title: Muscle-derived fibro-adipogenic progenitor cells for production of cultured bovine adipose tissue

status: Public on Jan 02 2022

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

department: Cell Biology

institute: Mosa Meat

summary: Cultured meat is an emergent technology with the potential for significant environmental and animal welfare benefits. Accurate mimicry of traditional meat requires fat tissue; a key contributor to both the flavour and texture of meat. Here, we show that fibro-adipogenic progenitor cells (FAPs) are present in bovine muscle, and are transcriptionally and immunophenotypically distinct from satellite cells. These two cell types can be purified from a single muscle sample using a simple fluorescence-activated cell sorting (FACS) strategy. FAPs demonstrate high levels of adipogenic potential, as measured by gene expression changes and lipid accumulation, and can be proliferated for a large number of population doublings, demonstrating their suitability for a scalable cultured meat production process. Crucially, FAPs reach a mature level of adipogenic differentiation in three-dimensional, edible hydrogels. The resultant tissue accurately mimics traditional beef fat in terms of lipid profile and taste, and FAPs thus represent a promising candidate cell type for the production of cultured fat.

overall_design: Comparison of bovine skeletal muscle-derived satellite cells and fibroadipogenic progenitor

first: Richard

last: Dohmen

first: Sophie

last: Hubalek

first: Johanna

last: Melke

first: Federica

last: Cantoni

first: Arianna

last: Mei

first: Rui

last: Hueber

first: Rada

last: Mitic

first: Dirk

last: Remmers

first: Panagiota

last: Moutsatsou

first: Mark

last: Post

first: Laura

last: Jackisch

first: Joshua

middle: E

last: Flack


title: ChIP-seq of H3K27acethylation of human aortic endothelial cells (HAECs) treated with Cobalt chloride (CoCl2)

status: Public on Nov 18 2021

city: Tokyo

first: Naoko

last: Hattori

address: 5-1-1 Tsukiji, Chuo-ku

department: Research Institute

country: Japan

institute: National Cancer Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Endothelial-to-mesenchymal transition (EndMT) is a fundamental process in vascular remodeling, and hypoxia is known to induce EndMT and involved in cardiovascular disease development. Cobalt chloride (CoCl2), a chemical inducer of hypoxia-inducible factor-1 (HIF-1) could influence cellular function and its differentiation. However, exact molecular mechanism how stabilization of HIF-1 by cobalt chloride in human primary ECs affects cellular behavior and EndMT process is largely unknown. In this study, we performed ChIP-seq for H3K27ac in human aortic endothelial cells (HAECs) treated with CoCl2

overall_design: H3K27ac profiles of HAECs were generated by ChIP-sequencing using Illumina HiSeqX.

first: Yoshito

last: Yamashiro

first: Yu-Yu

last: Liu


title: The human respiratory airways contain a distinct multipotent secretory cell lineage that can regenerate lung alveoli

status: Public on Dec 09 2021

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

country: USA

institute: Perelman School of Medicine at the University of Pennsylvania

type: Expression profiling by high throughput sequencing

summary: The human lung differs substantially from its murine counterpart, resulting in a distinct distal airway architecture affected by disease pathology in chronic obstructive pulmonary disease. In humans, the distal branches of the airway interweave with the alveolar gas exchange niche, forming an anatomical structure known as the respiratory airways. Due to the lack of a murine counterpart, the cellular and molecular characterization of the respiratory airways in the human lung remains an enigma. We show that human respiratory airways contain a unique secretory cell population that is distinct from cells in larger proximal airways. Stem cell modeling reveal that these respiratory airway secretory cells (RASCs) act as unidirectional progenitors for alveolar type 2 cells, which are essential for maintaining and regenerating the alveolar niche. RASC lineage differentiation into AT2 cells is regulated, in part, by Notch signaling. In COPD, RASCs are altered transcriptionally, corresponding to abnormal AT2 cell states. These data identify a distinct progenitor in a region of the human lung not found in mouse that plays a critical role in maintaining the gas exchange compartment and is altered in chronic lung disease.

overall_design: Survey of human adult lung from diseased and normal tissue using single cell RNA sequencing.

first: Maria

last: Basil

first: Justine

last: Carl

first: Edward

last: Morrisey


title: Lung microenvironments and disease progression in fibrotic hypersensitivity pneumonitis

status: Public on Jan 01 2022

city: New Haven

first: John

last: McDonough

state: CT

address: 300 Cedar St

institute: Yale School of Medicine

summary: Rationale: Fibrotic hypersensitivity pneumonitis (fHP) is an interstitial lung disease caused by sensitization to an inhaled allergen. Objectives: We aimed to identify the molecular determinants associated with progression of fibrosis. Methods: Nine fHP explant lungs and six unused donor lungs (as controls) were systematically sampled (4 samples/lung). According to microCT measures, fHP cores were clustered into a mild, moderate and severe fibrosis group. Gene expression profiles were assessed using Weighted Gene Co-expression Network Analysis (WGCNA), xCell, gene ontology and structure enrichment analysis. Gene expression of the prevailing molecular traits was also compared with IPF. The explant lung findings were evaluated in separate clinical fHP cohorts using tissue, bronchoalveolar lavage samples and computed tomography scans. Results: We found six molecular traits that associated with differential lung involvement. In fHP, extracellular matrix and antigen presentation/sensitization transcriptomic signatures characterized lung zones with only mild structural and histological changes, whereas signatures involved in honeycombing and B-cells dominated the transcriptome in the most severely affected lung zones. With increasing disease severity, endothelial function was progressively lost and progressive disruption in normal cellular homeostatic processes emerged. All six were also found in IPF, with largely similar associations with disease microenvironments. The molecular traits correlated with in vivo disease behaviour in a separate clinical fHP cohort. Conclusion: We identified six molecular traits which characterise the morphological progression of fHP and associate with in vivo clinical behaviour. Comparing IPF with fHP, the transcriptome landscape was determined considerably by local disease extent, rather than by diagnosis alone.

overall_design: We sampled multiple regions in human lungs collected following lung transplantation for severe EAA and IPF and determined the extent of fibrosis using microCT quantitative imaging and tissue histology to classify them as early, progressive, or end-stage fibrosis. We then performed RNA-seq profiling to determine gene expression at these selected stages and applied a linear mixed-effects model to identify differentially expressed genes

first: Laurens

last: DeSadeleer

first: Jonas

last: Schupp

first: Xiting

last: Yan

first: Bart

last: Vanaudenaerde

first: Naftali

last: Kaminski

first: Wim

last: Wuyts


title: Wild-type and Hsd3b6-deficient mouse meibomian gland transcriptome

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

summary: To dissect molecular mechanisms underlying Hsd3b6−/−meibomian gland phenotypes, we performed RNA-sequencing (RNA-seq) analysis using fluorescence-activated cell sorting (FACS)-purified meibomian gland cells. RNA-seq analysis was performed using FACS-purified Itgav(+);CD45(−) meibomian gland acinar cells from wildtype and Hsd3b6−/−mice.As revealed by gene ontology (GO) enrichment analysis, cells sorted from Hsd3b6−/−mice show increased expression of inflammation-related genes. On the other hand, downregulated genes exhibit the highest enrichment score for the GO term related to “regulation of anatomical structure morphogenesis”, a signature accounting for the phenotype of the meibomian gland atrophy of Hsd3b6−/− mice.

overall_design: RNA-seq analysis using FACS-purified meibomian gland cells from wild-type and Hsd3b6-/- mice

first: Doi

last: Masao

first: Manabe

last: Ichiro


title: Expression profiling by high throughput sequencing of NDP52

status: Public on Nov 17 2021

city: Sheffield

first: Chris

last: Toseland

address: Medical School

country: United Kingdom

institute: University of Sheffield

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

overall_design: Refer to individual Series


title: Expression profiling by high throughput sequencing of NDP52 I

summary: NDP52 is an autophagy receptor involved in the recognition and degradation of invading pathogens and damaged organelles. Although NDP52 was first identified in the nucleus and is expressed throughout the cell, to date, there is no clear nuclear function for NDP52.  Here, we use a multidisciplinary approach to characterise the biochemical properties and nuclear roles of NDP52. We found that NDP52 clusters with RNA Polymerase II (RNAPII) at transcription initiation sites and that its overexpression promotes the formation of additional transcriptional clusters. We also show that depletion of NDP52 impacts overall gene-expression levels in two model mammalian cells, and that transcription inhibition affects the spatial organisation and molecular dynamics of NDP52 in the nucleus. This directly links NDP52 to a role in RNAPII-dependent transcription.  Furthermore, we also show that NDP52 binds specifically and with high affinity to double-stranded DNA (dsDNA) and that this interaction leads to changes in DNA structure in vitro. This, together with our proteomics data indicating enrichment for interactions with nucleosome remodelling proteins and DNA structure regulators, suggests a possible function for NDP52 in chromatin regulation.   Overall, here we uncover novel nuclear roles for NDP52 in gene expression and DNA structure regulation.

overall_design: Total RNA was extracted from three replicates of WT (scrambled siRNA control) and NDP52  KD by siRNA in HeLa cells

first: Alia

last: dos Santos

first: Yukti

middle: H

last: Gupta

first: Christopher


title: Transcriptome data of B cells from patients with multiple sclerosis and healthy controls

status: Public on Dec 14 2021

city: Rostock

first: Michael

last: Hecker

address: Gehlsheimer Str. 20

department: Department of Neurology

country: Germany

institute: University of Rostock

summary:
We analyzed the transcriptome profile of B cells from patients with relapsing-remitting multiple sclerosis (RRMS), patients with primary progressive multiple sclerosis (PPMS) and healthy individuals.
High-density Clariom D Arrays for human were used to quantify the transcript levels. This GEO entry provides the processed Clariom D microarray data from the gene-level and exon-level workflows.

overall_design:
EDTA blood samples (n=121) were taken from MS patients (n=63) and healthy controls (n=28). Up to four blood samples were collected per patient.
Seven patients were about to switch to an immune reconstitution therapy (IRT). The other RRMS patient samples were taken under therapy with alemtuzumab (n=38), natalizumab (n=29) or cladribine (n=6).
Untouched B cells were isolated from each blood sample, and total RNA was extracted, labeled and hybridized to Clariom D microarrays to obtain gene-level and exon-level expression profiles.

first: Dirk

last: Koczan

first: Uwe

middle: K

last: Zettl


title: RNAseq analysis of DPSC-derived neurons from Neurotypical control subjects and PWS subjects

status: Public on Oct 26 2021

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

summary: A major challenge to the study and treatment of neurogenetic syndromes is the difficulty in gaining access to live neurons from individuals with these disorders. Although other sources of stem cells are currently available for differentiation into neurons, these can involve invasive procedures and be difficult or expensive to generate limiting their use on a broad scale, especially for rare syndromes which may not be well represented in the local population.  Dental pulp stem cells (DPSC) are neural crest derived multipotent stem cells that reside deep the pulp of shed (baby) teeth and have the potential for broad use in the study of neurogenetic disease. Here, we use DPSC-derived neurons to investigate the transcriptional differences between neurotypical controls and Prader-Willi syndrome (PWS) conferred by uniparental disomy (UPD) versus deletion. Additionally, we investigated the increased autism incidence within the UPD genotype by sequencing PW-UPD patients with and without autism.  Using this data, we defined a PWS molecular signature and discovered a global reduction in mitochondrial transcripts in the PW-UPD +ASD neurons.

overall_design: RNA-seq Analysis of DPSC derived neurons; 4 individuals per group of the following: neurotypical control, PWS deletion, PWS UPD -ASD, and PWS UPS +ASD

first: A

last: Victor

first: Winston

last: Miller

first: Martin

last: Donaldson

first: Lawrence

middle: T

last: Reiter


title: Transcriptomic analysis of primary CD105+CD90+CD13- and CD105+CD90+CD13+ mesenchymal cells in human lung

status: Public on Dec 24 2021

city: Lund

first: Gunilla

last: Westergren-Thorsson

address: Sölvegatan 19, BMC C12

country: Sweden

institute: Lund University

summary: Primary mesenchymal CD105+CD90+CD13- and CD105+CD90+CD13+ populations from human lung were isolated and characterized using bulk population mRNA sequencing to understand differences between these populations.

overall_design: Single cell suspensions from 4 normal human lungs were generated by enzymatic digestion of tissue and subsequently cryopreserved. After thawing cells, fluorescence-associated cell sorting was used to sort CD45-CD235a-CD105+CD90+CD13- and CD45-CD235a-CD105+CD90+CD13+ cells and total RNA was isolated using the PicoPure™ RNA Isolation Kit (Thermo Fisher Scientific, KIT0204). cDNA libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio) and Nextera XT DNA Library Preparation Kit (Illumina). A total of 8 libraries were pooled and run across two lanes of a NovaSeq 6000 S2 flow cell (Reagent Kit v1.5, 200 cycles, Illumina) on a NovaSeq 6000 System (Illumina).

first: Måns

last: Kadefors


title: Human lung tissue resident memory T cells are re-programmed but not eradicated with systemic glucocorticoids after acute cellular rejection

status: Public on Oct 15 2021

city: Pittsburgh

first: Mark

last: Snyder

address: 200 Lothrop Street, BST12

department: Medicine

institute: University of Pittsburgh

summary: Acute cellular rejection is common after lung transplantation and is associated with an increased risk of early chronic rejection.  We present combined single cell RNA and T cell receptor sequencing on recipient derived T cells obtained from the bronchoalveolar lavage of three lung transplant recipients with acute cellular rejection and compare them with T cells obtained from the same three patients after clinical treatment of rejection with high-dose, systemic glucocorticoids.  At the time of acute cellular rejection, we find an oligoclonal expansion of cytotoxic CD8+ T cells, that all persist as tissue resident memory T cells following successful treatment.  Persisting CD8+ allograft-resident T cells have reduced gene expression for cytotoxic mediators following therapy with glucocorticoids.  This clonal expansion is discordant with circulating T cell clonal expansion at the time of rejection, suggesting in-situ expansion.  These findings pose a potential biological mechanism linking acute cellular rejection to chronic allograft damage.

overall_design: Single cell RNA/TCR sequencing of recipient-derived T cells obtained from three lung translpant recipients at the time of ACR and after treatment with high dose glucocorticoids


title: Single-Cell, Single-Nucleus and Spatial RNA Sequencing of the Human Liver Identifies Hepatic Stellate Cell and Cholangiocyte Heterogeneity

status: Public on Oct 13 2021

city: Toronto

first: Tallulah

middle: Suzanne

last: Andrews

state: Ontario

address: MARS Building

country: Canada

institute: UHN Research

summary:
Comparison of single cell RNAseq and single nucleus RNAseq on four healthy human liver caudate lobes, with cell-types validated using one slice of a fifth healthy human for VISIUM Spatial Transcriptomics. Raw UMI count tables can be found here: https://figshare.com/projects/Human_Liver_SC_vs_SN_paper/98981
Processed Seurat Objects can be found here:
https://www.dropbox.com/sh/sso15ehqmrrh6mk/AACKHOsSlZW0_Zy9cbCkOmMfa?dl=0

overall_design: Four healthy human liver caudate lobes were removed prior to transplantation into living recipients. A potion of each lobe was frozen then nuclei were extracted and sequenced with 10X Chromium while another portion was dissociated immediately while still fresh and isolated cells were sequenced with 10X Chromium.

middle: S

first: Jawairia

last: Atif

first: Jeff

middle: C

last: Liu

first: Sonya

last: MacParland


title: RNA-next generation sequencing of intestine tissue from mice fed high fat diet or/and sugar drink

status: Public on Nov 25 2021

city: Seoul

first: Woo-Jeong

last: Shon

address: 103 Daehak-ro, Jongno-gu,

department: College of Medicine

country: South Korea

institute: Seoul National University

summary:
Purpose: NGS was used to determine if a distinct transcriptomic profile is observed among the experimental mice fed four different dietary components.
Methods: We carried out RNA-Seq analysis of ileum tissue from 6 weeks male mice ad libitum fed for 10 weeks a high liquid sugar (23% (w/v)) or/and high fat (60% Kcal from fat) diet. The combined effect of sugar drink and high fat diet (HF-Sugar) was compared with sugar drink only (NF-Sugar), or high fat diet only (HF), or control diet that was plain water and normal fat diet (NF).
Results: RNA-Seq revealed sample-specific clusters that included genes responding to each experimental diet. We found only addition of sugar drink to high fat group (HF-Sugar) not NF-Sugar and HF, there was a significant enrichment in biological functions relating to Inflammatory/Immune Responses, especially including dendritic cell (DC) and T cell related signaling pathway.
Conclusions: Taken together, our data demonstrate that sugar drink synergistically promotes and exacerbates inflammatory responses driven by the high fat diet.

overall_design: For investigation of the transcriptional changes in response to the experimental diet, three statistically independent RNA samples per group (total 12 samples) were sequenced.

first: Dong-Mi

last: Shin


title: Genome wide analysis of Suv4-20h1/2 depleted animal caps

status: Public on Sep 01 2021

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München


title: Genome wide analysis of Suv4-20h1/2 depleted animal caps [dataset3]

summary: Suv4-20h1/2 are histone methyltransferases that write the H4K20me2 and H4K20me3 marks. We knocked down these enzymes using translation blocking morpholinos in X. tropicalis animal caps and performed RNA-seq in order to investigate the impact of altering H4K20me state on epidermal differentiation. Knocking down Suv4-20h1/2 leads to a strong increase of H4K20me1 in bulk chromatin. To determine whether increased H4K20me1 is responsible for transcriptional changes in suv4-20h KD animal caps, we performed RNA-Seq for a rescue experiment with PHF8, an H4K20me1 demethylase.

overall_design: RNA-seq experiment of human Phf8 mRNA injection in Suv4-20H1/2 knock down or control conditions (i.e. control morpholino, LacZ mRNA) in 3 biological replicates.

first: Alessandro

last: Angerilli

first: Janet

last: Tait

first: Irina

last: Shcherbakova

first: Ralph

last: Rupp


title: CAR virus receptor mediates erythroid differentiation and migration and is downregulated in MDS

status: Public on Dec 01 2021

city: Linz

first: Johannes

last: Pröll

state: Upper Austria

address: Krankenhausstraße 7a

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University

summary:
The major Coxsackie-Adenovirus receptor, CAR, is specifically down-regulated in immature erythroid progenitor cells in patients with MDS
CAR mediates erythroid maturation in progenitor cells and their migration which may explain the maturation defect and pathology in MDS

overall_design: We analyzed CD 105-positive erythroid cells from reactive anemia and MDS subjects using the Affymetrix HG-U133 Plus 2 plattform. Array data was was processed by Affymetrix Array Computational Tool. No technical replicates were performed.

first: Karin

last: Bauer

first: Sigrid

last: Machherndl-Spandl

first: Lukas

last: Kazianka

last: Sadovnik

first: Sinan

last: Gültekin

first: Susanne

last: Suessner

last: Proell

first: Jeroen

last: Lauf

first: Gregor

last: Hoermann

last: Eisenwort

first: Norman

last: Häfner

first: Mathilde

last: Födermayr-Mayrleitner

first: Ann

last: Schmolke

first: Emiel

last: van der Kouwe

first: Uwe

last: Platzbecker

first: Thomas

last: Lion

first: Ansgar

last: Weltermann

first: Otto

last: Zach

first: Gerald

last: Webersinke

first: Ulrich

last: Germing

first: Christian

last: Gabriel

first: Wolfgang

middle: R

last: Sperr

first: Marie

last: Béné

first: Philipp

middle: B

last: Staber

first: Peter

last: Bettelheim

last: Valent


title: Evolution of drug resistance in cancer cells involves generation of numerous mutations in non-coding genome that reduces the chances of DNA breaks

status: Public on Nov 24 2021

city: Ariel

first: Santosh

last: Kumar

state: Ariel

address: RamatHa Golan Street 65'

department: Molecular Biology

country: Israel

institute: Ariel University

summary: Selection of drug-resistant mammalian cell mutants requires multiple drug exposures. Since cells in starting population could be genetically identical, selection of pre-existent mutations is unlikely. Therefore, adaptation must involve generation of drug-resistant mutations de-novo. Understanding how adaptive mutations are generated and protect cells is important for our knowledge of cancer biology and evolution. Here, we studied adaptation of cancer cells to topoisomerase (Top1) inhibitor irinotecan, which triggers DNA breaks, resulting in cytotoxicity. Resistance mechanism was based on gradual accumulation of recurrent mutations in non-coding DNA at sequence-specific Top1 cleavage sites. Repair of DSBs at these sites following initial irinotecan exposures created mutant sequences that were resistant to further Top1 cleavage. Therefore, by virtue of creating DNA breaks Top1 increases the rate of highly protective mutations specifically at such spots, thus explaining a puzzling need of dose escalation in resistance development.

overall_design:
To study the origin of resistance through drug dose adaptation in cancer cells.
PRJNA738674 contains related data with whole genome sequencing of HCT116 cell lines.

first: Valid

last: Gahramanov

first: Julia

last: Yagalom

first: Shivani

last: Patel

first: Lukasz

last: Kaczmarczyk

first: Ivan

last: Alexandrov

first: Gabi

last: Gerlitz

first: Mali

last: Salmon-Divon

first: Michael

last: Sherman


title: Reconstructing human Brown Fat developmental trajectory in vitro

status: Public on Oct 11 2021

city: Milan

first: Fabio

last: Marchiano

address: Via Alessandro Manzoni 56

country: Italy

institute: Humanitas

summary: Brown adipocytes represent a specialized type of mammalian adipocytes able to uncouple nutrients catabolism and ATP generation to dissipate energy as heat. They play an important role in mammals, allowing non-shivering thermogenesis to regulate body temperature in response to cold exposure. In humans, the brown fat tissue is dispersed in small depots found throughout the neck and trunk region. Increasing brown fat activity either with drug treatment or with cell therapy approaches are considered as potential approaches for the treatment of metabolic syndrome and obesity. The recent development of in vitro differentiation strategies relying on human pluripotent stem cells (hPSCs) offers in theory the possibility to produce unlimited amounts of BAT. A strategy efficiently applied to several tissues is to recapitulate step by step the development of the tissue of interest by exposing hPSCs to the signaling cues used during normal embryonic development. However, this strategy has proven difficult to implement for brown fat as the development of this tissue is poorly characterized. Here, we first used single cell RNA sequencing to characterize the development of interscapular brown fat in mouse. Our analysis identified a previously unrecognized population of brown adipocytes precursors characterized by expression of the transcription factor GATA6. We showed that this precursor population can be efficiently generated from hPSCs by modulating the signaling pathways identified our transcriptomic analysis in paraxial mesoderm precursors differentiated in vitro. These precursors can in turn be efficiently converted into functional brown adipocytes which can respond to adrenergic stimuli by increasing their metabolism resulting in heat production.

overall_design: Wildtype pluripotent stem cell line was differentiated into brown adipocytes as described in Rao et. al. iPSCs, terminally differentiated iPSC-derived brown adipocytes and human fetal brown adipose tissues were analyzed to investigate the characterstics of developing brown adipocytes in vitro and in vivo. To evaluate the differentation protocol performance we compare our terminally differentiated iPSC-derived brown adipocytes with the ones produced by Carobbio et al. (10.1016/j.stemcr.2021.01.013, GSE168387) and Zhang et al (10.1016/j.stem.2020.07.013, GSE131169). Moreover, to demostrate the specificity of the differentiation, we compared these samples to iPSCs differentiated to a late myogenic stage previously generated by us as reported in Al Tanoury et al. (https://doi.org/10.1073/pnas.2022960118, GSE164874).

first: Jyoti

last: Rao

first: Bianca

last: Habermann

first: Olivier

last: Pourquié


title: DNA methylation-based classification of MCD in the human brain

status: Public on Nov 30 2021

city: Erlangen

first: Katja

last: Kobow

state: Deutschland

address: Schwabachanlage 6

department: Neuropathology

institute: Universitätsklinikum Erlangen

summary: Genome wide DNA methylation profiling of human normal and epileptic brain tissue. The Illumina Infinium 850K Human DNA methylation Beadchip  was used to obtain DNA methylation profiles across approximately 850.000 CpGs in formalin-fixed paraffin-embedded surgical brain samples. Samples included 316 cases diagnosed with malformations of cortical development (MCD), non-MCD epilepsy or no-epilepsy autopsy controls.

overall_design: Bisulphite converted DNA from the 308 (215 NEW) human surgical brain samples were hybridised to the Illumina Infinium 850k Human Methylation Beadchip Arrays

first: Samir

last: Jabari

first: Tom

last: Pieper

first: Till

last: Hartlieb

first: Manfred

last: Kudernatsch

first: Tilman

last: Polster

first: Christian

last: Bien

first: Thilo

last: Kalbhenn

first: Matthias

last: Simon

first: Hajo

last: Hamer

first: Karl

last: Rössler

first: Martha

last: Feucht

first: Angelika

last: Mühlebner

first: Imad

last: Najm

first: José

last: Peixoto-Santos

first: Antonio

last: Gil-Nagel

first: Rafael

last: Delgado

first: Angel

last: Aledo-Serrano

first: Yanghao

last: Hou

first: Roland

last: Coras

first: Andreas

last: von Deimling

first: Ingmar

last: Blümcke


title: Expression of transport proteins in the rete mirabile of European silver and yellow eel

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

institute: University of Innsbruck

summary: We investigated transcriptional and translational changes in rete mirabile tissue of European yellow and silver eels. We therefore analyzed the transcriptome as well as the proteome of rete capillaries of specimens of both developmental stages. The results clearly show the presence of a large number of membrane transport proteins in the transcriptome as well as in the proteome. ATP required to energize ion and metabolite transport can be generated in the aerobic metabolism. A high ROS defense capacity is established in rete endothelial cells, probably connected to the hyperbaric oxygen partial pressures, generated in the rete by back-diffusion of oxygen.

overall_design: Using Illumina Sequencing to obtain RNA-Seq data and statistical Deseq analysis, the transcriptomes of European eel rete mirabile tissues of animals of different developmental stages were compared. Using LC-MS/MS and statistical analysis, the proteomes of European eel rete mirabile tissues of animals of different developmental stages were compared.

first: Victoria

last: Drechsel

first: Ron

middle: P

last: Dirks

first: Klaus

last: Faserl

first: Bettina

last: Sarg

first: Bernd

last: Pelster


title: Expression profiling by high throughput sequencing of NDP52 II

first: Chris

last: Toseland

overall_design: Total RNA was extracted from three replicates of WT (scrambled siRNA control) and NDP52  KD by siRNA in MCF7 cells

first: Alia

last: dos Santos

first: Yukti

last: Gupta

first: Christopher


title: Gene expression profiling of the striatum in drug naïve Diversity Outbred mice

status: Public on Oct 31 2021

city: Bar Harbor

first: Vivek

last: Philip

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: 416 J:DO drug naïve striatum were subjected to RNA sequencing towards profiling gene expression in these drug naïve straitums.

first: Elissa

middle: J

last: Chesler

middle: M


title: Transcriptome dynamics of Pseudomonas aeruginosa during growth in complex medium

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

summary: Transcriptiome dynamics of P. aeruginosa PA14 during batch growth in complex LB medium over the course of 10 h.

overall_design: Two to three biological replicates were grown in batch culture. Samples were taken every 60 min.

first: Kathrin

last: Alpers

first: Susanne

last: Häussler


title: A serum-free media formulation for cultured meat production supports bovine satellite cell differentiation in the absence of serum starvation

status: Public on Oct 22 2021

city: Maastricht

first: Tobias

last: Messmer

address: Watermolen 28

country: Netherlands

institute: Mosa Meat


title: A serum-free media formulation for cultured meat production supports bovine satellite cell differentiation in the absence of serum starvation [Timecourse]

summary:
Production of cultured meat requires the robust differentiation of satellite cells into mature muscle fibers without the use of animal-derived components. Current protocols induce myogenic differentiation in vitro through serum starvation, an abrupt reduction in serum concentration. Here, we used RNA sequencing to investigate the transcriptomic remodelling of bovine satellite cells during myogenic differentiation induced by serum starvation.
We characterized canonical myogenic gene expression, and identified surface receptors upregulated during the early phase of differentiation. Supplementation of ligands to these receptors enabled the formulation of a chemically defined media that induced differentiation in the absence of serum starvation and/or transgene expression.
Serum-free myogenic differentiation was of similar extent to that induced by serum starvation, as evaluated by transcriptome analysis, protein expression and the presence of a functional contractile apparatus. Moreover, the serum-free differentiation media supported the fabrication of mature three-dimensional bioartificial muscle constructs, demonstrating its suitability for cultured beef production.

overall_design: Satellite cells were cultured in growth media (GM) containing 20% FBS and abuptly switched to differentiation medium containing 2% FBS, a procedure known as serum-starvation. RNA samples were taken at 0 h, 24 h, 48 h, 72 h and 96 h of serum starvation in biological quadruplicates (A, B, C, D).

first: Iva

last: Klevernic

first: Carolina

last: Furquim

first: Ekaterina

last: Ovchinnikova

first: Arin

last: Dogan

first: Helder

last: Cruz

first: Mark

last: Post

first: Joshua

last: Flack


title: A serum-free media formulation for cultured meat production supports bovine satellite cell differentiation in the absence of serum starvation [SF_Diff]

overall_design: Satellite cells were cultured in either FBS-containing growth media (GM) containing 20% FBS or in serum-free growth media (SFGM). For the 72h myogenic differentiation, cells in GM were switched to differentiation media (DM) containing 2% FBS while cells in SFGM were either switched to serum-free base media (SFB), serum-free differentiation media with a DMEM/F-12 base (SFDM) or with a DMEM base (DMEM). RNA samples were taken from at 0 h from GM and SFGM, and at 72 h from DM, SFDM and DMEM in biological triplicates (A, B, C).


title: Recurrent frameshift neoantigen vaccine elicits protective immunity with reduced tumor burden and improved overall survival in a Lynch syndrome mouse model

status: Public on Aug 30 2021

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: DNA mismatch repair deficiency (MMRD) drives microsatellite instability (MSI). Cells with MSI accumulate numerous frameshift mutations. Frameshift mutations affecting cancer-related genes may promote tumorigenesis and, therefore, are shared among independently arising MSI tumors. Consequently, such recurrent frameshift mutations can give rise to shared immunogenic frameshift peptides (FSPs) that represent ideal candidates for a vaccine against MSI cancer. Pathogenic germline variants of mismatch repair genes cause Lynch syndrome (LS), a hereditary cancer syndrome affecting approximately 20-25 million individuals worldwide. LS individuals are at high risk of developing MSI cancer. Previously, we demonstrated safety and immunogenicity of an FSP-based vaccine in a Phase I/IIa clinical trial. However, the cancer-preventive effect of FSP vaccination in the scenario of LS has not been demonstrated so far.

overall_design: RNA-seq was performed on tumor and normal intestinal tissue from VcMsh2 mice, treated with NSAID, FSP-vaccination, or combination.

first: Johannes

last: Gebert

first: Magnus

last: von Knebel Doeberitz

first: Steven

last: Lipkin

first: Matthias

last: Kloor


title: WT BMDM M2 vs RON TK- BMDM M2

status: Public on Aug 10 2021

city: Cincinnati

first: Susan

last: Waltz

state: Ohio

address: 3125 Eden Ave

department: Cancer Biology

institute: University of Cincinnati

summary: Introduction: HGFL-Ron signaling is augmented in human breast cancer and is associated with poor overall prognosis. Here, we investigate the role of HGFL-Ron signaling in RON-modulated murine macrophages through RNA-sequencing of bone marrow-derived macrophages from FVB WT or FVB RON tyrosine kinase -/- mice. BMDM of each genotype M2-polarized via 72 hour treatment with IL-4 were submitted for transcriptomic characterization on the Illumina HiSeq 2500. High quality reads were aligned to the mm10 genome and quantified to generate RPKM

overall_design: Transcriptome profiles of RON-proficient and RON-deficient BMDM M2 cells through RNA-sequencing

first: Brian

last: Hunt

first: Jennifer

last: Bourn


title: Single nuclei RNAseq of rat area postrema and nucleus tractus solitarius

status: Public on Sep 09 2021

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

address: 125 S 31st St

institute: University of Pennsylvania

summary: We performed single-nuclei RNAseq of Sprague Dawley rat area postrema and nucleus tractus solitarius brain samples to identify cellular subtypes.

overall_design: We performed the 10x Genomics 3' gene expression assay (v3.1) on nuclei isolated from frozen Sprague Dawley rat area postrema and nucleus tractus solitarius combined brain punches. At the onset of the dark cycle, rats (n=4, ~400 g) were injected with saline (i.p.). After six hours, rats were deeply anesthetized with a triple cocktail of ketamine, xylazine and acepromazine (180 mg/kg, 5.4 mg/kg and 1.28 mg/kg, respectively; i.p.) in the middle of the dark phase. Brains were removed and snap-frozen in dry ice-cold hexane. Three adjacent micro-punch samples (each ~1 cubic mm) containing the AP and left and right NTS were collected from coronally-prepared brains on a cryostat, pooled together, and stored at -80°C until further processing. Nuclei were isolated by differential centrifugation and microfluidically captured using the 10x Genomics Chromium controller. Sequencing libraries were constructed and sequenced on an Illumina NovaSeq 6000.

first: Richard

last: Crist

first: Matthew

last: Hayes

first: Bart

last: De Jonghe

first: Tito

last: Borner


title: Functional antagonism of chromatin modulators regulates EMT

status: Public on Jul 16 2021

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

institute: Max-Delbrück-Centrum für Molekulare Medizin

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

overall_design: Refer to individual Series


title: Genome wide analysis of Suv4-20h1/2 depleted animal caps [dataset2]

first: Tamas

last: Schauer

overall_design: RNA-seq experiment of Xenopus Phf8 mRNA injection in Suv4-20H1/2 knock down or control conditions in 2 biological replicates.

first: Alessandro

last: Angerilli

first: Janet

last: Tait

first: Pawel

last: Smialowski

first: Ralph

last: Rupp


title: The ageing epigenome regulates stem cell fate via mitochondrial-derived vesicles delivery of citrate carrier to lysosomes [CUT&RUN_H3AC]

status: Public on Jul 08 2021

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

summary: We report that upon ageing MSC exhibit reduced metabolic rates, with lower lipid biosynthesis and elevated acetyl-CoA levels. However, aged cells display chromatin compaction and histone hypo-acetylation, particularly on enhancers of genes involved in osteogenesis. This is due to the lower levels of citrate carrier, resulting in impaired acetyl-CoA export from mitochondria to the cytosol, which concomitantly affects histone acetylation and osteogenesis. CiC gets degraded in the aged cells via an MVD-lysosomal pathway, which establishes a strong connection between mitochondrial quality control, chromatin and stemness.

overall_design: Description of aged-associated changes in metabolism, chromatin and stemness using mesenchymal stem cells isolated from young and old mice.

first: Andromachi

last: Pouikli

first: Swati

last: Parekh


title: Genome wide analysis of Suv4-20h1/2 depleted animal caps [dataset4]

overall_design: RNA-seq experiment of Suv4-20H1/2 and Control morpholino knock down in 3 developmental stages and in 2 or 3 biological replicates.


title: Genome wide analysis of Suv4-20h1/2 depleted animal caps [dataset1]

overall_design: RNA-seq experiment of Suv4-20H1/2 and Control morpholino knock down in 2 biological replicates.


title: Horizontal mitochondrial transfer from microenvironment increases glioblastoma tumorigenicity

status: Public on Aug 31 2021

city: Cleveland

first: Yadi

last: Zhou

address: 9500 Euclid Ave

institute: Cleveland Clinic

summary: Glioblastoma (GBM) cells acquire mitochondria from glial cells in vitro and in vivo. This transfer is accompanied by increased tumor-initiation capacity.

overall_design: GFP+ SB28 tumor cells were co-cultured with CellTrace Violet-stained astrocytes from mito::mKate2 mice at a 1:1 ratio for 2 days. Tumors with or without exogenous mitochondria and donor astrocyte population were sorted based on CellTraceViolet-GFP-+mKate- (astrocyte), CellTraceViolet+GFP-mKate2-(mKate_neg) and CellTraceViolet+GFP-mKate2+(mKate_pos) from 3 biological replicates.

first: Dionysios

last: Watson

first: Defne

last: Bayik

first: Justin

middle: D

last: Lathia


title: Pericytes exhibit a parallel pro-fibrotic response after vascular injury in the heart and brain

status: Public on Jun 19 2021

city: Los Angeles

first: Reza

last: Ardehali

state: CA

address: 675 Charles E Young Dr S

department: Internal Medicine, Division of Cardiology

institute: David Geffen School of Medicine at UCLA

summary: Ischemic injury leads to irreversible loss of neurons and cardiomyocytes in the brain and heart, respectively which ultimately results in fibrotic scar formation. Despite recent advances in tissue fibrosis, cellular mediators of scar formation in the heart and brain remain elusive. Pericytes are a heterogeneous population of mural cells that surround microvessels in various organs including the brain and heart. Their function beyond vascular integrity and contractility is poorly understood, although recent studies have suggested they may be a major contributor to tissue fibrosis. In both the heart and brain, differences in injury models, lack of proper transgenic mouse models for lineage tracing and absence of pericyte-specific markers have contributed to discrepancies in the literature regarding their direct contributions to fibrosis. Here, by performing a set of complementary experiments using a common pericyte transgenic model and clinically-relevant ischemic injury models of stroke and myocardial infarction, we demonstrated the parallel pro-fibrotic response of pericyte after vascular injury.

overall_design: single-cell RNA sequencing analysis of heart and brain of Tbx18CreER/+;Rosa26tdT/+ mice.

first: Thanh

last: Pham

first: Shuin

last: Park

first: Kamal

last: Kolluri

first: Lingjun

last: Wang

first: Peng

last: Zhao

first: Dana

last: Tran

first: Riki

last: Kawaguchi

first: Stanley

last: Carmichael


title: Deregulated mito-nuclear communication alters chromatin plasticity and osteogenic differentiation potential upon ageing in mesenchymal stem cells (MSCs) [RNA-seq]

summary: We report that upon ageing MSC undergo a metabolic switc, down-regulating glycolysis and inducing fatty acid oxidation, which results in elevated acetyl-CoA levels. However, aged cells exhibit chromatin compaction and histone hypo-aceylation. This is due to the lower levels of citrate carrier, resulting in impaired acetyl-CoA export from mitochondria to the cytosol, which concomitantly affetcs histone acetylation and osteogenesis.

overall_design: Description of aged-associated changes in metabolism, chromatin and stemness using mesenchymal stem cells from isolated from young and old mice.


title: Deregulated mito-nuclear communication alters chromatin plasticity and osteogenic differentiation potential upon ageing in mesenchymal stem cells (MSCs) [ATAC-seq]


title: Gene expression profiling of colorectal cancer tissue samples

status: Public on Jul 27 2021

city: Oslo

first: Anita

last: Sveen

address: P.O.Box 4953, Nydalen

department: Department of Molecular Oncology

country: Norway

institute: Institute for Cancer Research, Oslo University Hospital

summary: We have compared the gene expression profiles of primary colorectal cancers and colorectal liver metastases within the framework of the consensus molecular subtypes. This series represents a subset of the primary tumor samples.

overall_design: This series consists of tissue samples from 105 primary colorectal tumors analyzed on Affymetrix Human Transcriptome 2.0 Arrays.

first: Jonas

last: Langerud

first: Ragnhild

middle: A

last: Lothe


title: Single cell analysis reveals intra-tumor heterogeneity and microenvironment for clear cell renal cell carcinoma

city: Shanghai

first: Jia

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

country: China

institute: SJTU CHINA

summary: Here we performed 3’ transcriptome single cell sequencing on 7 ccRCC patients’ tumor and matched 5 adjacent normal samples. We identified two different functional subgroups in ccRCC tumor epithelial cells and two different gene transcriptional programs that were associated with survival across a TCGA cohort. We found important transcriptional factor regulons that played roles in ccRCC progression. We identified macrophage and T cell clusters whose higher infiltration in tumor was associated with overall survival. We also discovered some potentially targetable inhibitory interactions among tumor epithelial cells, the infiltrating T cell and myeloid compartments. Collectively, our data provided cell clusters and gene sets for predict clinical outcome and potential targets for ccRCC therapy.

overall_design: Single cell mRNA profiles of 7 primary tumors  and correspongding para-tumors from 7 patients with celar cell cancer were generated by 10X Genomics plartform, without technical replication, and sequenced by NovaSeq 6000 (Illumina)

first: Man

last: Zhang

first: Wei-Qiang

last: Gao


title: Deregulated mito-nuclear communication alters chromatin plasticity and osteogenic differentiation potential upon ageing in mesenchymal stem cells (MSCs)

first: Peter

last: Tessarz


title: Single cell gene expression analysis of zebrafish body elongation

status: Public on Aug 18 2021

city: New Haven

first: Scott

middle: A.

last: Holley

address: 219 Prospect St

department: Department of Molecular, Cellular and Developmental Biology

institute: Yale University

summary: scRNA-seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt, Fgf and BMP signaling pathway.

overall_design: We performed single cell RNA sequencing (scRNAseq) on dissected tails from 10-12 somite stage zebrafish embryos. We used wild-type embryos and embryos subject to treatments known to alter tailbud cell migration, specifically inhibition of FGF, BMP, or Wnt signaling. For each treatment, we prepared four biological replicates each consisting of 10 to 12 tailbuds and resulting in 30,000-35,000 single cell profiles.

first: Miriam

last: Genuth

first: Yasuhiro

last: Kojima


title: Custom NanoString Gene Expression Assay for Subtype Identification in Glioblastoma

status: Public on Jun 13 2021

city: Calgary

first: Sorana

last: Morrissy

state: Alberta

address: 3310 Hospital Dr NW

department: Biochemistry and Molecular Biology

institute: Univeristy of Calgary

summary: Using non-negative matrix factorization to identify glioblastoma subtypes from NanoString gene expression data

overall_design: RNA was extracted from tissue cores using the Qiagen Allprep DNA/RNA FFPE kit per manufacturer's protocol. 300 ng of total RNA of each sample were analyzed by NanoString gene expression assay using a custom codeset of 70 probes representing 4 housekeeping genes and 30 classifier genes corresponding to the classical (CL), mesenchymal (MES), proneural (PN), and neural (NL) subtypes. Raw counts were background subtracted then normalized using the geometric mean of the samples analyzed using NanoString nSolver.

first: Jennifer

last: Chan

first: Samuel

last: Brown

first: Nazanin

last: Tatari

first: Sheila

last: Singh

first: Chitra

last: Venugopal


title: USP29-mediated HIF1a stabilization promotes Sorafenib resistance of hepatocellular carcinoma cells by upregulating glycolysis

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

country: Switzerland

institute: University of Basel

summary: Understanding the mechanisms underlying evasive resistance in cancer is an unmet medical need to improve the efficacy of current therapies. In hepatocellular carcinoma (HCC), aberrant expression of hypoxia inducible factor 1 a (HIF1a) and increased aerobic glycolysis metabolism represent drivers of the development of resistance to therapy with the multi-kinase inhibitor Sorafenib. However, it has remained unknown how HIF1a is activated and how its activity and the subsequent induction of aerobic glycolysis promotes Sorafenib resistance in HCC. Here, we report the ubiquitin-specific peptidase USP29 as a new regulator of HIF1a and of aerobic glycolysis during the development of Sorafenib resistance in HCC. In particular, we have identified USP29 as a critical deubiquitylase (DUB) of HIF1a, which directly deubiquitinates and stabilizes HIF1a and, thus, promotes its transcriptional activity. Among the transcriptional targets of HIF1a is the gene encoding for hexokinase 2 (HK2), a key enzyme of the glycolytic pathway. The absence of USP29, and thus of HIF1a transcriptional activity, reduces the levels of aerobic glycolysis and reinstalls the sensitivity to Sorafenib treatment in Sorafenib-resistant HCC cells in vitro and in xenograft transplantation mouse models in vivo. Notably, the absence of USP29 and high HK2 expression levels correlate with the response of HCC patients to Sorafenib therapy. Together, the data demonstrate that, as a DUB of HIF1a, USP29 promotes Sorafenib resistance in HCC cells by upregulating glycolysis, thereby opening new avenues for therapeutically targeting Sorafenib-resistant HCC in patients.

overall_design: RNA-Seq of Huh7-Parental and established Huh7-IR, Huh7-CR cell lines

first: R

first: F

last: Tang

last: Kiran

last: Kalathur

first: G

last: Christofori


title: The critical role of heme synthesis in the regulation of pluripotent states is succinate-dependent

city: Leuven

first: Marino

last: Caruso

address: Herestraat 49

department: Oncology

country: Belgium

institute: KULeuven

summary: Investigation of the role of heme biosynthesis in the Naïve and primed mESCs pluripotent states by transcriptomic analysis.

overall_design: RNA-sequencing analysis of naïve and primed mESCs treated with heme biosynthesis inhibitor Succinylacetone (SA) or rescued by SA + Hemin supplementation

first: Damien

last: Detraux


title: Multi range ERK responses shape the proliferative trajectory of single cells following oncogenic induction

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

summary: Aberrant oncogene activation can promote cellular transformation and tumorigenesis, enabling cancer cells to grow and proliferate uncontrollably. For instance, activating Ras or Raf mutations bypass the need of growth factor stimulation, resulting in constitutive mitogenic signaling through the Ras or Raf to MAPK pathway. Surprisingly, in normal cells, the same oncogenic mutations typically cause cells to enter into a stable state of cell cycle arrest, a phenomenon known as oncogene-induced senescence. We hypothesized that players that mediate ERK activity-dependent cell fate decisions must themselves undergo some expression/activity changes in response to varying levels of ERK activity. To systematically identify gene expression changes associated with different levels of ERK activity, we performed deep RNA sequencing of RPE cells simultaneously treated, for varying lengths of time, with DOX (to induce BRAFV600E) and different concentrations of ERK inhibitors. The ERK inhibitor concentrations were chosen to include most dynamic ranges of proliferation response based on previous titration experiments. The time points include 0 (untreated control), 1, 2, 4, 8, 16 and 24h post DOX and drug treatment.  These time points were selected based on the observation that RPE cells already showed a bell-shaped correlation between ERK activity and proliferation as early as 24h after BRaf induction. Moreover, earlier time points allow enrichment of genes that are more directly responsive to ERK activity changes.

overall_design: RNA-seq of RPE cells treated with five different doses of ERK inhibitor (SCH772984) and/or induction of BrafV600E expression at baseline (0h) and six time points up to 24h post-perturbation

first: Jia-Yun

last: Chen

first: Sarah

last: Boswell

last: Sorger

first: Galit

last: Lahav


title: Self-organized yolk sac-like organoids allow for scalable generation of multipotent hematopoietic progenitor cells from human induced pluripotent stem cells

status: Public on May 05 2021

city: Davis

first: Stefan

last: Siebert

address: One Shields Avenue

institute: University of California, Davis

summary: The human definitive yolk sac is an important organ supporting the early developing embryo through nutrient supply and by facilitating the establishment of the embryonic circulatory system. However, the molecular and cellular biology of the human yolk sac remains largely obscure due to the lack of suitable in vitro models. Here, we show that human induced pluripotent stem cells (hiPSCs) co-cultured with various types of stromal cells as spheroids self-organize into yolk sac-like organoids without the addition of exogenous factors. Yolk sac-like organoids recapitulated a yolk sac specific cellular complement and structures as well as the functional ability to generate definitive hematopoietic progenitor cells (HPCs). Furthermore, sequential hemato-vascular ontogenesis could be observed during organoid formation. Notably, our organoid system can be performed in a scalable, autologous, and xeno-free condition, thereby providing an important model of human definitive yolk sac development and allows for efficient bulk generation of hiPSC-derived HPCs.

overall_design: RNAseq profiling of organoid development using bulk mRNA-seq comparing gene expression at timepoints 0, day 6 and day 13 and single-cell RNAseq for timepoints day 6 and day 13.

first: Naritaka

last: Tamaoki

first: Suman

last: Vodnala

first: Raul

last: Vizcardo

first: Nicholas

last: Restifo


title: The ageing epigenome regulates stem cell fate via mitochondrial-derived vesicles delivery of citrate carrier to lysosomes [CUT&RUN]

first: Peter

last: Tessarz

first: Andromachi

last: Pouikli

first: Swati

last: Parekh


title: High-throughput gene expression profilng of SMARCA4-mutated extra-cranial rhabdoid tumours (ECRT-SMARCA4), SMARCB1-mutated ECRT, ATRT and SCCOHT tumours by RNA sequencing

status: Public on Jun 02 2021

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

summary:
Purpose: Molecular characterization of ECRT-SMARCA4 tumours and their place within the constellation of ECRT-SMARCB1, ATRT and SCCOHT

Methods: Total RNA was obtained from 72 fresh-frozen tumour samples using the Qiagen RNAeasy kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s procedure. Barcode Illumina compatible libraries were generated from 750 ng of total RNA for each sample using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Libraries were sequenced using the Illumina HiSeq 2500 platform. RNA-seq data pre-processing was performed using an in-house pipeline developed at the Curie Institute Bioinformatics Core Facility. Read mapping and counting were performed using STAR, version 2.5.3) and the hg19 version of the human reference genome.

Results: Dimensionality reduction and hierarchical clustering algorithms applied to the transcriptomics dataset show that ECRT-SMARCA4 display molecular features intermediate between SCCOHT and ECRTS-MARCB1.

overall_design:
Seventy two tumour samples were analysed by RNA sequencing including 38 ATRTs (29 re-analyzed samples from Leruste et al., 2019), 19 ECRT_SMARCB1 (all re-analyzed from Leruste et al., 2019), 4 ECRT_SMARCA4 and 11 SCCOHT (10 re-analyzed from Loarer et al., 2015 which 3 are deposited in SRA SRP052896: SRX857513, SRX857516, SRX857514).

All previously published and re-analyzed data included in our study (as detailed in the published_re-analyzed_data.xlsx) have been directly provided by the authors as fastq files. For those already published in Leruste et al. (2019), the data are now under submission in the dbGAP database (phs001915.v1.p1) as mentioned in the Leruste et al. (2019) publication. Therefore, the accession numbers for each sample are not yet available. For the data from Loarer et al. (2015), only 3 are publicly available in SRA database under the accession number SRP052896.

first: Mamy

last: Andrianteranagna

first: Joanna

last: Cyrta

first: Franck

last: Bourdeaut


title: Radiation Therapy Inhances Immunotherapy Response in  Microsatellite-stable Colorectal and Pancreatic Adenocarcinoma in a Phase II Trial

status: Public on Jul 06 2021

city: Charlestown

first: David

last: Ting

department: Cancer Center

institute: Massachusetts General Hospital

summary: Immune checkpoint blockade has limited efficacy in microsatellite stable (MSS) colorectal (CRC) and pancreatic (PDAC) cancer. Preclinical models have demonstrated the use of radiation to activate the innate immune response and stimulate responsiveness to immune checkpoint blockade. Here, we describe a Phase 2 trial of radiation therapy combined with combined anti-CTLA4 (ipilimumab) and anti-PD1 (nivolumab) antibodies in MSS CRC and PDAC. In the per protocol analysis disease control rate was 37% (10/27) in CRC and 29% (5/17) in PDAC with an overall response rate of 15% (4/27) and 18% (3/17), respectively. Whole exome and RNA sequencing of biopsies from 17 patients revealed low tumor mutational burden in all tumors, but a notable upregulation of interferon stimulated genes with concordant high expression of multiple repeat RNA transcripts in responders. Altogether, this study provides foundational human proof of concept of radiation with combination immune checkpoint blockade therapy in otherwise immunotherapy resistant cancers.

overall_design: This is a phase II trial evaluating nivolumab and ipilimumab in microsatellite stable, chemorefractory colon cancer and pancreatic cancer.

first: Aparna

last: Parikh

first: Annamaria

last: Szabolcs

first: Jill

middle: N

last: Allen

first: Jeffrey

middle: W

last: Clark

first: Jennifer

middle: Y

last: Wo

first: Michael

last: Raabe

first: Hannah

last: Thel

last: Hoyos

first: Arnav

last: Mehta

first: Sanya

last: Arshad

last: Lieb

first: Lorraine

last: Drapek

first: Lawrence

last: Blaszkowsky

first: Bruce

last: Giantonio

first: Colin

last: Weekes

first: Andrew

middle: X

last: Zhu

first: Lipika

last: Goyal

first: Ryan

last: Nipp

first: Jon

last: Dubois

first: Emily

middle: E

last: van Seventer

first: Bronwen

last: Foreman

first: Lauren

last: Matlack

first: Leilana

last: Ly

first: Jessica

last: Meurer

first: Nir

last: Hacohen

last: Ryan

first: Beow

last: Yeap

last: Corcoran

first: Benjamin

last: Greenbaum

first: Theodore

last: Hong


title: Genome-wide DNA methylation profiling of SCCOHT and SMARCB1-mutated rhabdoid tumours

first: Nicolas

last: Servant

type: Methylation profiling by genome tiling array

summary: Extracranial rhabdoid tumours (ECRT) are an aggressive malignancy of infancy and early childhood. The vast majority of cases demonstrate inactivation of SMARCB1 (ECRT_SMARCB1) but, rarely, ECRT can harbour the alternative inactivation of SMARCA4 (ECRT_SMARCA4) instead of SMARCB1. To explore the place of ECRTSMARCA4 in the "rhabdoid tumour" spectrum, we generated and collected from previous studies genome-wide DNA methylation array data (n = 85) from Atypical/Teratoid Rhabdoid Tumours (ATRT), ECRT_SMARCB1, ECRT_SMARCA4 and small cell carcinomas of the ovary, hypercalcaemic type (SCCOHT) tumours. Using dimensionality reduction and unsupervised clustering approaches, our results demonstrate that ECRT_SMARCA4 display an intermediate DNA methylation profile between SCCOHT and ECRT_SMARCB1.

overall_design:
Eighty five tumour samples were profiled using illumina Infinium Human EPIC Beadchip including 54 ATRTs (24 re-analyzed samples from Leruste et al., 2019), 13 ECRT_SMARCB1 (12 re-analyzed samples from Leruste et al., 2019), 9 ECRT_SMARCA4 (4 re-analyzed from Leruste et al., 2019; 5 re-analyzed from GSE161692: GSM4912763, GSM4912765, GSM4912764, GSM4912767, GSM4912768) and 9 SCCOHT samples.

All previously published data included in our study (listed in the 'published_re-analyzed_data.xlsx') have been directly provided by the authors as IDAT files, and only 5 samples have the corresponding GEO records as indicated above.

first: Mamy

last: Andrianteranagna

first: Joanna

last: Cyrta

first: Franck

last: Bourdeaut


title: Sex-dependent gene expression patterns in control and Rspo1 gain-of-function mouse adrenals

status: Public on Jun 27 2021

city: Nice

first: Andreas

last: Schedl

address: Parc Valrose

department: iBV

institute: University of Nice

summary:
Purpose: Ectopic Rspo1 expression in the mouse adrenal gland (driven by Sf1-Cre) leads to a sexually dimorphic phenotype of adrenocortical hyperplasia and tissue degeneration. In order to gain a mechanistic understanding of the sexual dimorphism, we compared the gene expression profiles of Rspo1-overexpressing animals (Rspo1 GOF) with control littermates.
Methods: Total RNA was extracted from whole adrenals of male and female, control and Rspo1GOF mice during puberty (4 weeks). mRNA sequencing and differential gene expression analysis was conducted by Novogene Co. Hierarchical clustering  and principal component analysis were conducted using Phantasus. Gene set enrichment analysis was performed using Broad's institute GSEA and the Molecular Signatures database.
Conclusions: After Rspo1 transgene expression, sex is the second most important component that explains variability among the experimental groups. Genes specifically upregulated in female Rspo1GOF adrenals vs all the other groups are enriched in DNA proliferation and cell cycle genes, targets of E2F transcription factros and the DREAM complex. Genes specifically upregulated in male Rspo1GOF adrenals are related to immune system regulation. Verification of the RNA Seq results by experimental methods has showed that ectopic proliferation in the mutant adrenals is female-specific and that androgen receptor signalling plays a role in proliferation arrest in male animals.  Moreover, accumulation of abnormal foamy-like macrophages in the male adrenals leads to tissue degeneration.

overall_design: We provide expression data for four groups: male control, female control, male Rspo1GOF, female  Rspo1GOF. We analysed 4 biological replicates (individual mice) for each group.

first: Lyraki

last: Rodanthi

first: Anaëlle

last: Grabek


title: Assessing androgen sensitive RNA splicing patterns in LNCaP cells.

status: Public on Jun 04 2021

city: Montreal

first: Miltiadis

last: Paliouras

state: QC

address: 3755, ch de la cote st catherine

department: Endocrinology/Oncology

institute: Lady Davis Institute for Medical Research

summary: Our previous studies of proteomic-coupled-network analysis of AR protein interaction complexes (Paliouras et al., Integrative Biology, 2011) identified a number of proteins involved in RNA metabolism, specifically alternative RNA splicing.  We selected two interacting RNA splicing proteins, SAM68 and DDX5 to examine RNA splicing events in prostate cancer (PCa).  This analysis suggests a much more robust effect on RNA splicing with AR dictating either an exon-inclusion or -exclusion pathway.  To establish the true physiological roles of AR in alternative RNA splicing, we opted to further examine the changes in global splicing profiles of LNCaP PCa cells, stimulated with and without androgens in conjunction with overexpression studies of SAM68 and DDX5.

overall_design: LNCaP cells transfected with SAM68 or DDX5 expression contructs were stimulated with 10nM Mibolerone (a synthetic non-metabolizable androgen) and RNA collected after 2hrs, 6hrs or 18hrs stimulation.  Controls include untransfected and uinstimulated cells.  All experiments were performed in triplicate (n=3).


title: Endothelial cell infection and dysfunction, immune activation in severe COVID-19

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: SARS-CoV2 infects endothelial cells and induce the dysfunction of them.

overall_design:
I. We infected WT C57BL/6J or K18 hACE2 transegnic mice in both male and female mice with 2x10^5 pfu SARS-CoV2. Then those mice were eutanized 4 days post challenge and the lungs were removed and processed for total RNA preparation.
II. We infected female WT C57BL/6J or K18 hACE2 transgenic mice with  2x10^5 pfu SARS-CoV2. Then those mice were eutanized 4 days post challenge and the lungs were removed and processed for single cell suspensions.

first: Xuebin

last: Qin


title: Characterization of G-quadruplexes in the rice genome

status: Public on Jul 01 2021

city: Nanjing

first: Pengyue

last: Zhang

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argriculture University

summary: DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure functioning in various biological processes in mammals. G4 ChIP-seq assay, In this study, we developed a robust BG4-DNA ChIP-seq for global identification of DNA G4 in rice..We found that G4s harbored some functional motifs for binding of certain trans-factors, were co-localized with R-loops and DHSs in the rice genome. Importantly, G4s exhibited differential effects on DNA methylation between TE and non-TE genes in rice. Especially, G4 intensity-dependent enrichment occurred between DNA 5mC and 6mA.These DNA-related features suggest potential regulatory roles of G4 in rice. Thus, our study will pave the way for prompting intensive characterization towards identifying novel functions of G4 in plants, especially for agronomic important crops.

overall_design:
Two BG4-ChIP-seq biological replicates libraries, input library,  high resolution sequencing using Illumina HiSeq 2500
Two BioTASQ-ChIP biological replicates libraries, two biotin control libraries, sequenced using Illumina NovaSeq 6000

first: Yilong

last: Feng

first: Wenli


title: Survey of Functional Genes in the Arctic Soil

status: Public on Mar 11 2021

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

country: Japan

institute: National Polar Research Institute

summary: The objective of this study was to identify the different functional genes involved in key biogeochemical cycles in the low Arctic regions. Understanding the microbial diversity in the Arctic region is an important step to determine the effects of climate change on these areas.

overall_design: Soil samples were collected from low Arctic region of Salluit. At each sampling site five biological replicates were collected and DNA and RNA were subsequently extracted. The DNA and cDNA (synthesized from RNA samples) samples were shipped to the University of Oklahoma, where it was analyzed with the GeoChip microarray.

first: M

last: Uchida

first: S-K


title: SMARCA4-deficient rhabdoid tumours show intermediate molecular features between SMARCB1-deficient rhabdoid tumours and small cell carcinomas of the ovary, hypercalcaemic type.

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

overall_design: Refer to individual Series


title: Comprehensive transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis

status: Public on Mar 13 2021

city: Copenhagen

first: Reza

last: Yarani

address: Emdrupvej 111, 1-1

country: Denmark

institute: Steno Diabetes Center Copenhagen

type: Non-coding RNA profiling by high throughput sequencing


title: Comprehensive transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis [RNA-Seq]

summary: BACKGROUND & AIMS: Ulcerative colitis (UC) is an inflammatory bowel disorder with unknown etiology, and given its complex nature, an in vivo model to study its pathophysiology is vital. Animal models play an important role in molecular profiling necessary to pinpoint mechanisms that contribute to human disease. Thus, we aim to identify common conserved gene expression signatures and differentially regulated pathways between human UC and a mouse model hereof, which can be used to identify UC patients from healthy individuals and to suggest novel treatment targets and biomarker candidates. METHODS: Therefore, we performed high-throughput total and small RNA sequencing to comprehensively characterize the transcriptome landscape of the most widely used UC mouse model, the dextran sodium sulfate (DSS) model. We used this data in conjunction with publicly available human UC transcriptome data to compare gene expression profiles and pathways. RESULTS: We identified differentially regulated protein-coding genes, long non-coding RNAs and microRNAs from colon and whole blood of UC mice and further characterized the involved pathways and biological processes through which these genes may contribute to disease development and progression. By integrating human and mouse UC datasets, we suggest a set of 51 differentially regulated genes in UC colon and blood that may improve molecular phenotyping, as well as aid in treatment decisions, drug discovery and the design of clinical trials. CONCLUSION: Global transcriptome analysis of the DSS-UC mouse model supports its use as an efficient high-throughput tool to discover new targets for therapeutic and diagnostic applications in human UC through identifying relationships between gene expression and disease phenotype.

overall_design: Total RNA (minus small RNA) profiling of colon and blood of 3 dextran sulfate sodium mouse model of acute ulcerative colitis and 3 healthy controls

first: Oana

last: Palasca

first: Jan

last: Gorodkin

first: Flemming

last: Pociot


title: Healthy, adjacent normal and tumor colon cells

status: Public on Feb 09 2021

city: L'Hospitalet de Llobregat

first: Victor

last: Moreno

state: Barcelona

address: Granvia 199

department: Oncology Data Analytics Program

country: Spain

institute: Catalan Institute of Oncology


title: Comprehensive transcriptome profiling of ulcerative colitis mouse model suggests biomarkers and therapeutic targets for human colitis [miRNA-Seq]

overall_design: Small RNA profiling of colon and blood of 3 dextran sulfate sodium mouse model of acute ulcerative colitis and 3 healthy controls


title: Functional dissection of the Csn1s2b locus identifies complex redundant and non-redundant cytokine-activated enhancers in mouse mammary gland tissue

status: Public on Feb 11 2021

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

country: USA

institute: National Institutes of Health (NIH)

summary: Enhancers are transcription factor platforms that synergize with promoters to activate gene expression. While genome-wide chromatin studies can predict enhancers, only experimental genetics can reveal their in vivo significance and the respective contribution of individual transcription factors. Here we investigate the regulation of the Csn1s2b gene whose expression in the mouse mammary gland is induced several thousand-fold during pregnancy and lactation. Using ChIP-seq for activating histone marks and transcription factors, we identified candidate enhancers distal to the promoter and within an intron and one super-enhancer separated from the Csn1s2b gene by the Prr27 gene. Using experimental mouse genetics, we dissected the complex lactation-specific distal enhancer bound by the prolactin-activated transcription factor STAT5 and the mammary-enriched NFIB and the glucocorticoid receptor. Deletion of the canonical binding motifs for NFIB and STAT5, individually and combined, had a limited biological impact. Additional deletions revealed the importance of a non-canonical STAT5 binding site for enhancer activity throughout lactation. In contrast, the intronic enhancer activated gene expression only in late pregnancy and early lactation, likely by interacting with the distal enhancer. A downstream super-enhancer, which physically interacts with the distal enhancer, was required for the functional establishment of the Csn1s2b promoter and gene activation. Lastly, NFIB binding in the promoter region fine-tuned Csn1s2b expression. Our study provides comprehensive insight into the anatomy and biology of regulatory elements spanning 70 bp that employ the JAK/STAT signaling pathway and activate gene expression several hundred-fold during lactation.

overall_design: ChIP-seq for TFs and histone markers in the mammary tissues of wild type and mutant mice for Csn1s2b regulatory elements at day one and ten of lactation.

first: Hye

middle: K


title: Deep learning enables genetic analysis of the human thoracic aorta

status: Public on Jan 30 2021

first: Amelia

middle: Weber

last: Hall

address: 185 Cambridge St

department: Cardiology

summary: Enlargement or aneurysm of the aorta predisposes to dissection, an important cause of sudden death. We trained a deep learning model to evaluate the dimensions of the ascending and descending thoracic aorta in 4.6 million cardiac magnetic resonance images from the UK Biobank. We then conducted genome-wide association studies in 39,688 individuals, revealing 82 loci associated with ascending and 47 with descending thoracic aortic diameter, of which 14 loci overlapped. Transcriptome-wide analyses, rare-variant burden tests, and human aortic single nucleus RNA sequencing prioritized genes including SVIL, which was strongly associated with descending aortic diameter. A polygenic score for ascending aortic diameter was associated with thoracic aortic aneurysm in 385,621 UK Biobank participants (HR = 1.43 per SD; CI 1.32-1.54; P = 3.3·10-20). Our results illustrate the potential for rapidly defining quantitative traits with deep learning, an approach that can be broadly applied to biomedical images.

overall_design:
We incorporated an analysis of single-nucleus RNA sequencing (snRNA-seq) using paired samples from the ascending and descending aorta from 3 individuals to identify potentially relevant cell types for the genes at aortic GWAS loci. We sequenced the transcriptomes of 54,092 nuclei and identified 12 primary cell clusters. Through comparison of unique transcriptional profiles in each cluster to canonical cell markers, we identified populations comprising vascular smooth muscle cells, fibroblasts, three distinct types of endothelial cells, as well as macrophages and lymphocytes.
Please note that processed file is an h5ad file containing output from all samples

first: James

last: Pirruccello

first: Mark

last: Chaffin

first: Elizabeth

middle: L

last: Chou

first: Patrick

middle: T

last: Ellinor


title: Single cell RNA sequencing in Staphylococcus epidermidis-inoculated nasal epithelial cells

status: Public on Feb 26 2021

city: Seoul

first: Hyun Jik

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of otorhinolaryngology

institute: Seoul National University

summary: We report the application of single cell RNA sequencing technology for high-throughput profiling of nasal microbiome Staphylococcus epidermidis in human nasal epithelial cells.

overall_design: Examination of S. epidermidis-induced RNA expression in normal human nasal epithelial cells.

first: Hyun

first: Ara

last: Jo


title: RNA-seq analysis of pH-responsive gene expression in Helicobacter pylori [ArsS]

status: Public on Jan 19 2021

city: Nashville

first: John

last: Loh

state: TN

address: A2320 MCN VUMC

department: Infectious Diseases

institute: Vanderbilt University

summary: Purpose: Next-generation sequencing (NGS) was used to analyze pH-responsive gene expression in H. pylori. The goals of this study are to compare H. pylori pH-responsive gene expression in H. pylori strain 26695 and 26695 dervatives  containing  mutations to the ArsS, CrdS and FlgS sensor kinases.

overall_design: Analysis of transcriptional changes in H. pylori grown for 1 h in either pH 5.3 or pH 7.0 medium.

first: Timothy

last: Cover


title: Functional single-cell genomics of human cytomegalovirus infection

status: Public on Jan 22 2021

city: Vienna

first: Marco

middle: Yannic

last: Hein

address: Dr.-Bohr-Gasse 9

department: Max Perutz Labs

institute: Medical University of Vienna

summary: The complex life cycle of herpesviruses is orchestrated by the interplay of host factors and hundreds of viral genes. Understanding how they work together and how perturbations of viral and host factors impact infection represents both a fundamental problem in virology and the basis for designing antiviral interventions. Here, we use CRISPR screening to study infection of human cytomegalovirus (HCMV) in primary cells, comprehensively defining the functional contribution of each viral and host factor. We then record the transcriptomes of tens of thousands of single cells, and monitor how genetic perturbation of critical host and viral factors alters the timing, course, and progression of infection. We find that normally, the large majority of cells follow a stereotypical transcriptional trajectory. Perturbing critical host factors does not change this trajectory per se, but can either stall, delay or accelerate progression along the trajectory, allowing us to pinpoint systematically the stage of infection at which each host factor acts. Conversely, perturbation of viral factors can create distinct abortive trajectories. Our results reveal a dichotomy between the roles of host and viral factors and more generally provide a road map for functional dissection of host-pathogen interactions.

sample_organism:
Homo sapiens
Human herpesvirus 5 strain Merlin

overall_design: This repository includes six individual experiments, all conducted in human foreskin fibroblasts (HFFs) infected with human cytomegalovirus (HCMV).   (1) A pooled CRISPR nuclease (CRISPRn) screen with a library tiling the entirety of the HCMV genome, identifying viral factors that affect survival of infected cells.   (2) A pooled CRISPR interference (CRISPRi) screen with a human genome-wide library, identifying host factors that affect survival of infected cells.  (3) A pooled CRISPR nuclease (CRISPRn) screen with a human genome-wide library, identifying host factors that affect survival of infected cells.  (4) A time course of HCMV infection in genetically unperturbed fibroblasts, recorded by single-cell RNA sequencing.   (5) A pooled single-cell CRISPRi experiment (CRISPRi Perturb-seq) targeting host factors, recorded by single-cell RNA sequencing.   (6) A pooled single-cell CRISPRn experiment (CRISPRn Perturb-seq) targeting both viral and host factors, recorded by single-cell RNA sequencing.

first: Jonathan

middle: S

last: Weissman


title: Identification of Anticarin-β target gene expression in human osteosarcoma cells

status: Public on Feb 05 2021

city: kunming

first: Gan

last: Wang

address: jiaochang dobg lu 32#

institute: Kunming Institute of Zoology

summary: To gain insight into the  Anticarin-β target gene profile in osteosarcoma cells, we performed RNA-seq analysis in MG63 cells upon CCT4 siRNA-mediated knockdown (siCCT4) or  Anticarin-β.

overall_design: Transcriptomics analysis of CCT4 siRNA-mediated knockdown or Anticarin-β treatment expression in human osteosarcoma cells

first: Wang

last: Gan

first: Jin

last: Yang

first: Sheng

last: Xia

first: Zhang

last: Min


title: Fasting-Induced FOXO4 Blunts Human CD4+ T Helper Cell Responsiveness

status: Public on Jan 20 2021

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

summary: This fasting and refeeding pilot study was registered in ClinicalTrials.gov with the registration number NCT02719899 and approved by the National Heart and Lung Institute IRB.

overall_design: Subjects were screened in the ambulatory clinic and signed informed consent for the protocol prior to undertaking the study (Visit 1). Subjects initiated the study after an overnight fast with blood draw for the baseline immune response (Visit 2). After overnight fasting the study subjects consumed a fixed 500 calorie meal before 8am in the morning and fasted for 24 hours except for unrestricted water intake. Following a 24-hr. fasting blood draw (Fasting-Visit 3), the subjects ate another 500 calorie meal with post-prandial blood draws 3 hours later (Refed-Visit 3).

first: Michael

last: Sack

first: Komudi

last: Singh


title: Dual-function of beta-catenin in human tumor hepatocytes

city: Bordeaux

first: Violaine

last: Moreau

address: 146 Leo Saignat

institute: INSERM

summary: ß-catenin is part of the cell-cell adhesion complex, where it plays a structural role but is also the key effector of the Wnt pathway, where it is endowed with a transcriptional regulatory activity. Oncogenic mutations of ß-catenin are present in about one third of hepatocellular carcinoma. In most tumors, ß-catenin mutations are heterozygous meaning that mutated and wild-type proteins co-exist in tumor cells. We address here the interplay between wild-type and mutated ß-catenins in liver tumor cells. We have designed a RNA interference strategy in HepG2 cells that allows uncoupling of the two functions of ß-catenin in the same cellular background: nuclear/transcriptional activity, a function almost exclusively mediated by the mutated ß-catenin, and membrane/structural activity, which is mediated by the degradable WT ß-catenin.

overall_design: The N-terminus part of ß-catenin contains the GSK-3ß phosphorylation sites that are crucial for the regulation of its turnover. This region encoded by the exon3 of ß-catenin is deleted on one allele of the CTNNB1 gene in HepG2 cells. Thus, a high amount of a truncated form of 76kDa is co-expressed with a 92-kDa full-length ß-catenin in HepG2 cells. We designed small interfering RNAs (siRNAs), named “sißcat-WT”, “sißcat-mut” and “sißcat-both” to target, respectively and specifically, either the wild-type (WT), the mutated form of ß-catenin, or both. We performed a transcriptional analysis of HepG2 cells treated with each siRNA. This analysis was performed in triplicates.

first: Caroline

last: Gest

first: Sandra

last: Sena

first: Doulaye

last: Dembele


title: Unravelling the developmental roadmap towards human brown adipose tissue

status: Public on Mar 07 2021

city: Cambridge

first: Davide

last: Chiarugi

address: Box 289, Addenbrooke’s Hospital

department: Metabolic Research Laboratories

country: United Kingdom

institute: WT-MRC Institute of Metabolic Science

summary:
We have developed and characterised functionally and molecularly a new chemically-defined protocol for the differentiation of human pluripotent stem cells (hPSCs) into brown adipocytes (BAs) that overcomes current limitations
This protocol recapitulates step-by-step the physiological developmental path of human BAT.
The BAs obtained expresses brown adipocyte and thermogenic markers, are insulin sensitive, and responsive to β-adrenergic stimuli.
This new protocol is scalable, enabling the study of human BAs at early stages of development.

overall_design: mRNA profiles of the human embryonic stem celll line H9 and the human iPS cell line KOLF2-C1 at different stages of differentiation. Days of differentiation included D0, D2, D4. D8, D10, D12, D20 and D25 or D30. For H9 we have 3 biological replicates and for the KOLF2-C1, 5 biological replicates.

first: Stefania

last: Carobbio

first: Antonio

last: Vidal-Puig


title: Age-Related Injury Responses of Human Oligodendrocytes to Metabolic Insults: Link to BCL-2 and Autophagy Pathways

status: Public on Dec 31 2020

first: Jack

last: Antel

state: Quebec

address: 3801 University, Montreal Neurological Institut

country: Canada

institute: Montreal Neurological Institute


title: RNA-seq analysies of pH-responsive gene expression in Helicobacter pylori

first: John

last: Loh

summary: Purpose: Next-generation sequencing (NGS) was used to analyze pH-responsive gene expression in H. pylori. The goals of this study are to compare H. pylori pH-responsive gene expression in H. pylori strain 26695 and 26695 dervatives containing mutations to the ArsRS two component system.

first: Timothy

last: Cover


title: Depletion of PARP-2 in C2C12 cells

status: Public on Dec 18 2020

city: Debrecen

first: Judit

last: Márton

state: HajdU-Bihar

address: Egyetem tér

country: Hungary

institute: University Of Debrecen

summary: Poly(ADP-ribose) polymerase-2 (PARP-2) is acknowledged as a DNA repair enzyme; however, recently metabolic properties had been attributed to it. Hereby, we examined the metabolic consequences of PARP-2 ablation in skeletal muscle.

overall_design: PARP-2 silencing was performed employing shPARP-2 (small hairpin) and scPARP-2 (scrambled) shRNA by lentiviral delivery (Sigma) using 40 MOI lentiviruses coding shRNA sequence against PARP-2.

first: Peter

last: Bai


title: Age-Related Injury Responses of Human Oligodendrocytes to Metabolic Insults: Link to BCL-2 and Autophagy Pathways [Microarray]

summary: Myelin destruction and oligodendrocyte (OL) death consequent to metabolic stress is a feature of CNS disorders across the age spectrum. Using cells derived from surgically resected tissue, we demonstrate that young (<age 5) pediatric-aged sample OLs are more resistant to in-vitro metabolic injury than fetal O4+ progenitor cells, but more susceptible to cell death and apoptosis than adult-derived OLs. Pediatric but not adult OLs show measurable levels of TUNEL+ cells, a feature of the fetal cell response. The ratio of anti- versus pro-apoptotic BCL-2 family genes are increased in adult versus pediatric (<age 5) mature OLs and in more mature OL lineage cells. Lysosomal gene expression was increased in adult and pediatric compared to fetal OL lineage cells. Cell death of OLs was increased by inhibiting pro-apoptotic BCL-2 gene and autophagy activity. These distinct age-related injury responses should be considered in designing therapies aimed at reducing myelin injury.

overall_design: Comparison of autophagy and BCL2 family gene expression in oligodendrocyte-lineage cells derived from adult human brain tissue (N=3) under N1 control and low glucose conditions

first: Milton

middle: G

last: Fernandes

first: Julia

last: Luo

first: Qiao-Ling

last: Cui

first: Kelly

last: Perlman

first: Florian

last: Pernin

first: Moein

last: Yaqubi

first: Jeffrey

last: Hall

first: Roy

last: Dudley

first: Myriam

last: Srour

first: Charles

middle: P

last: Couturier

first: Kevin

last: Petrecca

first: Catherine

last: Larochelle

first: Luke

last: Healy

first: Jo-Anne

last: Stratton

last: Kennedy


title: Epigenetic regulation of gene expression in mouse skin after ionizing radiation damage

status: Public on Jan 31 2021

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Back skin from 8-10 weeks male mice was plucked to induce actively growing hair follicles. After 9 days, the back skin was irradiated with 5Gy ionizing radiation. Skin samples were collected for CHIP-seq analysis using a p53 antibody and H3K4me3 antibody. We compared wild type and Krt17 knock out mice for their epigenetic regulation of gene expression change in response to ionizing radiation

overall_design: Expression profile difference between back skin in their hair anagen after IR treatment.

first: Yue

last: Zhicao

first: Gao

last: Qingxiang


title: Ionizing radiation induced hair and skin damage

status: Public on Dec 22 2020

summary: Skin samples from back region and footpads were analyzed in 8-10 week old mice. For back skin, the hair was plucked in order to  induce active growing phase(anagen). After 9 days, the mice were irradiated for 5Gy IR. Krt17 knock out, p53 knock out, and wild type mice were compared. Samples were taken at time 0 (control), 6h, and 24h post-irradiation. For footpad skin, the mice were irradiated for 40 Gy IR. Krt17 knock out and wild type mice were compared.  Samples were taken at time 0 (control), 3 d, 6 d, 9 d post-irradiation.

overall_design: Expression profiling by high-throughput sequencing

first: ZhiCao

last: Yue


title: Creatine utilization as a sole nitrogen source in Pseudomonas putida KT2440 is transcriptionally regulated by CahR

status: Public on Dec 17 2020

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

summary: creatine regulon is small and electrophoretic mobility shift demonstrates specific CahR binding only at the creA promoter suggesting much of the regulon is due to induction by downstream products. This study identifies ligand specificity and provides biological function to a previously uncharacterized GATR, contributing to our understanding of bacterial organic nitrogen compound metabolism.

overall_design: Examination of growth and gene expression of Pseudomonas putida wild type and ∆cahR strains in response to creatine.

first: Lauren

last: Hinkel

first: Graham

last: Willsey

first: Sean

last: Lenahan

first: Korin

last: Eckstrom

first: Kristin

last: Schutz


title: Identification of functional regulatory variants implicates distinct transcriptional networks in dementia

status: Public on Dec 25 2020

city: Los Angeles

first: Yonatan

middle: Ariel

last: Cooper

state: California

address: 695 South Charles E Young Dr.  Gonda Building 2309

department: Neurology

institute: University of California, Los Angeles

summary: We used 2 massively parallel reporter assays to characterize 5,706 unique noncoding genetic variants derived from genome-wide association studies for two neurodegenerative disorders: Alzheimer’s disease (AD) and Progressive Supranuclear Palsy (PSP). Specifically, we synthesized a library consisting of both alleles of each SNV embedded within their native genomic context, which was cloned upstream of a minimal promoter within an expression vector. We then measured the transcriptional drive of each library element using next-generation sequencing of barcoded transcripts uniquely associated with each regulatory element. This enabled the identification of variants with significant transcriptional skew between alleles representing likely functional regulatory variants underlying disease risk.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design:
We first used next-generation sequencing to uniquely map barcodes to alleles to create a barcode-variant lookup table. We then assessed allelic expression by amplifying and performing next-generation sequencing of barcodes from library plasmid DNA and cDNA across multiple biological replicates.
Please note that the variant_list_MPRA* (i.e. MPRA*_variant_list.tsv) files have no associated raw data files and these files are actually variant ID metadata files needed to process the raw data.

first: Y

first: J

last: Davis

first: S

last: Kosuri

first: G

last: Coppola

first: D

middle: H

last: Geschwind


title: T47D shNT versus T47D shRON

status: Public on Dec 03 2020

city: Cincinnati

first: Susan

last: Waltz

state: Ohio

address: 3125 Eden Ave

department: Cancer Biology

institute: University of Cincinnati

summary: Introduction: HGFL-Ron signaling is augmented in human breast cancer and is associated with poor overall prognosis. Here, we investigate the role of HGFL-Ron signaling in RON-modulated human luminal A breast cancer cells T47D through RNA-sequencing, focusing on the impact of Ron knockdown through a short hairpin construct.  Methods: non-targeting shRNA (shNT) and RON-targeting shRNA (shRON) were submitted for transcriptomic characterization on the Illumina HiSeq 2500. High quality reads were aligned to the hg19 genome and quantified to generate RPKM

overall_design: Transcriptome profiles of RON-proficient and RON-deficient T47D cells through RNA-sequencing

first: Brian

last: Hunt

first: Jennifer

last: Bourn


title: Astrocytes respond to a reduction of extracellular Nerve Growth Factor levels by a phosphorylation of TrkA in the endoplasmic reticulum:  a microarray transcriptome study

status: Public on Dec 01 2020

city: Roma

first: Ivan

last: Arisi

address: viale Regina Elena 295

department: Bioinformatics Facility

institute: European Brain Research Institute

summary: The discovery that other cells besides neurons, like the glia cells, could respond to NGF and modulate the neuronal physiology broadened the possible NGF targets to potentially all the brain, boosting the comprehension of neuronal pathologies - like Alzheimer's disease - and supporting more therapeutical strategies. This microarray transcriptome analysis of primary astrocytes was performed to demonstrate a direct modulation of NGF activity on astrocyte cells. We investigated this modulation by neutralizing extracellular NGF by the alfaD11 monoclonal antibody and measuring the gene expression profile. Data analysis was performed using R-Bioconductor.

overall_design: A total of n=8 samples were processed. The samples are divided into 3 experimental groups: anti-NGF alfaD11 antibody treated samples (n=4), naive cells control samples (n=2), anti-V5 antibody treated control samples (n=2). Samples were treated for 24h.

first: Nicola

last: Carucci

first: Giovanna

last: Testa

first: Francesco

last: Gobbo

first: Caterina

last: Rizzi

first: Lucia

last: Galli-Resta

first: Mara

last: D'Onofrio

first: Rossella

last: Brandi

first: Simona

last: Capsoni

first: Antonino

last: Cattaneo


title: RNA-sequencing reveals transcriptional signature of pathological remodeling in the diaphragm of rats after myocardial infarction

city: Gainesville

first: Svetlana

last: Yegorova

state: FL

address: 1864 Stadium Rd

institute: University of Florida

summary:
Purpose: In the current study, we used RNA-Seq to determine the transcriptional changes and understand the genetic reprogramming of the diaphragm in the chronic phase post-myocardial infarction.
Methods: Rat diaphragm mRNA profiles 16 weeks post Sham and Myocardial infarction (MI) surgeries were generated by deep sequencing using llumina NextSeq 500. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat followed by Cufflinks.
Results: After quality control and data filtering, on average, 33,972,308 raw reads per sample were obtained. For each sample, 88.49 % to 91.70 % reads were uniquely mapped to the rat reference genome. Median CV coverage uniformity was 0.45± 0.01. Distribution of mapped reads over DNA regions showed 48% of reads mapped to coding region, 20% of reads mapped to untranslated region (UTR), 12% of reads mapped to intron region, and 20% reads mapped to intergenic region. The resulting Sham and MI transcriptomes, created from generated transcriptomes of each individual sample in each group and merged transcriptomes within the same group, were used for differential gene expression analysis. A total of 112 differentially expressed genes (DEGs) were identified out of a total of 9664 genes with measured expression in MI and Sham groups. Among DEGs, 42 were upregulated and 70 were downregulated in the MI group. Hierarchical clustering heat map, pathway enrichment and gene ontology (GO) analyses, and analysis of DEGs in the framework skeletal muscle-specific biological networks were performed.
Conclusions: Our study represents the first detailed analysis of diaphragm transcriptomes post-myocardial infarction generated by RNA-Seq technology.

overall_design: Diaphragm mRNA profiles of Sham and myocardial infarction rats were generated by deep sequencing using Illumina NextSeq 500 sequencer.

first: Oleg

last: Yegorov

first: Leonardo

middle: F

last: Ferreira