directs any cytotoxic T cell, regardless of its intrinsic specificity, to kill gp100-expressing tumor cells.  In patients with metastatic melanoma, tebentafusp showed anti-tumor activity and manageable and predictable side effects. Notably, tebentafusp induced an increase in serum CXCL10 (a T cell attractant), and a reduction in circulating CXCR3+ CD8+ T cells together with an increase in cytotoxic T cells in the tumor microenvironment (TME). Furthermore, the appearance of rash, likely due to cytotoxic T cells targeting of gp100-expressing skin melanocytes, or an increase in serum CXCL10 showed a positive association with patient survival.  Taken together, these results suggest that re-directing T cells using a gp100-targeting T cell receptor/anti-CD3 bispecific fusion protein may provide benefit to patients with metastatic melanoma.

overall_design: To assess the changes in the tumor immune micro-environment following tebentafusp more broadly, we analyzed gene expression from paired baseline and on-treatment biopsies. We compared within a subset of 9 patients (melanoma type: 1 uveal, 8 non-uveal), 2 responders (partial response) and 7 with progressive disease.


title: Ribosome pausing at the AT-rich codons regulates the protein expression of secondary metabolite gene clusters in the Streptomyces tsukubaensis NRRL 18488

status: Public on Oct 16 2019

city: Daejeon

first: Namil

last: Lee

address: Daehakro

department: Biological science

institute: KAIST

summary: Streptomyces tsukubaensis NRRL 18488 is the preferred strain for the production of immunosuppressant agent tacrolimus (FK506). To take full advantage of its genetic potential, systematic understanding of secondary metabolism and related regulatory mechanisms is highly demanded. Here, to this end, we complete its 7.9 Mbp linear genome sequence followed by integrating with multi-omics measurements. With accurate reannotation of FK506 gene cluster, total 2,389 transcription start sites were determined by using primary transcriptome analysis. Integrated analysis of transcriptome and translatome data revealed that secondary metabolic gene clusters, especially FK506 cluster, undergo translational control with decrease in translational efficiency according to the growth. Furthermore, we demonstrated that SD motif has little correlation with ribosome pausing but AT-rich codons delay the translational elongation. Strong ribosome pausing was observed in the rare TTA codon in FK506 cluster. This comprehensive genome-scale analysis provides insight to the translational regulation of secondary metabolism in S. tsukubaensis.

overall_design: Transcription abundance and ribosomal profiling analysis of Streptomyces tsukubaensis according to the growth phase

first: Yujin

last: Jeong

first: Jinkyoo

last: Chung

first: Young

first: Suhyung

last: Cho

first: Bernhard

last: Palsson

first: Byung-Kwan


title: RNA-Seq analysis of ileocecal valve and peripheral blood from Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis

status: Public on Sep 14 2019

city: Derio

first: MARTA

last: ALONSO-HEARN

state: Bizkaia

address: Berreaga 1

department: Animal Health

institute: NEIKER

summary:
Purpose: Since the peripheral blood (PB) is the most available physiological fluid for the detection of biomarkers, in the current we examine whether it recapitulates, at least in part, the transcriptome of the ileocecal valve (ICV), the primary site of MAP colonization. For this purpose, RNA-Seq was used to identify host genes differentially expressed (DE) in ICV and PB samples collected from PTB-infected animals with focal or diffuse lesions in gut tissues versus control animals.
Methods: RNA-Seq libraries were single-end sequenced in a 1x75 format using an Illumina NextSeq 500 sequencer. The raw reads were filtered by their length (minimum size 60 bp long) and percentage of ambiguous base N less than 5 % using Prinseq-lite. Trimmed reads were subsequently mapped to the Bos Taurus reference genome (Bos_taurus.UMD3.1. version 87) with TopHat mapper. The resulting alignment files were provided to Cufflinks to generate a transcriptome assembly for each condition. These assemblies were then merged together using Cuffmerge, which is included in the Cufflinks package. This merged assembly provided a uniform basis for calculating gene and transcript expression levels in each condition. The reads and merged assembly were fed to Cuffdiff which calculates expression levels and tested the statistical significance of each observed change in expression. The fold change (in log2 scale), P-values and false discovery rates (FDR) for each gene were obtained. The genes with a FDR-adjusted threshold ˂ 0.05 were considered differentially expressed (DE) when compared to the control group.
Results: Our results demonstrated both shared, and PB and ICV-specific gene expression in response to a natural Map infection. As expected, the number of differentially expressed (DE) genes was larger in the ICV than in the PB samples. Among the DE genes in the PB and ICV samples, there were some common genes irrespective of the type of lesion including the C-X-C motif chemokine ligand 8 (CXCL8/IL8), apolipoprotein L (APOLD1), and the interferon inducible protein 27 (IFI27). The biological processes (BP) enriched in the ICV gene expression profiles from the cows with focal lesions included the killing of cells of other organism, defense response, immune response and the regulation of neutrophil chemotaxis. Two of these BP, the defense and immune response, were also enriched in the ICV and PB from the cows with diffuse lesions. Metabolic analysis of the DE genes revealed that the N-glycan biosynthesis, bile secretion, one-carbon pool by folate and purine metabolism were significantly enriched in the ICV from the cows with focal lesions. In the ICV from cows with diffuse lesions; the valine, leucine and isoleucine degradation route, purine metabolism, vitamin digestion and absorption and the cholesterol routes were enriched
Conclusions: This study is the first to simultaneously describe transcriptomic changes in PB and ICV samples of cattle naturally infected with MAP. Several important observations were made. First, by comparing the transcriptomic profiles of two MAP-targeted tissues we described both unique and overlapping changes in the transcriptome of the infected cows versus the control group. Second, our study highlighted the ability of the RNA-Seq technology to reveal roles for genes that have not been previously implicated in the host response to MAP infection. Third, our transcriptomic analysis provided potential biomarkers for the development of future diagnostic tools, vaccines and therapeutics.

overall_design: RNA-Seq libraries were prepared from the PB and ICV of 14 animals within the three categories; with focal (N=6) or diffuse (N= 5) histopathological lesions in gut tissues and control (N=3).

first: Marta

last: Alonso-Hearn

first: Maria

last: Canive


status: Public on Jul 15 2019

city: Aurora

first: Matthew

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

institute: University of Colorado Anschutz Medical Campus

summary: Transcriptional responses to interferon require Mediator kinase-dependent pause release and mechanistically distinct functions of CDK8 and CDK19.

overall_design: Examination of 45 minute IFNgamma response in CDK8 analog sensitive HCT116 cells compared with wild type HCT116 cells with all the applicable controls.

first: Cecilia

last: Levandowski

first: Zdenek

last: Andrysik

first: Heather

last: Bender


title: Nonpregnant and term pregnant human myometrial tissues

status: Public on Nov 27 2019

first: Franco

last: Demayo


title: The histone H3-H4 tetramer is a copper reductase enzyme

status: Public on Jun 04 2019

city: Los Angeles

first: Oscar

middle: Antonio

last: Campos

address: 615 Charles Young Dr. South

department: Biological Chemistry

institute: University of California, Los Angeles

summary: We sought to examine whether nucleosomes participate in cellular copper homeostasis by directly catalyzing the reduction of copper, thereby producing the biousable cuprous ion. To test this hypothesis, we disrupted a potential copper coordination site of the nucleosome by mutating the histone H3 His113 residue to an asparagine (H113N) in the budding yeast. We observed that copper homeostasis was indeed perturbed in the H113N mutant. However, given the known roles of nucleosomes in regulating gene expression, it was reasonable to expect that the perturbation of copper homeostasis was due simply to a conincidental disrutpion of the tanscriptional regulation of genes important for copper metabolism. We performed polyA+ RNA sequencing of WT and H3H113N yeast strains in various conditions to assess whether gene expression alterations could account for the copper-related phenotypes.

overall_design: S. cerevisiae strains with or without the H3H113N mutation, and alone or in combination with CTR1 or CCS1 deletions, were grown in various liquid media conditions that tested their ability for proper copper utilization. The H3H113N mutation resulted in copper-dependent growth defects in several of the conditions. Total RNAs were extracted from these cells and subjected to library preparation and Illumina HiSeq sequencing.

first: Siavash

last: Kurdistani


title: Genome-wide analysis of the transcriptional profile of the CNS in MS patients.

first: Michael

last: Wheeler

summary:
We identify cellular heterogeneity during in MS patient samples from the CNS
Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: N=4 MS patients.

first: Emily

last: Tjon

first: Zhaorong

last: Li

first: Francisco

middle: J

last: Quintana


title: Genome-wide analysis of the transcriptional profile of the CNS during EAE in B6 mice by scRNA-seq [scRNA-seq]

summary:
We identify cellular heterogeneity during EAE in B6 mice.

Multiple sclerosis (MS) is an autoimmune neurologic disease leading to demyelination and neurologic dysfunction controlled by both genetic and environmental factors. In addition to CNS-infiltrating immune cells, CNS-resident cells, such as astrocytes, are thought to play an important role in MS pathogenesis. However, a comprehensive understanding of the extent to which gene expression is disrupted in astrocytes is not known. Here, we implement single-cell RNA sequencing, in vivo genetic perturbations, cell-specific RNA profiling by Ribotag, as well as single-cell RNA sequencing of human MS patient samples to identify a transcriptional regulatory network in astrocytes that controls the pathogenesis of EAE and potentially, MS. We defined an astrocyte subpopulation characterized by expression of the small Maf protein, MAFG, which represses NRF2-driven antioxidant mechanisms and promotes EAE pathogenesis. Mechanistically, MAFG suppresses NRF2-dependent antioxidant genetic programs by cooperating with its cofactor, MAT2a, to promote DNA methylation in the context of CNS inflammation, which in turn increases pathogenic signaling processes in astrocytes. MAFG/MAT2a astrocytes are controlled by GM-CSF signaling, which drives EAE pathogenesis and MAFG expression. MAFG is activated in astrocytes derived from MS patients, which are characterized by DNA methylation programs, pro-inflammatory signaling processes including GM-CSF signaling, and repressed NRF2 activation. Together, these data create a transcriptional and epigenetic framework to analyze CNS inflammation in MS and may provide new therapeutic targets.

overall_design: Naïve mice (n=6), CFA-only mice (n=3), EAE priming phase (n=6), EAE peak phase (n=6), EAE remission phase (n=6)


title: Characterizing transcriptomic differences between between primary colorectal adenocarcinomas and distant metastases reveals subtypes of metastatic colorectal cancer

status: Public on May 18 2019

city: Tampa

first: Stephanie

middle: L.

last: Schmit

state: FL

address: 12902 USF Magnolia Drive

department: Department of Cancer Epidemiology

institute: H. Lee Moffitt Cancer Center

summary: We present a novel approach for investigating transcriptomic differences between primary colorectal cancers (CRC) and distant CRC metastases, which may help to identify primaries at high risk for future dissemination and to inform the development of metastasis-targeted therapies. Eliminating tissue specificity of the “host” organs where tumors are located and adjusting for confounders such as exposure to chemotherapy and radiation, allows for an effective comparison of primary CRC and metastatic lesion transcriptomes at both the gene and pathway levels. Using this approach, our discovery-validation design identified that metastases are characterized by reduced epithelial-mesenchymal-transition (EMT) but increased MYC target and DNA repair pathway activities. The most significant gene-level expression differences between primaries and metastases were in FBN2 and MMP3, which showed over a 7-fold difference. In addition, we uncovered two distinct subtypes of CRC metastases that are characterized by either EMT-inflammatory or proliferative phenotypes, and demonstrated that none of the metastases examined were of consensus molecular subtype (CMS) 3 suggesting subtype exclusivity.  Highlighting transcriptome differences between primary tumors and CRC metastases delineates pathways that may be activated in metastases and may assist in the development and/or selection of existing targeted treatment regimens for individuals with metastatic disease.

overall_design: In the study presented here, surgical resections of tumor samples (primary tumors n=333 from the MCC dataset; primary tumors  n=545 from Consortium dataset; and n=184 metastases of CRC from the MCC dataset and n=73 metastases of CRC from the Consortium dataset ) from n=1120 patients with CRC in the discovery Moffitt Cancer Center (MCC) Cohort and the validation Consortium cohort are presented with 24497 genes detected. Of note, there are n=15 patients in the MCC dataset that have matched primary CRC and metastatic lesions of CRC.

middle: L

first: Hildreth

middle: R

last: Frost

first: Christopher

middle: I

last: Amos

first: Yasmin

last: Kamal

first: Hannah

last: Hoehn


title: From silence to song: Testosterone triggers extensive transcriptional changes in the female canary HVC

city: Seewiesen

first: Meng-Ching

last: Ko

state: Bayern

address: Eberhard-Gwinner-Str. 6a

department: Behavioral Neurobiology

institute: Max Planck Institute for Ornithology

summary: In this data set, we compared the expression data of song nuclei HVC dissected from adult female canaries (S. canaria) implanted with 7-mm SilasticTM tubes filled with testosterone for 6 periods (1h, 3h, 8h, 3d, 7d, and 14d) with control birds (implanted with empty tube) to identify testosterone effects on gene expression.

overall_design: A total of 39 HVC from adult female canaries (S. canaria) were sampled. The transcriptomes were compared by testosterone-treated birds with control birds.

first: Carolina

last: Frankl-Vilches

first: Antje

last: Bakker

first: Manfred

last: Gahr


title: Pancreas single cell patch-seq links physiologic dysfunction in diabetes to transcriptomic phenotypes

status: Public on Feb 18 2020

city: Gothenburg

first: Joan

last: Camunas-Soler

address: Medicinaregatan 9C

institute: University of Gothenburg

summary: Combined single-cell RNAseq and electrophysiological profiling of human pancreatic islet cells (pancreas patch-seq) to link transcriptomic phenotypes of islet cells to their physiologic properties.

overall_design: The dataset contains 1,369 pancreas patch-seq cells from human donors (nondiabetic and type II diabetes), 348 cryopreserved patch-seq cells (nondiabetic and type I diabetes) and 3,518 FACS islet cells from the same donors. In total cells from 18 nondiabetic , 7 T2D donors, 3 T1D (cryopreserved) and 3 nondiabetic donors (cryopreserved) were used. Single-cell RNA libraries are done using SmartSeq2.

first: Xiaoqing

last: Dai

first: Yan

last: Hang

first: Seung

middle: K

last: Kim

first: Patrick

last: MacDonald

first: Stephen

last: Quake


title: Lipoprotein Particle (LPP) exRNA Profiles Isolated from Plasma

status: Public on Dec 20 2018

city: San Francisco

first: Robert

last: Raffai

address: 4150 Clement Street

institute: University of California, San Francisco

summary: An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on lipoprotein particle (LPP) exRNA profiles obtained via sequential density ultracentrifugation (SD-UC) and fast protein liquid chromatography (FPLC).

overall_design: RNA-seq profiles of purified lipoprotein (LPP) carriers (HDL, VLDL, LDL, Chylomicron) were isolated from plasma using sequential density ultracentrifugation (SD-UC) and fast protein liquid chromatography (FPLC).

first: Allen

last: Chung

first: David

last: Wong

first: Srimeenakshi

last: Srinivasan

first: Clara

middle: D

last: Laurent

first: Louise


title: Integrated analysis of genetic variants regulating retinal transcriptome (GREx) identifies genes underlying age-related macular degeneration

status: Public on Feb 11 2019

city: Bethesda

first: Matthew

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

summary: Age-related macular degeneration (AMD) is a complex multifactorial disease with at least 34 loci contributing to genetic susceptibility.  To gain functional understanding of AMD genetics, we generated transcriptional profiles of retina from 453 individuals including both controls and cases at distinct stages of AMD.  We integrated retinal transcriptomes, covering 13,662 protein-coding and 1,462 noncoding genes, with genotypes at over 9 million common single nucleotide polymorphisms (SNPs) for expression quantitative trait loci (eQTL) analysis of a tissue not included in Genotype-Tissue Expression (GTEx) and other large datasets.  Cis-eQTL analysis revealed 10,474 genes under genetic regulation, including 4,541 eQTLs detected only in the retina.  We then integrated the AMD-genome-wide association studies (GWAS) data with eQTLs and ascertained target genes at six loci.  Furthermore, using transcriptome wide association analysis (TWAS), we identified 23 additional AMD-associated genes, including RLBP1, HIC1 and PARP12.  Our studies expand the genetic landscape of AMD leading to direct targets for biological evaluation and establish the Genotype-Retina Expression (GREx) database as a resource for post-GWAS interpretation of retina-associated traits including glaucoma and diabetic retinopathy.

overall_design: Retinal samples from 523 aged post-mortem human subjects from a spectrum of age-related macular degeneration (AMD) were RNA-seq profiled.

first: Rinki

last: Ratnapriya

first: Margaret

last: Starostik

first: Sosina

last: Kayode

first: Madeline

last: Kwicklis

first: Rebecca

last: Kapphahn

first: Lars

last: Fritsche

first: Ashley

last: Walton

first: Marios

last: Arvanitis

first: Linn

last: Geiser

first: Alexandra

last: Pietraszkiewicz

first: Sandra

last: Montezuma

first: Emily

last: Chew

first: Alexis

last: Battle

first: Gonçalo

last: Abecasis

first: Deborah

last: Ferrington

first: Nilanjan

last: Chatterjee

first: Anand

last: Swaroop


title: Ultracentifugation and nanoscale deterministic lateral displacement (nanoDLD) of samples for exRNA analysis

status: Public on Dec 13 2018

city: Yorktown Heights

first: Gustavo

last: Stolovitzky

address: P.O.Box 218

institute: Icahn School of Medicine

summary: An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on those samples obtained via ultracentrifugation and nanoscale deterministic lateral displacement (nanoDLD).

overall_design: Whole blood samples (2 to 5 ml) were collected by the team of Dr. Ashutosh Tewari at the Icahn School of Medicine at Mount Sinai, New York, Department of Urology by venipuncture from 9 consenting adult male Prostate Cancer patients under Institute Review Board approved protocols (GCO # 06-0996, 14-0318, and surgical consent) in purple capped tubes.  After blood collection, serum was isolated using BD Vacutainer blood collection tubes, serum separation tubes (Fisher Scientific, Cat # 368016) and kept at -80°C until further steps were taken for exosome isolation. Serum was rapidly thawed prior to EV isolation with both nanoDLD and UC.

first: Mehmet

middle: E

last: Ahsen

first: Carlos

last: Cordon-Cardo

first: Navneet

last: Dogra

first: Stacey

last: Gifford

first: Joshua

middle: T

last: Smith

first: Ashutosh

last: Tewari

first: Benjamin

last: Wunsch

first: Kamlesh

last: Yadav