title: In vivo transciptomic responses to bromobenzene exposure from liver and kidneys of Sprague Dawley rats

summary: In this study we tested the ability to identify early perturbations in the organ (liver and kidney) metabolism due to bromobenzene exposure at two early time points (5 and 10 h) using RNA-sequencing.

overall_design: We treated Sprague Dawley rats with a single dose of bromobenzene (0.4 g/kg) with corresponding controls given 2% saline as vehicle (n =8 each for control and treatment). Liver and kidney samples for RNA-sequencing were collected 5 and 10 h post bromobenzene/vehicle treatment. Total 32 rats were used with 8 replicates for each condition and time point.

first: Mohsin

last: Rahim

first: Chiyo


title: Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model.

status: Public on Apr 19 2023

city: Antwerp

first: Pieter

last: Meysman

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: University of Antwerp

type: Expression profiling by high throughput sequencing

summary: With Varicella-Zoster Virus (VZV) being an exclusive human pathogen, human induced pluripotent stem cell (hiPSC)-derived neural cell culture models are an emerging tool to investigate VZV neuro-immune interactions. Using a compartmentalized hiPSC-derived neuronal model allowing axonal VZV infection, we previously demonstrated that paracrine interferon (IFN)-α2 signalling is required to activate a broad spectrum of interferon-stimulated genes able to counteract a productive VZV infection in hiPSC-neurons. In this new study, we now investigated whether innate immune signalling by VZV-challenged macrophages was able to orchestrate an antiviral immune response in VZV-infected hiPSC-neurons. In order to establish an isogenic hiPSC-neuron / hiPSC-macrophage co-culture model, hiPSC-macrophages were generated and characterised for phenotype, gene expression, cytokine production and phagocytic capacity. Even though immunological competence of hiPSC-macrophages was shown following stimulation with the VZV mimic poly(dA:dT) or treatment with IFN-α2, hiPSC-macrophages in co-culture with VZV-infected hiPSC-neurons were unable to mount an antiviral immune response capable of suppressing a productive neuronal VZV infection. Subsequently, a comprehensive RNA-Seq analysis confirmed the lack of strong immune responsiveness by hiPSC-neurons and hiPSC-macrophages upon, respectively, VZV infection or challenge. This may suggest the need of other cell types, like T-cells or other innate immune cells, to (co-)orchestrate an efficient antiviral immune response against VZV-infected neurons.

overall_design: We generated bulk RNA-seq samples from both hiPSC-neurons and hiPSC-macrophages, stimulated with the pro-inflammatory pdAT or cell-free VZV-eGFP/ORF23.

first: Elise

last: Van Breedam

first: Tamariche

last: Buyle-Huybrecht

first: Jonas

last: Govaerts

first: Marlies

last: Boeren

first: Julia

last: Di Stefano

first: Thalissa

last: Caers

first: Hans

last: De Reu

first: Laura

last: Dirkx

first: Jolien

last: Schippers

first: Esther

last: Barholomeus

first: Marielle

last: Lebrun

first: Catherine

last: Sadzot

first: Paulina

last: Rybakowska

first: Concepcion

last: Maranon

first: Kris

last: Laukens

first: Peter

last: Delputte

first: Benson

last: Ogunjimi

last: Ponsaerts


title: A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [TC28_ZEB1_DRUGseq]

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

country: USA

institute: The Scripps Research Institute

summary: To investigate the role of ZEB1 in chondrocytes, we transfected an overexpression vector containing cDNA for ZEB1 (Sino Biological; HG17705-UT) into TC28a2 cells using Lipofectamine 3000. We then performed DRUG-seq analysis to determine the impact of ZEB1 on global gene expression.

overall_design: DRUG-seq (high throughput low-cost RNA-Seq) analysis of ZEB1 overexpression in chondrocyte cell line (TC28a2)

first: Hannah

last: Swahn

first: Kun

last: Li

first: Tomas

last: Duffy

first: Merissa

last: Olmer

first: Darryl

middle: D

last: D'Lima

first: Tony

middle: S

last: Mondala

first: Padmaja

first: Steven

middle: R

last: Head

first: Martin

middle: K

last: Lotz


title: A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [Cartilage_Meniscus_scRNAseq]

summary: Osteoarthritis (OA) affects all tissues in the knee joint but therapeutic targets have often been selected for their role in cartilage damage and inflammation and largely omitted consideration of mechanisms that are mediating meniscus damage and more importantly there have been insufficient efforts to determine whether pathogenic processes are shared between tissues. Several scRNA-seq analyses have been performed in OA knees but have been largely restricted to the analysis of a single joint tissue of articular cartilage, or meniscus with the exception of one study that analyzed cartilage and synovium. Here, we performed scRNA-seq analyses of healthy and OA-affected human knee cartilage and menisci to interrogate separate and shared mechanisms in cellular homeostasis and OA pathogenesis.

overall_design: Single cell level analysis of articular cartilage and meniscus tissues from human healthy (n=6, n=7) and osteoarthritis (n=6, n=6) knees.


title: The effect of crosslinking density on nasal chondrocytes' redifferentiation

city: Edmonton

first: Zhiyao

last: Ma

state: Alberta

country: Canada

institute: University of Alberta

summary: In this manucript, we investigate the effect of different crosslinking density of the thiolated hyalonric acid hydrogel as the supporting matrix for monolayer expanded chondrocyte's chondrogenic redifferentiation.A wide ragne of gene expression level was found to be correlated with teh level of crosslinking, and the biological processes and KEGG pathways associated with this panel of genes are related to cell death, immune response, and regulation of various foundamental developmental processes.

overall_design: A combination of thiolate hyaluronic acid and thiolate gelatin (1:1, 10mg/mL) solution was mixed with PEDGA crosslinker solution (10mg/mL) in a solid content ratio of 1:2, 1:4, 1:6, 1:8. Tissue engineered constructs were made from nasal chondrocytes mixed with these four hydrogels with different crosslinking density. The tissue engineered constructs were cultured for 6 weeks in normal oxygen condition (21% oxygen, NRX). After 6 weeks of culture, the constructs were assessed vis histology, immunofluorescence, GAG/DNA assays, RNA sequencing.

first: Xiaoyi

last: Lan

first: Melanie

last: Kunze

first: Aillette

last: Mulet-Sierra

first: Yaman

last: Boluk

first: Adetola

last: Adesida


title: Human iPSC-derived neural progenitor cells secreting GDNF provide protection in rodent models of ALS and retinal degeneration

city: Los Angeles

first: Shaughn

last: Bell

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

summary: Expanded populations of human fetal-derived neural progenitor cells transduced to produce GDNF (fNPC-GDNF) have now been shown to survive for over three years following injection into the human spinal cord and can provide neuroprotection in many animal models. However, low availability of starting material limits their widespread use. Human induced pluripotent stem cells (iPSCs) are an alternative, renewable cell source that can be differentiated into NPCs and transduced with GDNF (iNPC-GDNF). The goal of the current study was to characterize iNPC-GDNF cells and test their therapeutic potential and safety. Single nuclei RNA- seq showed that fNPC-GDNF and iNPC-GDNF had both overlapping and unique clusters of cells, suggesting that the two products were not identical. When transplanted into the subretinal space of a rodent model of retinal degeneration, iNPC-GDNF preserved photoreceptors and visual function. Transplantation of iNPC-GDNF into the lumbar spinal cord of a rodent model of ALS preserved motor neurons. Finally, to evaluate long-term safety and tolerability, iNPC-GDNF were transplanted into the spinal cord of athymic nude rats for 9 months. Surviving grafts secreting GDNF were found in all animals with no signs of tumor formation or cell proliferation. iNPC-GDNF survive long-term, are safe, and provide neuroprotection in models of both retinal degeneration and ALS, indicating their potential for clinical trials as a cell and gene therapy-based treatment for various neurodegenerative diseases.

overall_design: Single nucleus sequencing:  Two cell lines: 1) fetal-derived neural progenitors transduced to produce GDNF; 2) iPSC-derived neural progenitors transduced to produce GDNF.

first: Alexander

middle: H

last: Laperle

first: V

middle: A

last: Moser

first: Pablo

last: Avalos

first: Bin

last: Lu

first: Amanda

last: Wu

first: Aaron

last: Fulton

first: Stephany

last: Ramirez

first: Veronica

middle: J

last: Garcia

first: Ritchie

last: Ho

first: George

last: Lawless

first: Kristina

last: Roxas

first: Saba

last: Shahin

first: Oksana

last: Shelest

first: Soshana

last: Svendsen

first: Shaomei

last: Wang

first: Clive

middle: N


title: RNA-seq of CAF05s grown on different substrates

status: Public on Apr 18 2023

city: Urbana

first: Taher

last: Saif

state: IL

address: 105 S Mathews Ave

department: Grainger College of Engineering

institute: University of Illinois at Urbana-Champaign

summary: Almost all solid tumors become stiff with progression of cancer. Cancer Associated Fibroblasts (CAFs), most abundant stromal cells in the tumor microenvironment (TME), are known to mediate the stiffening. While the biochemical crosstalk between CAFs and cancer cells have been widely investigated, it is yet not clear whether CAFs in stiffer TME promote metastatic progression, and if so, how. To address this question, here we explore the role of mechanical stiffness and cell traction force in regulating human colorectal CAF (CAF05 cell line) gene expressions that are relevant to metastatic progression. We cultured CAFs on 2D polyacrylamide hydrogels with increasing elastic modulus (E) of 1, 10 and 40 kPa, and quantified corresponding cell spreading area and cytoskeletal force. We performed genome-wide transcriptome analyses in these cells to identify differentially expressed genes on 40 KPa compared to those on 1 kPa substrate. The latter represents normal tissue stiffness of colon.

overall_design: CAFs were grown on polyacrylamide hydrogel (PA gel) substrates of 1 kPa, 10 kPa and 40 kPa elastic modulus. Fibronectin coating were applied on the substrates. Cell were also grown on plastic dish that has an elastic modulus of 3.4 GPa. After 48 hrs of culture, RNA was extracted using Trizol reagent and then processed for RNAseq.

first: Bashar

last: Emon

first: You Jin

last: Song

first: Kannanganattu

middle: V

last: Prasanth

first: M

middle: T

last: A Saif


title: Gene expression profile at single cell level of B cells from the Peyer's patch (PP) in the small intestine of EWSR1 WT and BKO mice

city: Nanjing

first: Yanchuan

last: Li

state: Jiangsu

address: Nanjing Medical University

department: Department of Cell Biology

country: China

institute: School of Basic Medical Sciences, Nanjing Medical University

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of PP B cells  in the small intestine.

overall_design: PP cells from PP cells from WT and Ewsr1 BKO mice (three 8-week-old) male mice together as one sample for each group) were stained for 15 min with anti-CD45 FITC, anti-CD19 APC antibodies, and Dead marker (PI) for live-dead discrimination. Viable B cells (CD45+CD19+Dead-) were sorted on a FACSARIA sorter.


title: Mechano-hypoxia conditioning with TGF-β3 withdrawal promotes stable, non-hypertrophic chondrogenesis of human mesenchymal stem cells

first: Zhiyao

last: Ma

summary: We hypothesize that the combination of mechanical loading with hypoxia culture and TGF-β3 growth factor withdrawal will promote stable, non-hypertrophic chondrogenesis of hBM-MSC embedded in an HA-hydrogel. To this end, we first assessed static hypoxia culture with growth factor withdrawal against static normoxia (20% O2) culture at the global transcriptome and tissue matrix level. We then assess two modalities of mechanical loading (dynamic compression, DC and cyclic hydrostatic pressure, CHP) with growth factor withdrawal against static culture, all under hypoxia. Results showed that Mechanical stimulation and TGF-β3 withdrawal under hypoxia promoted a strong chondrogenic and non-hypertrophic phenotype of hBM-MSC.

overall_design: Tissue-engineered constructs were made from frozen human BM-MSCs seeded on HyStem-C hydrogel. Constructs were precultured for three weeks in a 3% oxygen (HYP) condition with the supplement of TGF-β3. After pre-culture, two separate experiments were conducted. In experiment I, constructs were cultured in 3% and 20% (NRX) oxygen environment with/without the supplement with TGF-β3 for 3 weeks. In experiment II, constructs were cultured under dynamic compression or cyclic hydrostatic pressure with/without the supplement with TGF-β3 for 3 weeks. After the 6 weeks period, constructs were assessed via histology, immunofluorescence, GAG/DNA assays, RNA sequencing, and testing of mechanical properties.

first: David

middle: X

first: Alexander

last: Szojka

first: Xiaoyi

last: Lan

first: Melanie

last: Kunze

first: Aillette

last: Mulet-Sierra

first: Lindsey

last: Westover

first: Adetola

middle: B

last: Adesida


title: A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus [TC28_FAP_DRUGseq]

first: Padma

last: Natarajan

summary: To investigate the role of FAP in chondrocytes, we transfected an overexpression vector containing cDNA for FAP (Sino Biological; HG10464-UT) into TC28a2 cells using Lipofectamine 3000. We then performed DRUG-seq analysis to determine the impact of FAP on global gene expression.

overall_design: DRUG-seq (high throughput low-cost RNA-Seq) analysis of FAP overexpression in chondrocyte cell line (TC28a2)

first: Hannah

last: Swahn

first: Kun

first: Tomas

last: Duffy

first: Merissa

last: Olmer

first: Darryl

last: D'Lima

first: Tony

last: Mondala

first: Padmaja

first: Steven

last: Head

first: Martin

last: Lotz


title: Multiplexed inactivation of endogenous genes by base-editor-mediated multi-stop system

city: Shanghai

first: Qing

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

institute: Chinese Academy of Science

summary: Base editor is also a powerful tool to introduce early stop codons to simultaneously silence multiple genes to study family gene function in embryo development. Here, we identified the highest efficiency base editing system (hA3A-eBE-Y130F) with few sgRNA independent off-target sites among six well-established base editors in mouse embryo. Further, we developed a Multi-Stop system to simultaneously knock-out all Ten-eleven translocation (TET) family of dioxygenase genes (Tet1, Tet2 and Tet3) in zygotic genome leads embryo die before 10.5 days of gestation. Moreover, we showed that inactivation of three DNA methyltransferases genes (Dnmt1, Dnmt3a and Dnmt3b) in zygote leads to gastrulation failure. We also obtained multiple TET and DNMT family genes (6KO: Dnmt1/3a/3b and Tet1/2/3; 5KO: Dnmt3a/3b and Tet1/2/3; 4KO: Dnmt1 and Tet1/2/3) deactivated mouse embryos in one step, which indicated that Dnmt1 or Dnmt3a/b is indispensable for mouse gastrulation.

overall_design: We used the deep sequencing to evaluate the mutant efficiency of all the mutant embryos.

first: Li

last: Jinsong

last: Qing

first: Yan

last: Meng


title: Asynchronous transcription and translation of neurotrasmitter-related genes characterize the initial stages of neuronal maturation in Drosophila

city: Portugal

first: Catarina

middle: CF

last: Homem

address: Rua Campo Mártires da Pátria, 130

country: Portugal

institute: CEDOC - NMS

summary: Neuron specification and maturation are essential for proper central nervous system development. However, the precise mechanisms that govern neuronal maturation, essential to shape and maintain neuronal circuitry, remain poorly understood. Here, we analyse early-born secondary neurons in the Drosophila larval brain revealing that the early maturation of secondary neurons goes through three consecutive phases: 1) Immediately after birth, neurons express pan-neuronal markers but do not transcribe terminal differentiation genes; 2) Transcription of terminal differentiation genes, such as neurotransmitter-related genes VGlut, ChAT or Gad1, starts shortly after neuron birth, but these transcripts are however not translated; 3) Translation of neurotransmitter-related genes only begins several hours later in mid pupa stages in a coordinated manner with animal developmental stage, albeit in an ecdysone independent-manner. These results support a model where temporal regulation of transcription and translation of neurotransmitter-related genes is an important mechanism to coordinate neuron maturation with brain development.

overall_design: scRNA-Seq profile of neuronal lineages of central brain and ventral nerve cord collected at 105h after larval hatching (2 samples)

middle: C

first: Graça

last: Marques


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [scRNA-seq]

first: Isaac

middle: F.

last: López-Moyado

address: 9420 Athena Cir

department: Division of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

summary: The three mammalian TET dioxygenases oxidize the methyl group of 5-methylcytosine (5mC) in DNA, and the oxidised methylcytosines are essential intermediates in all known pathways of DNA demethylation. To define the in vivo consequences of complete TET deficiency, we inducibly deleted all three Tet genes in the mouse genome. Tet1/2/3 inducible TKO (iTKO) mice succumbed to acute myeloid leukaemia by 4-5 weeks. Single-cell RNA sequencing of Tet iTKO bone marrow cells revealed the appearance of new myeloid cell populations characterised by a striking increase in expression of all members of the stefin/cystatin gene cluster on mouse chromosome 16. In patients with acute myeloid leukaemia, high stefin/cystatin gene expression correlates with poor clinical outcomes. Increased expression of the clustered stefin/cystatin genes was associated with a heterochromatin-to-euchromatin compartment switch with readthrough transcription downstream of the clustered stefin/cystatin genes as well as other highly expressed genes but only minor changes in DNA methylation. Our data highlight new roles for TET enzymes that are distinct from their established function in DNA demethylation, and instead involve increased transcriptional readthrough and changes in three-dimensional genome organisation.

overall_design: Single cell RNA-seq analysis in Control and Tet TKO CD11b+ cells

middle: F

first: Hiroshi

last: Yuita


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [WGBS]

type: Methylation profiling by high throughput sequencing

overall_design: WGBS (MethylC-seq) analysis in Control and Tet TKO CD11b+ cells


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [polyA+ RNA-seq]

overall_design: polyA+ RNA-seq analysis in Control and Tet TKO CD11b+ cells


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [Hi-C]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Hi-C analysis in Control (Tet1/2/3 f/f) and Tet iTKO (Tet1/2/3 f/f CreERT2) CD11b+ cells


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [ATAC-seq]

overall_design: ATAC-seq on Lin- c-Kit+ Sca-1+ (LSK) cells from Tet2f/f Tet3f/f Mx1-Cre (Tet2/3 f/f, Tet2/3 iDKO) mice 3 weeks after poly-I:C treatment

first: James

last: Scott-Browne

first: Myunggon

last: Ko


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch [Ribodepleted RNA-seq]

overall_design: Total ribodepleted RNA-seq analysis in Control, Tet2/3 DKO and Tet TKO CD11b+ cells


title: Characterization of the genes that were regulated by feeding with B. subtilis (natto) strains

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

summary: In the present study, we investigated the effect of Bacillus subtilis var. natto on lifespan using Caenorhabditis elegans as a model animal. The lifespan of the adult C. elegans fed Bacillus subtilis var. natto MI-OMU01 strain was significantly longer than that of animals fed OP50 (control). Transcriptional profiling comparing MI-OMU01- and control-fed animals suggested that genes related to “innate immune system” were upregulated by MI-OMU01.

overall_design: Transcriptional profiling of three-day-old worms that were fed OP50 or B. subtilis (natto) MI-OMU01 for one day, by deep sequencing, using Illumina HiSeq.


title: GPR101 loss promotes insulin resistance and diet-induced obesity risk

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary: G-protein-coupled receptors (GPCRs) represent targets for improved low-side-effect therapies to tackle the evolving Western obesity epidemic. The orphan (o) GPCR GPR101 emerged as an attractive candidate in this regard. Expressed on cells in brain areas regulating energy homeostasis, including the hunger-suppressing proopiomelanocortin (POMC) + neurons, it is minimally expressed outside the brain. To understand the function of this receptor in vivo, we herein generated and comprehensively characterized a Gpr101 knockout mouse line, either under standard feeding conditions or with chronic high-fat diet (HFD) access (16 weeks). GPR101 loss accelerated the risk for diet-induced obesity (DIO), hyperinsulinemia and disrupted glucose homeostasis. Hypothalamic transcriptomic analysis revealed also decreased Pomc activation with HFD suggesting impaired hunger suppression. Moreover, on a standard diet, there was a molecular signature of downregulated tristetrapolin (TTP) pathway gene activation suggesting impaired inflammation resolution and one of aberrant microglial phagocytosis and lipid metabolism on HFD. Morphometry revealed altered hypothalamic arcuate nucleus microglial morphology consistent with the transcriptomic profile. We discuss how the GPR101 specialized pro-resolving mediator (SPM) receptor capacity likely underlies the aberrant microglial function and contributes to DIO risk. Thus, this evidence shows that GPR101 is a potential therapeutic target for DIO through, among other factors, effects on hypothalamic inflammation resolution.

overall_design: We analysed hypothalamic tissue of Gpr101 knock-out and control mice treated with high-fat or control diets

first: Lillian

last: Garrett

last: Irmler

first: Angela

last: Baljuls

first: Birgit

last: Rathkolb

first: Nathalia

last: Dragano

first: Raffaele

last: Gerlini

first: Adrian

last: Sanz-Moreno

first: Antonio

last: Aguilar-Pimentel

first: Lore

last: Becker

first: Markus

last: Kraiger

first: Rosa

last: Reithmeir

first: Julia

last: Calzada-Wack

first: Wolfgang

last: Wurst

first: Helmut

last: Fuchs

first: Valerie

last: Gailus-Durner

first: Tina

last: Zimmermann

first: Sabine

middle: M

last: Hölter

last: Hrabě de Angelis


title: A senescent cell population with ZEB1 transcription factor as its main regulator promotes osteoarthritis in cartilage and meniscus

first: Padma

last: Natarajan

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

overall_design: Refer to individual Series


title: Altered DNA Methylation and Gene expression predict Disease Severity in Patients with Aicardi-Goutières Syndrome

city: Pavia

first: Jessica

last: Garau

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

summary:
Aicardi-Goutières Syndrome (AGS) is a rare neuro-inflammatory disease characterized by increased expression of interferon-stimulated genes (ISGs). Disease-causing mutations are present in genes associated with innate antiviral responses. Disease presentation and severity vary, even between patients with identical mutations from the same family.  This study investigated DNA methylation signatures in PBMCs to understand phenotypic heterogeneity in AGS patients with mutations in RNASEH2B. AGS patients presented hypomethylation of ISGs and differential methylation patterns (DMPs) in genes involved in “neutrophil and platelet activation”. Patients with “mild” phenotypes exhibited DMPs in genes involved in “DNA damage and repair”, whereas patients with “severe” phenotypes had DMPs in “cell fate commitment” and “organ development” associated genes. DMPs in two ISGs (IFI44L, RSAD2) associated with increased gene expression in patients with “severe” when compared to “mild” phenotypes.  In conclusion, altered DNA methylation and ISG expression as biomarkers and potential future treatment targets in AGS.
This project aimed at testing  the hypothesis that DNA methylation may influence gene expression, thereby affecting associated clinical phenotypes in AGS patients with the same mutation (RNASEH2B p.A177T).

overall_design: Genome wide DNA methylation profiles were analyzed in PBMCs from patients with Aicardi-Goutières Syndrome (Mild or Severe form) and healthy control patient

first: Amandine

last: Charras

first: Simona

last: Orcesi

first: Costanza

last: Varesio

first: Francesca

last: Dragoni

last: Galli

first: Elisa

last: Fazzi

first: Stella

last: Gagliardi

first: Orietta

last: Pansarasa

first: Cristina

last: Cereda

first: Christian

last: Hedrich


title: Off-target effect of engineered AsCas12f variants

status: Public on Apr 24 2023

city: Chicago

first: Tong

last: Wu

state: Illinois

address: 929 E 57th St. GCIS E335

institute: University of Chicago

summary: Cells were transfected with plasmids containing AsCas12f variants and sgRNAs for gene-editing. Off-target effect was determined using GUIDE-seq on an Illumina Nextseq platform.

overall_design: GUIDE-seq

first: Ruitu

last: Lyu

first: Weixin

last: Tang


title: mRNAseq of undifferentiated iPSCs, iPSC-derived skeletal muscles induced by dox-inducible MYOD1 expression, and those derived from human myoblast cell line (Hu5/KD3)

city: Nagakute

first: Yohei

last: Okada

state: Aichi

address: 1-1 Yazakokarimata

department: Department of Neural iPSC Research, Institute for Medical Science of Aging

institute: Aichi Medical University

summary: We sequenced mRNA from skeletal muscles derived from MYOD1-hiPSCs generated by different selection methods, and compared the results with those derived from human myoblast cell line (Hu5/KD3). This analysis enables us to understand the effects of different selection methods on the generation of MYOD1-hiPSCs and skeletal muscle differentiation from them. mRNAs from undifferentiated MYOD1-hiPSCs were also sequenced.(*RAW data not provided due to patient privacy concerns)

overall_design:
Global transcriptome analysis by RNA sequencing was carried out in both bulk and clonal MYOD1-hiPSCs (201B7) established through transduction of a piggyBac transposon vector for the doxycycline (Dox)-inducible expression of human MYOD1 tagged to 3 x HA (Dox-3HA-hMYOD1) with a selection by G418 or puromycin. 409B2-MYOD1-hiPSCs and human myoblast cell line (Hu5/KD3), as controls, and several other MYOD1-hiPSC (EKN3, YFE16, and TIGE9) generated in the bulk manner with the selection with Puromycin were also examined.

>>>Submitter states: Due to privacy concerns, raw data are not provided<<<

first: Muhammad

last: Irfanur Rashid

first: Fuyuki

last: Miya


title: SCENIC+: identification of enhancers and gene regulatory networks using single-cell multiomics (EAD)

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

institute: VIB

summary: Joint profiling of chromatin accessibility and gene expression of individual cells provides an opportunity to decipher enhancer-driven gene regulatory networks (eGRN). Here we present a new method for the inference of eGRNs, called SCENIC+. SCENIC+ predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. To improve both recall and precision of TF identification, we curated and clustered more than 40,000 position weight matrices that we could associate with ~1,500 human TFs. We validated and benchmarked each of the SCENIC+ components on diverse data sets from different species, including human peripheral blood mononuclear cell types, human ENCODE cell lines, human melanoma cell states, and Drosophila retinal development. Next, we exploit SCENIC+ predictions to study conserved TFs, enhancers, and GRNs between human and mouse cell types in the cerebral cortex. Finally, we provide new capabilities that exploit the inferred eGRNs to study the dynamics of gene regulation along differentiation trajectories; to map regulatory activities onto tissues using spatial omics data; and to predict the effect of TF perturbations on cell state. SCENIC+ provides critical insight into gene regulation, starting from multi-ome atlases of scATAC-seq and scRNA-seq. The SCENIC+ suite is available as a set of Python modules at scenicplus.readthedocs.io.

overall_design: 10x scATAC-seq on the Drosophila third instar larvae eye disc

first: Carmen

last: González-Blas

first: Seppe

last: De Winter

first: Stein

last: Aerts


title: SCENIC+: identification of enhancers and gene regulatory networks using single-cell multiomics (cell lines)

overall_design: A mix of 11 wild type melanoma cell lines (MM050, MM099, MM116, MM001, MM011, MM057, MM087, MM031, MM047 and MM029) were analysed using 10x scATAC-seq experiments


title: SCENIC+: identification of enhancers and gene regulatory networks using single-cell multiomics (Cortex)

overall_design: 10x single cell multiome on the mouse cortex


title: Transglutaminase 2 regulates terminal erythroid differentiation via cross-linking activity

status: Public on Apr 23 2023

city: Beijing

first: Xiang

last: Lv

state: Beijing

address: No.5, Dongdan Santiao, Dongcheng District, Beijing

department: School of Basic Medicine

institute: Peking Union Medical College

summary: To gain the whole picture of terminal erythroid differentiation, bone marrow erythroblasts of different maturation stages including proerythroblasts (Pro),basophilic erythroblasts (Baso), polychromatic erythroblasts (Poly) and orthochromatic erythroblasts (Ortho) were isolated and sorted.Transcriptomic analysis of these four stages of cells was performed.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for proerythroblasts (Pro), basophilic erythroblasts (Baso), polychromatic erythroblasts (Poly) and orthochromatic erythroblasts (Ortho).

first: Xuehui

last: Liu

first: Yingying

last: Zhang

first: Lifang

last: Shi

first: Ke

last: Yang

first: Donglin

last: Yu


title: The Mitochondrial Protein Mitofusin 2 Stabilizes Adherens Junctions and Suppresses Endothelial Inflammation via Modualtion of β-catenin Signaling

first: Jalees

last: Rehman

address: 909 S. Ashland Ave. MBRB 2072, Mailcode 669

department: Biochemistry and Molecular Genetics

institute: UIC

summary: Endothelial barrier integrity is ensured by the stability of the adherens junction (AJ) complexes  comprised of VE-cadherin as well as accessory proteins such as β-catenin and p120-catenin.  Disruption of the endothelial barrier due to disassembly of AJs results in tissue edema and the  influx of inflammatory cells. Using three-dimensional structured illumination microscopy (3D-  SIM), we found that the mitochondrial protein Mitofusin-2 (Mfn2) co-localizes at the plasma  membrane with VE-cadherin and β-catenin in endothelial cells during homeostasis. Upon  inflammatory stimulation, Mfn2 is sulfenylated, the Mfn2/β-catenin complex disassociates from  the AJs and translocates into the nucleus where Mfn2 negatively regulates the transcriptional  activity of β-catenin. Endothelial-specific deletion of Mfn2 resulted in inflammatory injury,  indicating an anti-inflammatory role of Mfn2 in vivo. Our results suggest that Mfn2 acts in a non-  canonical manner to suppress the inflammatory response by stabilizing cell-cell adherens  junctions and by binding to the transcriptional activator β-catenin.

overall_design: Total RNA was isolated by using  phenol/chloroform and TRIzol Reagent, and its quality was evaluated with gel QC. Bulk RNA  sequencing for 4 samples with 3 biological replicates each was performed with 3’ mRNA seq, 50  bp single end sequencing for coding genes at Core Genomic Facility in University of Illinois at  Chicago. The sequenced reads from all samples were aligned to the human (hg38) reference  genome with STAR v. 2.4.2, and the aligned reads were used to quantify mRNA expression by  using HTSeq-count v. 0.6.1. Gene symbols were mapped to the ENSEMBL features using the  biomaRt package v. 2.26.1.

first: Young-Mee

last: Kim

first: Ankit

last: Jambusaria


title: Crnic Institute Human Trisome Project - Trisomy 21 Model Atlas: PolyA RNA-seq from C57BL/6 and Dp16 adult mouse brain tissue ± JAK1/2 inhibition with baricitinib

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

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

summary: Analysis of steady-state mRNA levels in adult mouse brain tissue at 7-11 weeks  from wild-type C57BL/6 and Dp16 mice ± treatment with the JAK1/2 inhibitor baricitinib. This dataset is part of the Human Trisome Project - Trisomy 21 Model Atlas run by the Linda Crnic Institute for Down Syndrome at the University of Colorado Anschutz Medical Campus. http://www.trisome.org/

overall_design: Comparison of wild-type+vehicle (n=2), wild-type+baricitinib (n=2), Dp16+vehicle (n=4), Dp16+baricitinib (n=4).

first: Kelly

last: Sullivan

first: Joaquin

last: Espinosa


title: Induction of astrocytic Slc22a3 regulates sensory processing through histone serotonylation

status: Public on Apr 17 2023

city: Houston

first: Debosmita

last: Sardar

address: 1 Baylor Plaza

institute: Baylor College of Medicine


title: Induction of astrocytic Slc22a3 regulates sensory processing through histone serotonylation (ChIP-Seq)

summary:
To profile Sox2 and Sox9 binding sites in Gq-DREADD expressing CNO treated brains in comparison to control. Furthermore, we also aimed to profile Sox9 binding sites in odor treated vs. control olfactory bulbs.
An additional goal of this study was to profile histone serotonylation mark in Slc22a3-cKO olfactory bulb in comparison to control.

overall_design: Chromatin immunoprecipitation (ChIP-Seq) for Sox2, Sox9 and histone serotonylation in mouse brain.

first: Benjamin

last: Deneen


title: Identification of RoxS targets

city: Paris

first: Sylvain

last: Durand

address: 13 rue Pierre et Marie Curie

country: France

institute: CNRS

summary: To identify RoxS targets and do the comparison with RoxS targets identified by pulsed SILAC experiment

overall_design: Comparative gene expression profiling analysis of RNA-seq data in Bacillus subtilis strain CCB1243 (∆roxS, amyE::pXsa) vs CCB1244 (∆roxS, amyE::pXsa-RoxS). Experiment was made in triplicate

first: Delphine

last: Allouche

first: Gergana

last: Kostova

first: Marion

last: Hamon

first: Christophe

last: Marchand

first: Mathias

last: Caron

first: Sihem

last: belhocine

first: Ninon

last: Christol

first: Violette

last: Charteau

first: Ciaran

last: Condon

first: Hugo

last: Varet

first: Saliha

last: Azebi

first: Jean

middle: Y

last: Coppée


title: Characterization of SigH, ComK1 and ComK2 regulons during competence development in Staphylococcus aureus

city: GIF SUR YVETTE

first: Nicolas

last: Mirouze

address: Avenue de la Terrasse

institute: Institute for the Integrative Biology of the Cell

summary: To investigate the central competence regulators (SigH, ComK1 and ComK2) regulons, wt and KO strains were grown to competence in CS2 medium. We then performed gene expression profiling analysis using data obtained from RNA-seq of these four strains (wt and 3 KOs) at one time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wt N315 strain (St29) and its KO derivative (deltasigH, St61; deltacomK1, St40 and deltacomK2, St41)

first: Shi

last: Y Feng

first: Yolande

last: Hauck


title: Transcriptomic profiling of 293T and A549 COVGT#5 reporter cell lines treated with COVGT#5 inducers and synergistic drug combinations.

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

department: Molecular Oncology

institute: Max Delbrück Center for Molecular Medicine

summary: 293T and A549 COVGT#5 reporter cell lines treated with COVGT#5 inducers IFN mix or 3p-hpRNA and synergistic drug combinations to identify co-regulated genes upon COVGT#5 modulation.

overall_design: 293T and A549 COVGT#5 reporter cells were induced with IFN mix (20ng/ml IFNa-2a, 20ng/ml IFNa-2b, 20ng/ml IFNb, 10ng/ml IL-28, 5ng/ml IFNg) or 3p-hpRNA (0.1µg/ml) followed by TOPi (30nM Topotecan, 100nM Etoposide) or JAKi (100nM Baricitinib, 300nM Tofacitinib) treatment, sorted by FACS based on mCherry (reporter gene) intensity (as indicated in sample name) and subjected to RNA-sequencing.

first: Ben

last: Jiang

first: Matthias

last: Schmitt

first: Yuliia

last: Dramaretska

first: Michela

last: Serresi


title: Induction of astrocytic Slc22a3 regulates sensory processing through histone serotonylation (RNA-Seq)

first: Debosmita

last: Sardar

summary:
To profile gene expression differences in astrocytes after chemogenetic neuronal activation in different mouse brain regions.
Furthermore, we also sought to profile gene expression differences between control and Slc22a3 conditional knockout astrocytes in the mouse olfactory bulb.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FACS purified astrocytes from mouse brain tissue

first: Benjamin

last: Deneen


title: Different roles of dural macrophages subpopulations to systemic viral infection

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

summary: To investigate different responses of dural macrophage subsets to systemic viral infection, we collected the dura mater from mice 12 h after systemic LCMV infection and macrophages were sorted

overall_design: Dural macrophages were FACS sorted and single-cell libraries were made

first: Gou

last: Koh

first: Kim

last: Chan

first: Myung


title: Differential Contributions of Distinct Free Radical Peroxidation Mechanisms to the Induction of Ferroptosis

city: Seattle

first: Libin

last: Xu

address: 1705 NE Pacific St

institute: University of Washington

summary: Ferroptosis is a form of regulated cell death driven by lipid peroxidation of polyunsaturated fatty acids (PUFAs). Endogenous PUFAs are nonconjugated PUFAs and their peroxidation proceeds via the hydrogen-atom transfer (HAT) mechanism. We previously reported that lipids with conjugated double bonds undergo lipid peroxidation mostly via a different mechanism, peroxyl radical addition (PRA), and were much more readily oxidizable than nonconjugated ones. In this study, we aim to elucidate the effects of various unsaturated lipids in sensitizing ferroptosis. We found that while some peroxidation-reactive lipids, such as 7-dehydrocholesterol, vitamins D3 and A, and coenzyme Q10, suppress ferroptosis, both nonconjugated and conjugated PUFAs enhanced cell death induced by RSL3, a ferroptosis inducer. Importantly, we showed that conjugated linolenic acid (CLA 18:3) could act as a ferroptosis inducer by itself and conjugated linoleic acid (CLA 18:2) was more potent in sensitizing cells to RSL3-induced cell death than any nonconjugated PUFAs. We next sought to elucidate the mechanism underlying the different ferroptosis-inducing potency of conjugated and nonconjugated PUFAs. Lipidomics revealed that conjugated and nonconjugated PUFAs are incorporated into distinct cellular lipid species. Furthermore, the different peroxidation mechanisms predict the formation of higher levels of reactive electrophilic aldehydes from conjugated PUFAs than nonconjugated PUFAs, which was confirmed by aldehyde-trapping and mass spectrometry. RNA sequencing revealed that protein processing in the endoplasmic reticulum and proteasome are among the most significantly upregulated pathways in cells treated with CLA 18:3, suggesting increased ER stress and activation of unfolded protein response. Significantly, using click chemistry, we observed increased protein adduction by oxidized lipids in cells treated with an alkynylated CLA 18:2 probe. These results suggest that protein damage by lipid electrophiles is a key step in ferroptosis.

overall_design: Four independent replicates of HT-1080 cells incubated overnight with vehicle (DMSO), 10 nM RSL3, 80 uM LA, 80 uM CLA 18:2, 10 nM RSL3 + 80 uM LA, 10 nM RSL3 + 80 uM CLA 18:2, or 5 uM CLA 18:3 and total RNA were sequenced.

first: Quynh

last: Do

first: Rutan

last: Zhang

first: Gavin

last: Hooper


title: Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer [ChIP-seq]

city: Clayton

first: Joe

last: Cursons

state: VIC

address: 19 Innovation Walk

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

summary: Epithelial-mesenchymal transition (EMT) is a reversible transcriptional program subverted by cancer cells to drive cancer progression. Transcription factor ZEB1 is a master regulator of EMT, driving disease recurrence in poor outcome triple negative breast cancer (TNBC).  Here, we silence ZEB1 in TNBC models by CRISPR-mediated epigenetic editing, resulting in nearly complete repression of ZEB1 in vivo, accompanied by long-lasting tumor inhibition. Integrated transcriptomic and epigenetic profiling identified a ZEB1-dependent gene-signature associated with transcriptional up-regulation, promoter DNA demethylation and enhanced chromatin accessibility in core cell adhesion loci, demonstrating epigenetic reprogramming towards a more epithelial state. Epigenetic shifts induced by ZEB1-silencing are enriched in a subset of human breast tumors, illuminating a clinically-relevant hybrid-like state. Thus, the synthetic epi-silencing of ZEB1 induces stable “lock-in” epigenetic reprogramming of mesenchymal tumors associated with a distinct epigenetic landscape. We outline approaches to stably reprogram EMT for targeting poor outcome breast cancers driven by oncogenic transcription factors.

overall_design: Native chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K9me3 and H3K4me3 in SUM159 cells with pLV-KRAB and a combination of 4 gRNAs targeting the promoter of ZEB1 or empty vector (control).

first: Waryah

last: Charlene

first: Blancafort

last: Pilar


title: Inducible disruption of Tet genes results in myeloid malignancy, readthrough transcription, and a heterochromatin-to-euchromatin switch

city: La Jolla

first: Isaac

last: López-Moyado

overall_design: Refer to individual Series


title: Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer [RNA-seq]

overall_design: RNA-sequencing (RNA-seq) data for SUM159 cells and MDA-MB-231 cells with the following conditions: wildtype cells, and cells with pLV-KRAB either with no targeting gRNAs (No targeting gRNA), a combination of 4 gRNAs targeting the promoter of ZEB1 (All 4 gRNAs), or a single gRNA targeting the promoter of ZEB1 (gRNA #4).


title: Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer


title: Circadian protein TIMELESS regulates synaptic plasticity and memory by modulating cAMP signaling

city: NEW YORK

first: Estibaliz

last: Barrio Alonso

state: NY

address: 455 MAIN STREET, 8A, 8A

institute: Weill Cornell Medicine

summary: Regulation of neurons by circadian clock genes is thought to contribute to the maintenance of neuronal functions that ultimately underlie animal behavior. However, the impact of circadian genes on cellular and molecular mechanisms that influnce synaptic plasticity and cognitive function remain to be identified. Here, we show that conditional deletion of the circadian gene Timeless in the adult forebrain leads to an impairment in working and fear memory in mice. These cognitive phenotypes were accompanied with LTP attenuation of hippocampal Schaffer-collateral synapses. We discovered TIMELESS protein acts as a transcriptional factor regulating phosphodiesterase 4B (PDE4B) expression. Through Pde4b transcription, TIMELESS negatively regulates cAMP signaling to modulate AMPA receptor GluA1 function and fine-tune synaptic plasticity. Our data provide insights into the neuron-specific function of mammalian TIMELESS by defining a mechanism that regulates synaptic plasticity and cognitive function.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for TIMELESS. Adult mice hippocampal samples (Sample 1, Sample 2 and Sample 3) were fixed and immonoprecipitated with anti-TIMELESS antibody (Abcam, ab72458). Input 1 is an hippocampal sample from adult mouse but without undergoing immunoprecipitation.

last: Barrio-Alonso

first: Pablo

last: Lituma

first: Michael

last: Notaras

first: Robert

last: Albero

first: Youcef

last: Bouchekioua

first: Natalie

last: Wayland

first: Isidora

last: Stankovic

first: Tanya

last: Jain

first: Sijia

last: Gao

first: Diany

middle: P

last: Calderon

middle: E

last: Castillo

first: Dilek

last: Colak


title: SCENIC+: identification of enhancers and gene regulatory networks using single-cell multiomics

first: Gert

last: Hulselmans

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

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus


title: Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer [methylation array]

last: Cursons

summary: Infinium MethylationEPIC (850K) BeadChip data for wildtype SUM159 cells (2 replicates), SUM159 cells transfected with plV-KRAB (dCas9 CRISPRi system; 3 replicates), and SUM159 cells transfected with dCas9-KRAB and 4 targeting gRNAs against the ZEB1 promoter (3 replicates)

overall_design: 8 samples. 2 Wildtype control. 3 vector control. 3 vector+targeting gRNAs (ZEB1 suppressive).

last: Charlene


title: Increased risk of mammary cancer recurrence in socially isolated rats is linked to upregulation of IL6/JAK/STAT3 and inhibition of oxidative phosphorylation signaling, activities blocked by the herbal mixture Jaeumganghwa-tang

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

summary: While multifactorial in origin, one of the most prevalent and impactful consequences of social isolation is an increase in cancer mortality. Using a preclinical model in Sprague Dawley rats, we found that social isolation increased the risk of mammary tumor recurrence after completion of antiestrogen therapy. The increased recurrence risk was associated with an upregulation of IL6/JAK/STAT3 signaling in the mammary glands and tumors and suppression of mitochondrial oxidative phosphorylation (OXPHOS) pathway. Also inhibited were genes involved in mitochondrial pyruvate transport and the conversion of pyruvate to acetyl CoA but lactate levels were not altered. In addition, social isolation increased the expression of receptor for advanced glycation end-products (RAGE), consistent with the impaired insulin sensitivity and weight gain linked to social isolation. All these changes are commonly associated with aging. In socially isolated animals  consumption of the anti-inflammatory 12 herb mixture Jaeumganghwa-tang (JGT) inhibited IL6/JAK/STAT3 signaling, upregulated OXPHOS signaling, suppressed expression of the RAGE ligands S100a8 and S100a9, and prevented the increased risk of mammary cancer recurrence. In summary, increased breast cancer mortality among socially isolated survivors may be most effectively prevented by focusing on the period following the completion of endocrine therapy using tools that inhibit IL6/JAK/STAT3 inflammatory cytokine signaling and reverse disrupted OXPHOS.

overall_design: Estrogen receptor positive (ER+) mammary tumors were induced in 50-day-old Sprague Dawley rats by administrating 10 mg of 7,12-dimethylbenz[a]anthracene (DMBA). When a rat developed a palpable mammary tumor, it was either socially isolated (SI) by housing a rat singly or it remained group-housed (GH). Tamoxifen (TAM) or TAM + Jaeumganghwa-tang (JGT) treatment started when the first mammary tumor per rat reached a size of ~11 mm in diameter. TAM was provided at the concentration of 340 ppm via AIN93G diet and JGT at the dose of 500 mg/kg via drinking water. The tumor responses were assessed and TAM treatment was stopped when a rat had exhibited a sustained complete or partial response for nine weeks. Tumor recurrences after TAM therapy were monitored during up to nine additional weeks

first: Fabia

last: de Oliveira Andrade

first: Leena

last: Hilakivi-Clarke


title: Kinetics of transcriptome during hepatic conversion [RNA-seq]

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: Cell plasticity endows differentiated cells with competence to be reprogrammed to other identities. While reprogramming factors-induced epigenetic changes have been characterized, intrinsic chromatin features underlying cell plasticity remain elusive. By characterizing kinetics of high-order chromatin structures during transdifferentiation from fibroblasts to hepatocytes, we identified contiguous compartment switchable regions (CSRs). Compartment B to A CSRs (B-to-A CSRs), enriched with hepatocyte genes and demarcated by loop anchors, displayed a chimeric status of pre-existing chromatin accessibility in repressive compartment in fibroblasts. Pre-existing accessibility allowed the occupancy of pioneer factor Foxa3 to B-to-A CSRs, triggering compartment switch, H3K27ac gain and H3K27me3 reduction, and hepatocyte gene activation. Moreover, chimeric chromatin status appeared to be related with fibroblasts reprogramming to neurons, cardiomyocytes and pluripotent stem cells. Together, pre-existing accessibility in compartment B defines a chimeric chromatin status that may constitute intrinsic attribute for cell plasticity.

overall_design: Examination of chromatin structures by Hi-C, chromatin status by ATAC-seq, H3K27ac and H3K27me3 ChIP-seq  and transcriptome by RNA-seq. Examination of protein binding of Foxa3, Gata4, Hnf1a and CTCF by CHIP-seq. Hi-C, ATAC-seq and RNA-seq were performed with replicates for each time point in our study.

first: Xiaolong

last: Ma

first: Xuan

last: Cao

first: Lingying

last: Zhu

first: Gang

last: Wei


title: Responding to ACL Injury and its Treatments: Comparative Gene Expression between Articular Cartilage and Synovium

city: Boston

first: Martha

last: Murray

state: Massachusetts

address: 300 Longwood Avenue

department: Department of Orthopedic Surgery

institute: Boston Children's Hospital

summary: The current study compared the transcriptomes of knee joint articular cartilage and synovium in a large animal model one year following posttraumatic osteoarthritis induction and multiple surgical treatment modalities.

overall_design: Thirty-six Yucatan minipigs underwent transection of the anterior cruciate ligament. Subjects were randomized to no further intervention, ligament reconstruction, or ligament repair augmented with an extracellular matrix (ECM) scaffold, followed by RNA-sequencing of the articular cartilage and synovium at 52 weeks after harvest. Twelve intact contralateral knees served as controls.

first: Jonah

middle: I

last: Donnenfield

first: Braden

last: Fleming


title: Kinetics of chromatin accessibility during hepatic conversion


title: Synthetic epigenetic reprogramming of mesenchymal to epithelial states using the CRISPR/dCas9 platform in triple negative breast cancer [ATAC-seq]

first: Joe

overall_design: Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) SUM159 cells with pLV-KRAB and a combination of 4 gRNAs targeting the promoter of ZEB1 or empty vector (control).

first: Waryah

first: Blancafort

last: Pilar


title: Control of bacterial phenotype and chromosomal gene expression by single plasmids of Lactococcus lactis IL594

status: Public on Apr 16 2023

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: Plasmid-free Lactococcus lactis IL1403 is one of the best-characterized representatives of lactic acid bacteria (LAB), intensively used in broad microbiology worldwide. Its parent strain, L. lactis IL594, contains seven plasmids (pIL1-pIL7) with resolved DNA sequences and an indicated role for overall plasmid load in enhancing host adaptive potential. To determine how individual plasmids manipulate the expression of phenotypes and chromosomal genes, we conducted global comparative phenotypic analyses combined with transcriptomic studies in plasmid-free L. lactis IL1403, multi-plasmid L. lactis IL594 and its single-plasmid derivatives. The presence of pIL2, pIL4 and pIL5 led to the most pronounced phenotypic differences in the metabolism of several carbon sources, including some β-glycosides and organic acids. The pIL5 plasmid also contributed to increased tolerance to some antimicrobial compounds and heavy metal ions, especially those in the toxic cation group. Comparative transcriptomics showed significant variation in the expression levels of up to 189 chromosomal genes due to the presence of single plasmids, and 435 unique chromosomal genes that are resultant of the activity of all plasmids, which may suggest that the observed phenotypic changes are not only the result of direct action of their own genes, but also originate from indirect actions through cross-talk between plasmids and the chromosome. The data obtained here indicate that plasmid maintenance leads to the development of important mechanisms of global gene regulation that provide changes in the central metabolic pathways and adaptive properties of L. lactis, and suggest the possibility of a similar phenomenon among other groups of bacteria.

overall_design: The comparison of transcriptomes of the Lactococcus lactis IL1403 strain containing no plasmids to strains, IL1618, IL1421, IL2661, IL1619, IL1420, IL1530 containing single plasmids, or IL1392 strain containing a subset of four plasmids pIL1, pIL2, pIL3, pIL5, or IL594 strain containing seven plasmids (pIL1 to pIL7). Bacteria cells were grown in the medium with cellobiose as carbon source to mid-exponential growth phase (OD600 0.6-0.7). For every sample, two biological replicates were performed; for each of them two technical replicates with dye swapping were done.

first: Katarzyna

last: Kosiorek

first: Anna

last: Koryszewska-Bagińska

first: Tamara

last: Aleksandrzak-Piekarczyk


title: Blood transcriptome analysis suggests an indirect molecular association of early life adversities (ELA) and adult social anxiety disorder (SAD) by immune-related signal transduction

city: Tuebingen

first: Susanne

last: Edelmann

address: Calwerstraße 14

institute: University of Tuebingen

summary: Social anxiety disorder (SAD) is a psychiatric disorder characterized by severe fear in social situations and avoidance of these. Multiple genetic as well as environmental factors contribute to the etiopathology of SAD. One of the main risk factors for SAD is stress, especially during early periods of life (early life adversity; ELA). ELA leads to structural and regulatory alterations contributing to disease vulnerability. This includes the dysregulation of the immune response. However, the molecular link between ELA and the risk for SAD in adulthood remain largely unclear. Evidence is emerging that long-lasting changes of gene expression patterns play an important role in the biological mechanisms linking ELA and SAD. Therefore, we conducted a transcriptome study of SAD and ELA performing RNA sequencing in peripheral blood samples. Analyzing differential gene expression between individuals suffering from SAD with high or low levels of ELA and healthy individuals with high or low levels of ELA, 13 significantly differentially expressed genes (DEGs) were identified with respect to SAD whilst no significant differences in expression were identified with respect to ELA. The most significantly expressed gene was MAPK3 (p=0.003) being upregulated in the SAD group compared to control individuals. In contrary, weighted gene co-expression network analyses (WGCNA) identified only modules significantly associated with ELA (p≤0.05), not with SAD. Furthermore, analyzing interaction networks of the genes from the ELA-associated modules and the SAD-related MAPK3) revealed complex interactions of those genes. Gene functional enrichment analyses indicate a role of signal transduction pathways as well as inflammatory responses supporting an involvement of the immune system in the association of ELA and SAD. In conclusion, we did not identify a direct molecular link between ELA and adult SAD by transcriptional changes. However, our data indicate an indirect association of ELA and SAD mediated by the interaction of genes involved in immune-related signal transduction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in peripheral blood samples of individuals suffering from SAD with and without a history of ELA and healthy controls with or without a history of ELA.

first: Ariane

last: Wiegand

first: Thomas

last: Hentrich

first: Sarah

last: Pasche

first: Julia

last: Schulze-Hentrich

first: Matthias

middle: H

last: Munk

first: Andreas

last: Fallgatter

first: Benjamin

last: Kreifelts

first: Vanessa

last: Nieratschker


title: Kinetics of chromatin accessibility during hepatic conversion [ATAC-seq]

first: Lijian

last: Hui

first: Xiaolong

last: Ma

first: Xuan

last: Cao

first: Lingying

last: Zhu

first: Gang

last: Wei


title: Cold plasma pretreatment reinforces the lignocellulose-derived aldehyde inhibitors tolerance and bioethanol fermentability for Zymomonas mobilis

status: Public on Apr 15 2023

city: Changzhou

first: Xia

last: Yi

address: Gehu Middle Road #21

institute: Changzhou University

summary:
To investigate the molecular mechanism of the increased bioethanol fermentability, we carried out RNA-Seq sequencing assays for the wild and mutant strain Z. mobilis after pretreated with cold plasma.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at one time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the wild Z. mobilis cells and its pretreated mutant Z. mobilis cells.


title: GDF15 reduces NAFLD through mechanisms that are independent of the suppression of food intake

status: Public on Apr 14 2023

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

institute: McMaster University

summary: The effects of recombinant human GDF15 and matched caloric restriction in pair-fed controls on obesity and NAFLD in mice fed western diet high in both fat and fructose and housed at thermoneutrality (TN, 29 °C).

overall_design: We then performed gene expression profiling analysis using data obtained from liver tissue of mice treated with vehicle, GDF15, or were pair-fed the same weight of food matched to GDF15 treatment group.

first: Gregory

middle: R

last: Steinberg


title: Alemtuzumab treatment exemplifies discordant immune effects of blood and cerebrospinal fluid in multiple sclerosis

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

institute: University Hospital Muenster

summary: We here analyzed CSF and blood from two relapsing-remitting multiple sclerosis (RRMS) patients early after peripheral leukocyte depletion with the anti-CD52 antibody alemtuzumab compared to untreated RRMS and control patients using single cell RNA-sequencing.

overall_design: Single-cell RNA sequencing data of paired cerebrospinal fluid and blood of two RRMS patients after alemtuzumab treatment.

first: Luisa

last: Müller-Miny

first: I-Na

last: Lu

first: Gerd

last: Meyer zu Hörste


title: GDF15 increases cAMP/PKA signaling in tibialis anterior (TA) muscle compared to pair-fed controls

summary: The effects of recombinant human GDF15 on Sympathetic Nervous System (SNS) signalling in skeletal muscle during the caloric restriction in mice.

overall_design: We then performed gene expression profiling analysis using data obtained from tibialis anterior (TA) muscle of mice treated with vehicle, GDF15, or were pair-fed the same weight of food matched to GDF15 treatment group.


title: mNET-seq on INTS11-degron cells

city: Beijing

first: Hua

address: 38 Xueyuan Rd

institute: Peking University

summary: We measured the the dwell time of existed paused RNAPII at the promoter by mammalian native elongating transcript sequencing (mNET-seq).

overall_design: In order to examine and monitor the effects of INTS11 on the temporal stability of promoter RNAPII, we performed the mammalian native elongating transcript sequencing (mNET-seq) on INTS11-FKBP dTAG degron cells.


title: Kinetics of chromatin accessibility during hepatic conversion [ChIP-seq]


title: Effect of 2 mM and 17 mM 7-day intermittent EtOH exposure on human excitatory neurons

city: New York

first: Paul

last: Slesinger

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary:
To investigate the impact of EtOH exposure on human excitatory neurons, we induced NGN2 expression in 4 neural progenitor cell lines.
We then conducted a 7-day intermittent EtOH exposure protocol starting at Day 21 post-induction using two concentrations: 2 mM (0.01 BAC equivalent) and 17 mM (0.08 BAC equivalent). RNA was harvested at Day 28 post induction.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for NGN2 neurons treated with 0 mM, 2mM, or 17mM EtOH

first: Iya

last: Prytkova

first: Yiyuan

last: Liu

first: Alison

last: Goate


title: Sexual dimorphism in the response to chronic circadian misalignment (ChIP-Seq)

city: Philadelphia

first: Antonijo

last: Mrčela

state: Pennsylvania

address: 3400 Civic Center Boulevard

department: Institute for Translational Medicine and Therapeutics

institute: University of Pennsylvania

summary: Longitudinal studies associate shiftwork with cardiometabolic disorders but do not establish causation nor elucidate mechanisms of disease. We developed a mouse model based on shiftwork schedules to study circadian misalignment in both sexes, where misaligned mice undergo an 8-hour phase advance every week for 15 weeks. Behavioral and transcriptional rhythmicity were preserved in female mice despite exposure to misalignment. Females were protected against the cardiometabolic impact of circadian disruption seen in males. The liver transcriptome and proteome revealed discordant pathway perturbations between the sexes. Tissue-level changes were accompanied by gut microbiome dysbiosis only in male mice. In the UK biobank, female shiftworkers showed stronger circadian rhythmicity in activity and a lower incidence of metabolic syndrome than males. Thus we show that female mice are resilient to chronic circadian misalignment, and that these differences are conserved in humans.

overall_design: Liver BMAL1-DNA interaction profiles of male control, male misaligned, female control and female misaligned mice taken at two time points, ZT0 and ZT12. One biological replicate was analyzed per timepoint per group.

first: Seán

last: Anderson

first: Hu

last: Meng

first: Thomas

middle: G

last: Brooks

first: Soon

last: Tang

first: Soumyashant

last: Nayak

first: Dimitra

last: Sarantopulou

last: Grant

first: Garret

middle: A

last: FitzGerald


title: Glucose partitioning in the bone marrow micro-environment in acute myeloid leukaemia [single-cell RNA-seq]

city: Guangzhou

first: Suqi

last: Deng

state: Guangdong

address: Huangpu Avenue, Tianhe District, Guangzhou, China

institute: Jinan University

summary: To identify the metabolic transcriptome landscape within leukaemic cells we performed scRNA-Seq on the sorted leukaemia cells (GFP+) cells from MLL-AF9 mice.

overall_design: MLL-AF9/GFP driven leukaemic cells were isolated by FACS-sorted GFP+ cells and analyzed using scRNAseq.

first: Hui

last: Zeng

first: Juan

last: Du


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [DOGMAseq_PT1]

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

summary: Large deletions in mitochondrial DNA (mtDNA) have been linked to a variety of clinical pathologies, including somatic emergence in congenital disorders such as Pearson Syndrome (MIM:557000), a mitochondrial disease characterized by sideroblastic anemia and exocrine pancreas dysfunction. Here, we develop a multi-omics approach to quantify mtDNA deletion heteroplasmy and cell state features in thousands of single cells. By profiling primary hematopoietic cells from three patients with Pearson Syndrome, we resolve the interdependence between pathogenic mtDNA heteroplasmy and cell lineage, including purifying selection against mtDNA deletions in effector-memory CD8 T-cell populations. We further observe widespread Pearson-specific transcriptomic changes in peripheral blood mononuclear cells. Additionally, single-cell analyses of in vivo and in vitro cultured bone marrow mononuclear cells reveal multi-faceted clonal dynamics and purifying selection in a patient with both Pearson Syndrome and Myelodysplastic Syndrome (MDS). Our results identify specific molecular perturbations underlying Pearson Syndrome and more generally provide a powerful framework to utilize multi-omics in the study of evolution in disease within single cells.

overall_design: Peripheral blood mononuclear cells were obtained from human patients and processed for single cell genomics

first: Leif

last: Ludwig


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [Tcell_scATAC_ASAP]

overall_design: Peripheral blood mononuclear cells were obtained from two human patients and cultured before processing for single-cell genomics.


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [NAMDC_scATAC]

overall_design: Peripheral blood mononuclear cells were obtained from three human patients with CPEO or KSS and processed for single cell genomics using a joint mtDNA/scATAC-seq workflow.


title: Regulatory role and mechanisms of lymphoid IKK1 in kidney ischemia-reperfusion injury

city: Hamburg

first: Ning

last: Song

state: Hamburg

address: Martinistrasse 52

institute: University Medical Center Hamburg-Eppendorf

summary: To investigate the mechanism of  CD4IKK1Δ mice are protected from kidney IRI,We performed RNA sequencing on sorted CD4+Tcells from CD4cre and CD4IKK1Δ mice 2 days after IRI.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD4+T cells from CD4cre, CD4IKK1Δ and CD4NIKΔmice.

first: Friedrich

last: Thaiss


title: Kinetics of chromatin structures during hepatic conversion [Hi-C]

first: Lijian

last: Hui

overall_design: Examination of chromatin structures by Hi-C, chromatin status by ATAC-seq, H3K27ac and H3K27me3 ChIP-seq  and transcriptome by RNA-seq. Examination of protein binding of Foxa3, Gata4, Hnf1a and CTCF by CHIP-seq. Hi-C, ATAC-seq and RNA-seq were performed with replicates for each time point in our study.

first: Xiaolong

last: Ma

first: Xuan

last: Cao

first: Lingying

last: Zhu

first: Gang

last: Wei


title: BAZ2A-RNA dependent association with TOP2A and KDM1A represses gene expression in prostate cancer

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

summary: BAZ2A represses rRNA genes (rDNA) that are transcribed by RNA polymerase I. In prostate cancer (PCa), BAZ2A function goes beyond this role because it represses genes frequently silenced in metastatic disease. However, the mechanisms of this BAZ2A-mediated repression remain elusive. Here, we show that BAZ2A represses genes through its RNA-binding TAM domain using mechanisms differing from rDNA silencing. Although the TAM domain mediates BAZ2A recruitment to rDNA, in PCa, this is not required for BAZ2A association with target genes. Instead, the BAZ2A-TAM domain in association with RNA mediates the interaction with topoisomerase 2A (TOP2A) and histone demethylase KDM1A, whose expression positively correlates with BAZ2A levels in localized and metastatic PCa. TOP2A and KDM1A pharmacological inhibition up-regulate BAZ2A-repressed genes that are regulated by inactive enhancers bound by BAZ2A, whereas rRNA genes are not affected. Our findings showed a novel RNA-based mechanism of gene regulation in PCa. Furthermore, we determined that RNA-mediated interactions between BAZ2A and TOP2A and KDM1A repress genes critical to PCa and may prove to be useful to stratify prostate cancer risk and treatment in patients.

overall_design: RNA seq in human PC3 cells

first: Marcin

last: Roganowicz

first: Dominik

last: Bär

first: Cristiana

last: Bersaglieri

first: Rossana

last: Aprigliano


title: Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets

city: Madison

first: Sushmita

last: Roy

state: Wisconsin

address: 330 N Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin-Madison

summary: Cell type-specific gene expression patterns are outputs of transcriptional gene regulatory networks (GRNs) that dynamically reconfigure to drive diverse cellular states. Single-cell transcriptomic technologies, such as single cell RNA-sequencing (scRNA-seq) and single cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq), can examine the transcriptional state at individual cell resolution, allowing the study of cellular heterogeneity and cell-type specific gene regulation in dynamic  processes such as cell fate specification. However, current approaches to infer cell type-specific gene regulatory networks from these datasets are limited in their ability to integrate scRNA-seq and scATACseq measurements and to model network dynamics on a cell lineage. To address this challenge, we have  developed single-cell Multi-Task Network Inference (scMTNI), a multi-task learning framework to infer the gene regulatory network for each cell type on a lineage from scRNA-seq and scATAC-seq data. Using simulated, published, and newly collected single cell omic datasets, we show that scMTNI is able to accurately infer gene regulatory networks and captures meaningful network dynamics that identify GRN components associated with cell type transitions. Application of our method to mouse cellular reprogramming identified key regulators associated with cell populations that reprogram versus those that are stalled. Taken together, scMTNI is a powerful framework to infer cell type-specific gene regulatory networks and their dynamics from scRNA-seq and scATAC-seq datasets.

overall_design: Analysis of single-cell ATAC-seq data from MEF reprogramming populations

first: Shilu

last: Zhang

first: Saptarshi

last: Pyne

first: Stefan

last: Pietrzak

first: Alireza

last: Siahpirani

first: Rupa

last: Sridharan


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [Invitro_scATAC]

first: Caleb

last: Lareau

overall_design: Bone marrow mononuclear cells were obtained from a human patient, in vitro differentiated and processed for single cell genomics

first: Leif

last: Ludwig


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [BMMNC_scATAC_ASAP]

overall_design: Bone marrow mononuclear cells were obtained from a human patient and processed for single cell genomics


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [PBMC_scRNA]


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [Invitro_scRNA]


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [PBMC_scATAC]


title: DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [DNA methylation]

city: Pohang

first: Ildoo

last: Hwang

state: Kyungbuk

address: 77 Cheongam-Ro, Hyoja-dong, Nam-gu,

department: Department of Life Sciences

institute: POSTECH

summary:
Background: Plants memorize previous pathogen attacks and are ‘primed’ to produce a faster and stronger defense response, which is critical for defense against pathogens. In plants, cytosines in transposons and gene bodies are reported to be frequently methylated. Demethylation of transposons can affect disease resistance by regulating the transcription of nearby genes during defense response, but the role of gene body methylation (GBM) in defense responses remains unclear.
Results: Here, we find that loss of the chromatin remodeler decrease in DNA methylation 1 (ddm1) synergistically enhances resistance to a biotrophic pathogen under mild chemical priming. DDM1 mediates gene body methylation at a subset of stress-responsive genes with distinct chromatin properties from conventional gene body methylated genes. Decreased gene body methylation in loss of ddm1 mutant is associated with hyperactivation of these gene body methylated genes. Knockout of glyoxysomal protein kinase 1 (gpk1), a hypomethylated gene in ddm1 loss of function mutant, impairs priming of defense response to pathogen infection in Arabidopsis. We also find that DDM1-mediated gene body methylation is prone to epigenetic variation among natural Arabidopsis populations, and GPK1 expression is hyperactivated in natural variants with demethylated GPK1.
Conclusions: Based on our collective results, we propose that DDM1-mediated GBM provides a possible regulatory axis for plants to modulate the inducibility of the immune response.

overall_design: Whole genome bisulfite DNA methylation profiling was performed for Col and ddm1 mutant plants under four conditions - no treatment (control), sub-optimal β-aminobutyric acid treatment (BA_sub), Pseudomonas syringae pathovar tomato DC3000 infection (DC), and BA_sub treatment followed by DC infection (BA_sub+DC).

first: Seungchul

last: Lee

first: Jaemyung

last: Choi

first: Jihwan

last: Park

first: Chang

last: Hong

first: Daeseok

first: Tae-Young

last: Roh

first: Daehee


title: Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [Celline_scATAC]

overall_design: Patient-derived fibroblast cell lines were in vitro cultured and used for single cell genomics library preparation.


title: Sexual dimorphism in the response to chronic circadian misalignment (RNA-Seq)

first: Antonijo

last: Mrčela

overall_design: Liver mRNA profiles of male control, male misaligned, female control and female misaligned mice taken at 6 time points. Three biological replicates were analyzed per timepoint per group.

first: Seán

middle: T

last: Anderson

first: Hu

last: Meng

first: Thomas

last: Brooks

first: Soon

last: Tang

first: Soumyashant

last: Nayak

first: Dimitra

last: Sarantopulou

first: Gregory

last: Grant

first: Garret

last: FitzGerald


title: DDM1-mediated gene body DNA methylation is associated with inducible activation of defense-related genes in Arabidopsis [expression]

first: Ildoo

overall_design:
Gene expression profiling was performed for Col and ddm1 mutant plants under four conditions.
- no treatment (control), sub-optimal b-aminobutyric acid treatment (BA_sub), Pseudomonas syringae pathovar tomato DC3000 infection (DC), and BA_sub treatment followed by DC infection (BA_sub+DC). Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.


title: Gene expression profile of a C. elegans Anchor cell invading through Basement Membrane

status: Public on Apr 13 2023

city: Durham

first: David

last: Sherwood

state: North Carolina

address: Science Drive

department: Biology

institute: Duke University

summary: Cell invasion through basement membrane is crucial for development and immune cell trafficking, and is misregulated in many human diseases, such as cancer.  Understanding the gene expression profile of invading cells is challening, because cell invasion events are often stochastic and rare. Thus, it has been difficult to isolate cells during the act of basement membrane invasion. Here, we have taken advantage of the stereotyped timing of anchor cell invasion in C. elegans, along with synchronized animal culturing, Fluorescence activated cell sorting (FACS), and RNA-Seq and identified the gene expression profile of an invasive cell at the time of basement membrane breaching.

overall_design: Comparing gene expression profiling analysis or RNA-seq data for C. elegans anchor cells and whole body cells.

first: Daniel

middle: S

last: Costa

first: Isabel

middle: W

last: Kenny-Ganzert

first: Qiuyi

last: Chi

first: Kieop

first: Laura

last: Kelley

first: Aastha

last: Garde

middle: Q

last: Matus

first: Junhyun

first: Shaul

last: Yogev

first: Bob

last: Goldstein

first: Theresa

middle: V

last: Gibney

first: Ariel

last: Pani


title: Glucose partitioning in the bone marrow micro-environment in acute myeloid leukaemia [bulk RNA-seq]

first: Suqi

last: Deng

summary: We used a positron emission tomography (PET) tracer 18F fluorodeoxyglucose ([18F]-FDG) and transcriptomic analysis to detect glucose uptake by cells in the bone marrow micro-environment with an MLL-AF9-induced mouse model. Leukaemic cells had the greatest glucose uptake. To determine whether glucose uptake is driven by intrinsic demand, we applied RNA-seq of sorted leukaemia cells (GFP+) and bone marrow micro-environment myeloid cells (GFP-CD11b+) from the MLL-AF9 transduced mouse model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MLL-AF9/GFP driven leukaemic cells (flow-sorted GFP+ cells) and non-leukaemic BMME myeloid cells (MACS-sorted CD45.2-CD11b+ cells).

first: Hui

last: Zeng

first: Juan

last: Du


title: G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nat Genet (2023). https://doi.org/10.1038/s41588-023-01437-4

city: Montpellier

first: Amal

last: Makrini

address: 1919 route de mende

institute: IGMM

summary: Metazoan promoters are highly enriched in secondary structure forming motifs, among which G-quadruplexes (G4s). We describe G4access, a novel approach to isolate and sequence G4s when associated to open chromatin, based on their resistance to Micrococcal nuclease. G4access is an antibody- and crosslink-independent procedure that allows for high enrichment of predicted G4s (PG4s) motifs, most of which can be confirmed in vitro. Using this technique in several human and mouse cell lines, we were able to show a cell-specific enrichment that both relates to apparent nucleosome depletion and transcription at promoters. G4access allows scoring for PG4 pattern variation linked to nucleosome positioning changes that occur following treatment with a G4 ligand. It also reveals an unexpected role of G4s in hybrid mouse ES cells in the context of imprinting control regions, in which we propose that they will hallmark allelic active loci. Finally, we extended our procedure to non-mammalian species showing less annotated G4s in their genome. We found a decreased but still substantial G4 enrichment and confirmed their association to open and transcriptionally active regions of the yeast genome. Overall, our study not only provides a novel tool for studying G4 forming sequences in the cellular context but also indicates their essential roles as promoter elements, in chromatin opening and nucleosome positioning.

sample_organism:
Saccharomyces cerevisiae
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: We developed G4access, a novel, efficient and Ab and crosslinking-independent method coupled to high-throughput sequencing, that enriches for G4 forming sequences associated to open chromatin in cells. Taking advantage of the sequence preference of the Micrococcal nuclease. G4access signals were then compared to RNA Polymerase II signals upon KM05283 and Tryptolid (Two transcription inhibitors) and Pyridostatin (a G4 ligand).

first: Encar

last: Garcia-Oliver

first: Cyril

last: Esnault

middle: Z

last: El Aabidine

first: Talha

last: Magat

first: Anne

last: Cucchiarini

last: Lleres

first: Lutz

last: Goerke

first: Yu

last: Luo

first: Daniela

last: Verga

first: Laurent

last: Lacroix

first: Robert

last: Feil

first: Salvatore

last: Spicuglia

first: Jean

middle: L

last: Mergny

middle: C

last: Andrau


title: Glucose partitioning in the bone marrow micro-environment in acute myeloid leukaemia

last: Deng

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of dendritic cells (DC) from the lung of neonatal (NEO) or adult (AD) mice

city: Birmingham

first: Aaron

last: Silva Sanchez

state: AL

address: 1825 University Boulevard

department: Medicine

institute: The University of Alabama at Birmingham

summary: Multiple mechanisms restrain inflammation in neonates. Here we identify a population of pulmonary dendritic cells (DCs) that appear in the lungs and lung−draining lymph nodes between birth and two weeks of age and express intermediate levels of CD103 (CD103int). CD103int DCs express XCR1, CD205, and require the transcription factor, Batf3, suggesting that they belong to the cDC1 lineage. They also constitutively express CCR7 and spontaneously migrate to the lung−draining lymph node, where they promote stromal cell maturation and lymph node expansion, independently of microbial exposure and Trif− or MyD88−dependent signaling. CD103int DCs are transcriptionally related to efferocytic and tolerogenic DCs as well as mature, regulatory DCs. CD103int DCs efficiently acquire apoptotic cells and become activated through Mertk signaling, which also impairs CD8+ T cell activation. The appearance of CD103int DCs coincides with a temporal wave of apoptosis in developing lungs and explains, in part, impaired pulmonary immunity in neonatal mice.

overall_design:
Sorted lung zbtb46+ YFP+ cells from neonatal (7 days old) and adult (8 weeks old) zbtb46-cre x rosa26-yfp mice. Two samples per group were compared. Each sample was prepared independently, pooling at least five mice per pool.
Barcode 1: Neo_1
Barcode 2: Neo_2
Barcode 3: AD_1
Barcode 4: AD_2

first: Mingyong

last: Liu


title: Sexual dimorphism in the response to chronic circadian misalignment

first: Antonijo

last: Mrčela


title: The Mediator complex regulates enhancer-promoter interactions [ChIP-seq]

city: Goettingen

first: Shyam

last: Ramasamy

address: Am Fassberg 11

department: Genome Organization and Regulation

institute: Max Planck Insitute for Multidisciplinary Sciences

summary: Enhancer-mediated gene activation generally requires physical proximity between enhancers and their target gene promoters. However, the molecular mechanisms by which interactions between enhancers and promoters are formed are not well understood. Here, we investigate the function of the Mediator complex in the regulation of enhancer-promoter interactions, by combining rapid protein depletion and high-resolution MNase-based chromosome conformation capture approaches. We show that depletion of Mediator leads to reduced enhancer-promoter interaction frequencies, which are associated with a strong decrease in gene expression. In addition, we find increased interactions between CTCF-binding sites upon Mediator depletion. These changes in chromatin architecture are associated with a re-distribution of the Cohesin complex on chromatin and a reduction in Cohesin occupancy specifically at enhancers. Our results indicate that enhancer-promoter interactions are dependent on an interplay between the Mediator and Cohesin complexes and provide new insights into the molecular mechanisms by which communication between enhancers and promoters is regulated.

overall_design: ChIP-seq. Details are described in the Methods section of the paper.

first: A

middle: M

last: Oudelaar


title: PRDM1 DNA-binding zinc finger domain is required for normal limb development and is disrupted in Split Hand/Foot Malformation

city: Aurora

first: Brittany

last: Truong

department: Craniofacial Development

institute: University of Colorado Denver Anschutz Medical Campus

summary: Split Hand/Foot Malformation (SHFM) is a rare limb abnormality with clefting of the fingers and/or toes. For many patients, the genetic etiology is unknown. Through whole exome and targeted sequencing, we detected three novel variants in a transcription factor, PRDM1 that arose de novo in families with SHFM or segregated with the phenotype. PRDM1 has been shown to be required for limb development; however, its role is not well understood, and it is unclear how the PRDM1 variants affect protein function. Using transient and stable overexpression rescue experiments in zebrafish, we show that the variants have reduced function compared to wildtype PRDM1 likely due to disruption of the proline/serine-rich and DNA-binding zinc finger domains. Through expression assays, RNA-seq, and CUT&RUN in isolated pectoral fin cells, we demonstrate that Prdm1a directly binds to and regulates genes required for limb induction, outgrowth, and anterior/posterior patterning, such as fgfr1a, dlx5a, dlx6a, and smo. Together, these results improve our understanding of the role of PRDM1 in the limb gene regulatory network and help predict the pathogenicity of PRDM1 variants in humans

overall_design:
RNA-seq: Comparative gene expression analysis from isolated pectoral fins of Tg(Mmu:Prx1-EGFP) wildtype and Tg(Mmu:Prx1-EGFP);prdm1am805/m805 mutant zebrafish embryos at 48 hours post fertilization (hpf). CUT&RUN: Cleavage Under Targets and Release Using Nuclease (CUT&RUN) for IgG, H3K27Ac, and Prdm1a in isolated pectoral fin cells of wildtype and prdm1am805/m805 zebrafish embryos at 24 hpf
contributor: University of Washington Center for Mendelian Genomics

first: Lomeli

last: Shull

first: Ezra

last: Lencer

first: Eric

last: Bend

first: Michael

last: Field

first: David

last: Everman

first: Charles

last: Schwartz

first: Heather

last: Flanagan-Steet

first: Kristin

middle: B

last: Artinger


title: The Mediator complex regulates enhancer-promoter interactions [ATAC-seq]

overall_design: ATAC-seq. Details are described in the Methods section of the paper.


title: The Mediator complex regulates enhancer-promoter interactions [Cut&Tag]

overall_design: Cut&Tag. Details are described in the Methods section of the paper. Experiments were performed for five replicates that were derived from three biologically independent samples.


title: DNA Methylome and 3D Chromatin Landscape of Cell Types Across the Mouse Brain [10A_190423]

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 117 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 117 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (10A).

first: Hanqing

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

first: Julia

middle: K

last: Osteen

first: Jordan

last: Altshul

first: Mia

last: Kenworthy

first: Rosa

last: Castanon

last: Nery

first: Peter

last: Berube

first: Huaming

last: Chen

last: Nunn

first: Jesse

last: Dixon

first: M

last: Behrens


title: The Mediator complex regulates enhancer-promoter interactions

first: Shyam

last: Ramasamy


title: H4K16ac activates retrotransposons and contributes to their cis regulatory function

city: London

first: Pradeepa

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

country: United Kingdom

institute: Queen Mary University of London


title: The Mediator complex regulates enhancer-promoter interactions [Capture C]

overall_design: Capture-C. Details are described in the Methods section of the paper.

first: A

last: Oudelaar


title: ATAC-seq of Notch signaling response in RTE cells

status: Public on Apr 12 2023

city: Toronto

first: Juan Carlos

last: Zuniga-Pflucker

address: 2075 Bayview Avenue

department: Immunology

institute: University of Toronto

summary: We report the gene expression profile of recent thymic emigrant (RTE) that are either responsive to Notch signals, or unresponsive to Notch signals during their maturation process. Notch responsiveness is controled by the expression of RBPJ, a key mediator of the Notch signaling pathway.

overall_design: Wild type mature T cells (WT) and RTE from RBPJind mice that were Notch responsive (ON) and Notch unresponsive (OFF) during maturation stage were FACS sorted.  These cells were sent for ATAC sequencing.

first: Sintia

last: Teichman

first: Helen

last: Wang

first: Christina

last: Lee

first: Mahmood

last: Mohtashami

first: Elisabeth

last: Foerster

first: Ashton

last: Trotman-Grant

first: Shawn

last: Winer

first: Hubert

last: Tsui

first: Dana

middle: J

last: Philpott

first: Juan

last: Zúñiga-Pflücker


title: The Mediator complex regulates enhancer-promoter interactions [Tiled-Micro-Capture-C]

overall_design: Tiled-Micro-Capture-C (Tiled-MCC). Details are described in the Methods section of the paper.


title: Dual gene activating and repressive functions of TET1 in germ layer lineage bifurcation distinguished by genomic context and dependence on 5-methylcytosine oxidation [RNAseq2]

city: Leuven

first: Bernard

middle: Klaas

last: van der Veer

state: Vlaams-Brabant

address: Herestraat 49 - box 804

department: Department of Development and Regeneration

institute: KU Leuven

summary: Gastrulation initiates when the epiblast differentiates into either definitive ectoderm or primitive streak. During the lineage bifurcation, the DNA dioxygenase TET1 plays dual roles in both transcriptional activation and repression, but how it exerts this bipartite control via 5-methylcytosine (5mC) oxidation-dependent and independent activities remains unclear. Here, we perform a monolayer differentiation of mouse embryonic stem cells (ESCs) into neuronal precursors to define at single-cell resolution how Tet1-/- cells undergo a lineage switch to primitive streak and subsequently form mesoderm and endoderm. We identify the Wnt repressor Tcf7l1 as a direct target of TET1 that controls a signaling cascade of Wnt/β-catenin upstream of Nodal. Disrupting the endogenous catalytic site of Tet1 in ESCs contributes to activation of Nodal and subsequently Wnt/β-catenin signaling, promoting tri-lineage differentiation into ectoderm, mesoderm and endoderm. Catalytically dead TET1 is sufficient in sustaining open neuroectoderm enhancers, by which gene expression is uncoupled from enhancer DNA demethylation, and indirectly keeping primitive streak enhancers inaccessible to Wnt regulators and effectors. DNA hypermethylation caused by TET1 catalytic dysfunction instead promotes precocious primitive streak gene activation when associated with CpG islands overlapping bivalent gene promotors. Moreover, hypermethylated regions amplify in numbers in the absence of TET1 through differentiation to affect genes associated with neurological functions. Our results reveal two-way safeguarding activities of TET1 separable by genomic features, where at CpG-poor distal enhancers TET1 maintains accessible chromatin permissive for neural fate independently of 5mC oxidation; at CpG-rich bivalent promoters it prevents premature gene activation inducing alternative fates by harnessing 5mC oxidation in Polycomb gene repression.

overall_design: WT, Tet1 MUT and Tet1 KO mESCs were converted to EpiLCs.


title: MAPT expression is regulated by long-range interactions with cis-regulatory elements [ChIP-seq]

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

summary: Tau is encoded by MAPT and abnormal aggregates of tau are a hallmark of a group of neurodegenerative diseases called tauopathies. MAPT is lowly expressed in neural progenitor cells (NPCs), but it is more highly expressed in oligodendrocytes, astrocytes, and neurons that derive from NPCs. This expression switch at differentiation suggests that MAPT expression is controlled by transcription factors and cis-regulatory elements specific to these differentiated cell types, including neurons.

overall_design: We performed HiC and three-dimensional chromatin conformation capture (Capture-C), single-nucleus multiomics (RNA-seq and ATAC-seq), bulk ATAC-seq, and ChIP-seq for H3K27Ac and CTCF in neurons differentiated from human iPSC cultures. From these methods, we nominated candidate cis-regulatory elements (cCREs) for MAPT in human NPCs, NPCs differentiated to neurons, and pure inhibitory or excitatory neuron cultures. We then functionally assessed nominated regions using luciferase assays and CRISPR dCas9-KRAB inhibition experiments to assess the effect of nominated regions on MAPT expression.

first: Brianne

last: Rogers

first: Ashlyn

last: Anderson

first: J

middle: N