title: The Ewing sarcoma cell line atlas (ESCLA) - The relevance of the transcription factors GATA2 and E2F2 in a Ewing sarcoma cell line model

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

summary:
Cell lines have been essential for major discoveries in cancer including Ewing sarcoma (EwS). EwS is a highly aggressive pediatric bone or soft-tissue cancer characterized by oncogenic EWSR1-ETS fusion transcription factors converting polymorphic GGAA-microsatellites (mSats) into neo-enhancers. However, further detailed mechanistic evaluation of gene regulation in EwS have been hindered by the limited number of well-characterized cell line models. Here, we present the Ewing Sarcoma Cell Line Atlas (ESCLA) comprising 18 EwS cell lines with inducible EWSR1-ETS knockdown that were profiled by whole-genome-sequencing, DNA methylation arrays, gene expression and splicing arrays, mass spectrometry, and ChIP-seq for EWSR1-ETS and histone marks.
Systematic analysis of these multi-dimensional data identified GATA2 and E2F2 as EWSR1-ETS-driven putative co-regulatory transcription factors. To evaluate the relevance of these transcrition factors, RNA interference in a Ewing sarcoma cell line was employed with subsequent Affymetrix Exon array profiling. The expression data were analysed in synopsis with the effects of EWSR1-FLI1 in the same cell line.

overall_design: The Ewing sarcoma cell line A673 was transfected with 30 nM siPools targeting E2F2 or GATA2, or with 30nM of a non-targeting control siRNA pool (all siTOOLs Biotech, Planegg, Germany) using Opti-MEM (Thermo Fisher) and lipofectamine RNAiMax reagent according to the manufacturer’s recommendations (Thermo Fisher). 48 h after the first transfection, cells were re-transfected. 96 h after the first transfection, total RNA was isolated from three replicates, each. The transcriptome was profiled on Affymetrix Clariom D Human microarrays. Raw data were processed using the Transcriptome Analysis Console (version 4.0) by ThermoFisher, the SST-RMA analysis algorithm and the manufacturer's array description file (version 2).

first: Martin

last: Orth

first: Ohmura

last: Shunya

middle: P

last: Grünewald


title: Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage

status: Public on Aug 22 2022

city: Cold Spring Harbor

first: Gayan

middle: Indhu

last: Balasooriya

address: 1 Bungtown Road

country: USA

institute: Cold Spring Harbor Laboratory

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effect of obesity on mouse atrial gene expression.

status: Public on Aug 18 2022

city: Boston

first: Aneesh

last: Bapat

state: Massachusetts

address: 55 Fruit Street

department: CVRC

institute: Massachusetts General Hospital

overall_design: We performed RNA sequencing of atrial tissue from mice fed a HFD for 10 weeks, as compared to age-matched control mice fed a contol chow.

first: Ashish

last: Yeri

first: David

last: Milan

first: Saumya

last: Das


title: High throughput quantitative whole transcriptome analysis of E18.5 mouse distal lung mesenchyme and endothelium

status: Public on Aug 17 2022

city: ROCHESTER

first: Douglas

middle: Glenn

last: Brownfield

state: Minnesota

address: 200 1ST ST SW

department: PCCM

institute: Mayo Clinic

summary: We used microfluidic single cell RNA-seq on 42 individual mouse lung mesenchymal and 69 endothelial cells at E18.5 to measure the transcriptional state. We were able to classify these cells into distinct populations as well as map their signaling interactions with the distal lung epithelium. In this manner, single cell RNA-seq can be used to unbiasedly determine the signals the dictate construction and maintenance of the alveolus.

sample_organism:
Mus musculus
synthetic construct

platform_organism:
Mus musculus
synthetic construct

overall_design: 42 single-cell mesenchymal and 69 endothelial transcriptomes from E18.5 mouse lung were analyzed in total and NTC and three 200-cell bulk control sample; All single cell and control samples contain 92 external RNA spike-ins; In a single E18.5 timepoint, 111 transcriptomes were isolated; In addition,three 200-cell bulk control sample was prepared for E18.5;All single cell samples were processed on the microfluidic platform, 200-cell-bulk control sample was processed in microliter volumes in PCR tubes.

middle: G


title: RNAseq study of JDM patients and controls

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

summary: Highly enriched N cells, T cells, and B cells from PBMCs of JDM patients and controls

overall_design: Groups of four Highly enriched N cells, T cells, and B cells and controls were compared

first: Anthony

last: French


title: Effect of Tup1, Xbp1, Isw2, and Sds3 on transcription in diauxic shift and stationary phase.

city: Eugene

first: Laura

middle: Emily

last: McKnight

state: Oregon

address: 1318 Franklin Blvd Room 273 Onyx Bridge

department: Institute of Molecular Biology

institute: University of Oregon

summary: To investigate the effect of Tup1, Xbp1, Isw2, and Sds3 on transcription we generated knockout strains and measured their transcript abundance compared to wild type during diauxic shift and stationary phase.

overall_design: Cells were grown in 25 mL YPD at 30 °C until they reached diauxic shift or stationary phase.  We then compared transcript abundance between wild type cells and kockouts.

first: Bailey

last: Thomas

first: McKnight

last: Laura


title: Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage (scRNA-Seq)

summary: We reported the allele-specific single cell RNA sequencing in highly morphogenic (C57Bl6J-maternal x CASTEiJ-paternal) male F1 mouse embryonic stem cells (mESC) and in vitro mESC derived six cardiac lineage cell types. We demonstrated distinctive gene regulation based on the parental origin of the alleles. We showed that deterministic and stochastic monoalleleic gene classes are distinctive in regulation and are involved in unique processes. In this study we highlighted the importance of parental origin-specific gene expression in development, homeostasis and disease.

overall_design: Examination of allele-specific gene expression in cardiac cell lineage.

middle: I

middle: L

last: Spector


title: Epigenetic reprogramming of Kaposi’s sarcoma-associated herpesvirus during hypoxic reactivation

status: Public on Aug 15 2022

city: Philadelphia

first: Erle

middle: S

last: Robertson

state: Pennsylvania

address: Johnson Pavilion, 3610 Hamilton Walk

department: Otorhinolaryngology

institute: University of Pennsylvania

summary: Chromatin Immuno-precipitaion sequencing was performed using H3-Ac, H3K4Me3, H3K9Me3, H3K27Me3, LANA, RTA and DNA Polymerase 1 alpha antibodies to investigate its enrichment on Kaposi's sarcoma associated herpesvirus (KSHV) genome in BC3 cells under normoxic or hypoxic conditions

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for H3-Ac, H3K4Me3, H3K9Me3, H3K27Me3, LANA, RTA and DNA Polymerase 1 alpha in BC3 cells.

first: Rajnish

last: Kumar Singh


title: Tup1 binding during log phase, diauxic shift, and stationary phase.

summary: To determine where Tup1 binds to chromatin during log phase, diauxic shift and stationary phase, we performed ChIP-seq.

overall_design: Myc epitope tagged Tup1 yeast strains were used to determine where Tup1 binds to chromatin during log, diauxic shift, and stationary phase.


title: Long non-coding RNA ncRuPAR regulates gastric cancer cell proliferation and apoptosis via phosphoinositide 3-kinase/protein kinase B signaling

status: Public on Aug 19 2022

city: Shanghai

first: Jiahui

last: Yu

address: No.800, Xiangyin Road, Yangpu District, Shanghai

country: China

institute: Faculty of Traditional Chinese Medicine, Naval Medical University, Shanghai, China

summary:
Objective: To determine the effect and mechanism of the long non-coding RNA (lncRNA) ncRuPAR (non-protein coding RNA, upstream of coagulation factor II thrombin receptor [F2R]/protease-activated receptor-1 [PAR-1]) in human gastric cancer.  Methods: HGC-27-ncRuPAR overexpression and MGC-803-ncRuPAR-RNAi knockdown gastric cancer cell lines were established. We assessed the effect of ncRuPAR on cell proliferation, apoptosis, migration, and invasion using Cell Counting Kit 8, flow cytometry, scratch and transwell assays, respectively. Differentially expressed genes in HGC-27-ncRuPAR overexpression and HGC-27-empty vector cell lines were identified using Affymetrix GeneChip microarray analysis. Ingenuity Pathway Analysis (IPA) of the microarray results was subsequently conducted to identify ncRuPAR-enriched pathways, followed by validation using real time-quantitative PCR (RT-qPCR). As one of the top enriched pathways, phosphoinositide 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway was further examined by western blotting to determine its role in ncRuPAR-mediated regulation of gastric cancer pathogenesis.
Results: ncRuPAR inhibited human gastric cancer cell proliferation and induced G1/S phase arrest and apoptosis, but did not affect migration or invasion in vitro. Overexpression of ncRuPAR in vitro was found to inhibit its known target PAR-1, as well as PI3K/Akt signaling. The downstream targets of PI3K/Akt, cyclin D1 was downregulated, but there was no change in expression level of B-cell lymphoma 2 (Bcl-2).  Conclusions: We showed that lncRNA-ncRuPAR  could inhibit tumor cell proliferation and promote apoptosis of human gastric cancer cells, potentially by inhibiting PAR-1, PI3K/Akt signaling, and cyclin D1. The results suggest a potential role for lncRNAs as key regulatory hubs in GC progression.

first: Xiaoqiang

last: Yue


title: Effects of HCV JFH-1 on gene expression during 48 hour infection of Primary Human Hepatocytes

city: Miami

first: Emmanuel

state: Florida

address: 1550 NW 10th Ave Rm 119, Papanicalaou Bldg

department: Department of Pathology

institute: University of Miami Miller School of Medicine

summary: To investigate the underlying effects of HCV JFH-1 on cellular innate immune response, primary human hepatocytes were infected for 48 hours and analyzed for whole-cell total RNA. Gene expression profiling analysis was subsequently performed using data obtained from Illumina NextSeq 2500 bulk RNA-sequencing of 4 different cell populations.

overall_design: Primary human hepatocytes obtained and plated from patient liver resections were either uninfected or infected with Hepatitis C Virus JFH-1 MOI = 1 in duplicate.

first: Jasmine

last: Edwards

first: Stephanie

last: Delablat

first: Alejandro

middle: D

last: Badilla

first: Robert

middle: A

last: Burgess

first: Dennis

last: McDuffie


title: Allele-specific differential regulation of monoallelically expressed autosomal genes in the cardiac lineage (Bulk RNA-Seq)

first: Gayan

last: Balasooriya

summary: We reported the allele-specific bulkl RNA sequencing in highly morphogenic (C57Bl6J-maternal x CASTEiJ-paternal) male F1 mouse embryonic stem cells (mESC) and in vitro mESC derived six cardiac lineage cell types. We demonstrated distinctive gene regulation based on the parental origin of the alleles. We showed that deterministic and stochastic monoalleleic gene classes are distinctive in regulation and are involved in unique processes. In this study we highlighted the importance of parental origin-specific gene expression in development, homeostasis and disease.

first: David


title: ALKBH8 suppresses oxidative stress and ameliorates inflammation via blocking NFκB/NLRP3 axis in Sepsis

city: Xi'an

first: Zhengliang

last: Zhang

address: No. 157, Xiwu Road, Xincheng District

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

summary:
The molecular mechanisms underlying sepsis pathogenesis and its regulation are incompletely understood. Here we demonstrated that human AlkB homologue, ALKBH8, plays a critical role in sepsis.
we demonstrated that inhibition of Reactive oxygen species (ROS) production by using N-acetylcysteine (NAC) antagonized the effect of ALKBH8 knockdown on inflammation response and NFκB/NLRP3 signaling activation in THP-1 cells.

overall_design: A total of 10 patients with acute sepsis and 10 health donors were recruited to take the next-generation RNA-seq analysis and total RNA was purified from blood samples from sepsis patients (n = 5) and healthy control subjects (n = 5).

first: Ni

last: Yang

first: Li

first: Junhua

last: Lv

first: Zequn

last: Niu

first: Jie

last: Liu

first: Ping

last: Li


title: Tup1, Xbp1, Isw2, and Sds3

first: Laura

last: McKnight


title: Effect of Tup1 and Isw2 on nucleosome positions in stationary phase.

summary: We used MNase-seq to measure nucleosome positions in wild type, tup1 knockouts, and isw2 knockouts.

overall_design: We crosslinked cells after 3 days or growth in YPD at 30 °C.

first: Bailey

last: Thomas

first: McKnight

last: Laura


title: Effect of Tup1, Xbp1, Isw2, and Sds3 on H3K23ac in stationary phase.

summary: To investigate the effect of Tup1, Xbp1, Isw2, and Sds3 on H3K23acc we generated knockout strains and measured H3K23ac levels during stationary phase.

overall_design: Cells were grown in 25 mL YPD at 30 °C until they reached stationary phase.  We then compared H3K23ac levels between wild type cells and kockouts.


title: Xbp1 binding during log phase and stationary phase.

summary: To determine where Xbp1 binds to chromatin during log phase and stationary phase, we performed ChIP-seq.

overall_design: flag epitope tagged Xbp1 yeast strains were used to determine where Xbp1 binds to chromatin during log phase and stationary phase.


title: A cohesin traffic pattern genetically linked to gene regulation [RNA-Seq]

city: Worcester

first: Anne-Laure

last: Valton

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

summary: Cohesin-mediated loop extrusion folds interphase chromosomes at the ten to hundreds kilobases scale. This process produces structural features such as loops and topologically associating domains. We identify three types of cis-elements that define the chromatin folding landscape generated by loop extrusion. First, CTCF sites form boundaries by stalling extruding cohesin, as shown before. Second, transcription termination sites form boundaries by acting as cohesin unloading sites. RNA polymerase II contributes to boundary formation at transcription termination sites. Third, transcription start sites form boundaries that are mostly independent of cohesin, but are sites where cohesin can pause. Together with cohesin loading at enhancers, and possibly other cis-elements, these loci create a dynamic pattern of cohesin traffic along the genome that guides enhancer-promoter interactions. Disturbing this traffic pattern, by removing CTCF barriers, makes cells sensitive to deletion of genes involved in transcription initiation, such as the SAGA and TFIID complexes, and RNA processing such DEAD-Box RNA helicases. In the absence of CTCF, several of these factors fail to be efficiently recruited to active promoters. We propose that the complex pattern of cohesin movement along chromatin contributes to appropriate promoter-enhancer interactions and localization of transcription and RNA processing factors to active genes.

overall_design: We engineered a HAP1-derived human cell line in which CTCF or RNApolII (RPB1) could efficiently be removed using an auxin-inducible degron system. We depleted the DDX55 and TAF5L proteins in HAP1-CTCFdegron-TIR1 cells in two ways: siRNA and knock-outs. We performed Hi-C on control cells, cells depleted for CTCF or RPB1 or DDX55 or TAF5L or combinations of CTCF depletions with DDX55 or TAF5L depletion.

first: Sergey

middle: V

last: Venev

first: Barbara

last: Mair

first: Eraj

last: Khokhar

first: Amy

middle: H

last: Tong

first: Matej

last: Usaj

first: Katherine

last: Chan

first: Athma

last: Pai

first: Jason

last: Moffat

first: Job

last: Dekker


title: A cohesin traffic pattern genetically linked to gene regulation [ChIP-Seq]

overall_design: We engineered a HAP1-derived human cell line in which CTCF could efficiently be removed using an auxin-inducible degron system. We performed ChIP-seq on this CTCF degron in presence and absence of CTCF (non-treated and auxin treated) using CTCF, RAD21, DDX55 and TAF5L antibodies.


title: microRNA cerebrospinal fluid profile during the early brain injury period as a biomarker in subarachnoid hemorrhage patients

status: Public on Aug 13 2022

city: BARCELONA

first: Leire

last: Pedrosa

state: Barcelona

address: Carrer del Villarroel 170

country: Spain

institute: IDIBAPS

summary: Delayed cerebral ischemia (DCI) is a dreadful complication present in up to 30% of patients with spontaneous subarachnoid hemorrhage (SAH). Indeed, DCI is one of the main causes of long-term disability in SAH, yet its prediction and prevention are troublesome in poor-grade SAH cases. In this prospective study, we explored the potential role of micro ribonucleic acid (microRNA, abbreviated miRNAs), – small non-coding RNAs involved in clue gene regulation at the post-transcriptional level – as biomarkers of neurological outcomes in SAH patients. We analyzed the expression of several miRNAs present in the cerebrospinal fluid (CSF) of SAH patients during the early stage of the disease (third-day post-hemorrhage). NanoString Technologies were used for the characterization of the CSF samples. We found an overexpression of miRNAs in the acute stage of 57 SAH in comparison with 10 non-SAH controls. Moreover, a differential expression of specific miRNAs was detected according to the severity of clinical onset, but also regarding the development of DCI and the midterm functional outcomes. These observations reinforce the potential utility of miRNAs as prognostic and diagnostic biomarkers in SAH patients. In addition, the identification of specific miRNAs related to SAH evolution might provide insights into their regulatory functions of pathophysiological pathways, such as the TGF-β inflammatory pathway and blood-brain barrier disruption

overall_design: We have studied the miRNA expression of CSF samples from the third day of hemorraghe onset of SAH patients and CSF samples from healthy patients.

first: Jhon

last: Hoyos

first: Luis

last: Reyes

last: Llull

first: Daniel

last: Santana

first: Nicolás

last: deRiva

first: Ricard

last: Mellado

first: Xavier

last: Sala

first: Ana

last: Rodríguez-Hernández

first: Joaquim

last: Enseñat

first: Sergio

last: Amaro

first: Ramon

last: Torné


title: A cohesin traffic pattern genetically linked to gene regulation [Hi-C]

first: Anne-Laure

last: Valton

first: Sergey

last: Venev

first: Barbara

last: Mair

first: Eraj

last: Khokhar

first: Amy

last: Tong

last: Usaj


title: devCellPy: A machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data

status: Public on Aug 14 2022

city: Stanford

first: Francisco

middle: Xavier

last: Galdos

state: CA

address: 265 Campus Dr.

department: Cardiovascular Institute

institute: Stanford University

summary: A major informatic challenge in single cell RNA-sequencing analysis is the precise annotation of datasets where cells exhibit complex multilayered identities or transitory states. Here, we present devCellPy a highly accurate and precise machine learning-enabled tool that enables automated prediction of cell types across complex annotation hierarchies. To demonstrate the power of devCellPy, we construct a murine cardiac developmental atlas from published datasets encompassing 104,199 cells from E6.5-E16.5 and train devCellPy to generate a cardiac prediction algorithm. Using this algorithm, we observe a high prediction accuracy (>90%) across multiple layers of annotation and across de novo murine developmental data. Furthermore, we conduct a cross-species prediction of cardiomyocyte subtypes from in vitro-derived human induced pluripotent stem cells and unexpectedly uncover a predominance of left ventricular (LV) identity that we confirmed by an LV-specific TBX5 lineage tracing system. Together, our results show devCellPy to be a powerful tool for automated cell prediction across complex cellular hierarchies, species, and experimental systems.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Development, testing, and application of machine learning algorithm for the automated prediction of developmental cell types in multilayered scRNA-seq datasets.

middle: X

first: Sidra

last: Xu

first: Sean

middle: M

last: Wu


title: Checkpoint blockade-induced dermatitis and colitis are dominated by tissue resident memory T cells and  Th1/Tc1 cytokines

status: Public on Aug 08 2022

city: Chicago

first: Thomas

last: Gajewski

state: IL

address: 929 E 57th St

institute: University of Chicago

summary:
Immune checkpoint blockade (ICB) is therapeutically successful in multiple cancer types. However, immune-related adverse events (irAE) frequently occur and can sometimes be life-threatening.
It is critical to understand the immunologic mechanisms of irAEs with the goal of finding novel treatment targets. Therefore, we studied tissues from irAE dermatitis cases using multiparameter immunofluorescence (IF), spatial transcriptomics,
and RNA in situ hybridization. Skin psoriasis cases were studied as a comparison, as a known Th17-driven disease, and colitis was investigated as a comparison. IF analysis revealed that CD4+ and CD8+ tissue resident memory T (TRM) cells
were preferentially expanded in the inflamed portion of skin in cutaneous irAEs compared to healthy skin controls. Spatial transcriptomics allowed focusing attention on areas containing TRM cells to discern their functional phenotype,
and revealed expression of Th1-associated genes in irAE, compared to Th17-asociated genes in psoriasis. Expression of a range of inhibitory checkpoint molecules was observed, including PD-1, CTLA-4, LAG-3, and TIGIT.
RNA in situ hybridization (RISH) technology combined with IF confirmed expression of IFN-γ, CXCL9, CXCL10, and TNF-α in additional irAE dermatitis cases and allowed us to identify production of IFN-γ within TRM cells specifically. The Th1-skewed phenotype was confirmed in irAE colitis cases compared to healthy colon.

overall_design: spatial transcriptomics: skin irAE vs. Psoriasis, colon irAE vs. healthy colon

first: Robin

last: Reschke

middle: F

first: Jovian

last: Yu

first: Sherin

middle: J

last: Rouhani

last: Olson

first: Yuanyuan

last: Zha

first: Jason

middle: W

last: Shapiro


title: Atoh1 is repurposed from neuronal to hair cell determinant by Gfi1 acting as a coactivator without redistribution of its genomic binding sites

status: Public on Aug 10 2022

city: Edinburgh

first: Aida

last: Santos da Costa

state: Edinburgh

address: Old College, South Bridge

country: United Kingdom

institute: University of Edinburgh

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

overall_design: Refer to individual Series


title: Effects of ein2-1 mutation on the miRNA expression during callus formation after submergence

status: Public on Aug 06 2022

city: Daejeon

first: Hyo-Jun

last: Lee

address: Gwahak-ro

department: Plant Systems Engineering Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

type: Non-coding RNA profiling by high throughput sequencing

summary: Col-0 and ein2-1 seedlings were submerged for 1 hour and then leaf explants was incubated on CIM for 7 days. The upper half of the explants were harvested for the small RNA sequencing.

overall_design: Three biological replicates for Col-0 and ein2-1 samples were analyzed. Control: Col-0

first: Seung

last: Shin

first: Su-Jin

last: Park

first: Ji-Sun

first: Ki-Beom

last: Moon

first: Hyun-Soon

last: Kim

first: Jae

last: Jeon

first: Hye

last: Cho


title: Gene expression profile at single cell level of FACS sorted CD8+ T cells from subcutaneous MC38 tumors from WT and Susd2-/-  mice

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

institute: The Ohio State University Wexner Medical Center

summary: Tumor-infiltrating CD8+ T cells are phenotypically heterogeneous with varying degrees of functional defects. We used single cell RNA sequencing (scRNA-seq) to analyze their sex differences.

overall_design: Tumor-infiltrating CD8+ T cells in  WT and Susd2-/-   mice were isolated by Fluorescence-Activated Cell Sorting (FACS) from MC38 s.c. tumors on Day 18 post inoculation according to their Cd8a, Trbc1, and Trbc2 expression and analyzed using scRNA-seq

first: Bao

last: Zhao

first: Haitao

last: Wen


title: Analyses of the individual and combinatorial transcriptional effects mediated by Atoh1, Pou4f3 and Gfi1 overexpression during embryoid body differentiation in vitro

summary: To gain new insights into the genetic networks regulating hair cell development, we developed a new transcriptional programming strategy to promote in vitro hair cell differentiation, starting from mouse embryonic stem cells (mESCs). In vivo, Atoh1 is the only transcription factor (TF) known to be necessary and sufficient for HC differentiation, but in vitro its overexpression induces neuronal rather than hair cell differentiation. We discovered that Atoh1 expression combined with two other TFs (Pou4f3, Gfi1) resulted in efficient hair cell generation. This work offers a new paradigm to understand the molecular mechanisms governing transcription factor specificity. For example, how do Pou4f3-Gfi1 modulate Atoh1 activity to orchestrate a HC differentiation program? To address this question, we have engineered several mESCs lines containing Atoh1, Gfi1 and/or Pou4f3 in a doxycycline-inducible locus to allow a controllable overexpression of every combination of these 3 transcriptional factors either using a polycistronic approach (mESCs lines: iG+A, iG+P, iP+A and iGPA) or by promoting their individual overexpression (mESCs lines: iAtoh1, iGfi1 and iPou4f3). These findings highlight the diversity of mechanisms by which one TF can redirect the activity of another to enable combinatorial control of cell identity.

overall_design:
7 different doxycycline-inducible mESCs lines containing every combination of Atoh1, Gfi1 and Pou4f3 were analysed at day 6 of embryoid body differentiation. Doxycycline-inducible mESCs lines were labelled using the following criteria: 1) iAtoh1- Atoh1 overexpression only; 2) iGfi1- Gfi1 overexpression only; 3) iPou4f3- Pou4f3 overexpression only; 4) iG+A- Gfi1 and Atoh1 combined overexpression; 5) iG+P- Gfi1 and Pou4f3 combined overexpression; 6) iP+A- Pou4f3 and Atoh1 combined overexpression; 7) iGPA- Gfi1, Pou4f3 and Atoh1 combined overexpression.
In order to promote overexpression of these TFs, 2 µg/ml of doxycycline was added to all doxycycline-inducible mESCs lines at day 4 of embryoid body differentiation and maintained until day 6. In parallel, a control group was generated by not adding doxycycline to the culture media but subjecting embryoid bodies to the same differentiation conditions. Please note that doxycycline treatment and control groups are indicated in Sample titles (e.g. *Dox* and *Ctrl*)
For each doxycycline-inducible mESCs lines, 2 independent biological replicates were performed using different clones for the same mESCs line and these are indicated in Sample titles (e.g. *Rep1 and *Rep2). In summary, a total of 28 samples comprising of 7 different doxycycline-inducible mESCs lines, 2 experimental groups (control and doxycycline treatment) and 2 independent biological replicates were analysed. All samples are present in 4 lanes of sequencing, reads from which were demultiplexed and provided here.

last: Costa

first: Andrew

last: Jarman

first: Sally

last: Lowell


title: Analyses of the Atoh1, Pou4f3 and Gfi1 genome binding profile during hair cell and neuronal differentiation


title: MicroRNA profiling of paediatric AML with FLT-ITD or MLL-rearrangements: expression signatures and in-vitro modulation of miR-221/222 with BRD4/HATs inhibitors.

status: Public on Jul 30 2022

first: Carlo

middle: M.

last: Croce

state: Ohio

address: 460 West 12th Avenue

department: Department of Cancer Biology and Genetics

institute: The Ohio State University

summary: Novel therapeutic strategies are needed for paediatric patients affected by Acute Myeloid Leukaemia (AML), especially for high-risk patients, characterized by high relapse incidence. MicroRNAs (miRs) have been extensively studied as biomarkers in cancer and haematological disorders, and their expression has been correlated to the presence of recurrent molecular abnormalities, expression of oncogenes, as well as to prognosis/clinical outcome. In this work, we identified different miRs expression signatures related both to presence of MLL and FLT3-ITD rearrangements and to paediatric AML patients clinical outcome. Notably, miR-221/222 resulted as a possible relapse-risk related miR. Thus, we investigated miR-221/222 expression modulation by using BRD4 and HAT inhibitors (JQ1 and curcumin), alone or in association. JQ1 modulates miR 221/222 expression in AML with a synergic effect when associated with curcumin. Moreover, we observed changes in the expression of CDKN1B, a known target of miR-221/222, increase in apoptosis and impaired colony forming capacity of AML cell lines and CD34+ AML primary cultures. Altogether, these findings suggest that several miRs expression signatures may be potentially useful as risk stratification indicators and relapse prediction markers of paediatric AML. Epigenetic drugs, deserving additional research for enhancing activity, bioavailability and safety, could represent a novel therapeutic strategy for high-risk paediatric AML patients

overall_design: Twenty-three patients aged 1 to 18 years, who received a diagnosis of AML harbouring FLT3-ITD or MLL rearrangement were enrolled in the study.  Bone marrow (BM) samples were collected at Bambino Gesù Children Hospital (OPBG) in Rome and at Department of Paediatrics, University in Padua, at diagnosis and at disease recurrence from the 13 patients who underwent relapse (REL-D and REL-R groups, respectively) and at diagnosis from the 10 patients who did not display relapse (NREL group).   Eight frozen age-matched BM samples from healthy children (HD) (unused aliquots from healthy BM donors) were retrieved from the tissue bank at OPBG as a control population.


title: Gene expression altered by E4bp4 deficiency of mice on high-fat diet feeding

status: Public on Jul 31 2022

city: Ann Arbor

first: Sujuan

state: MI

address: 2800 Plymouth Road

department: Molecular & Integrative Physiology

institute: University of Michigan

summary: To identify hepatic genes specifically regulated by E4bp4. Lipid droplet binding genes are downregulated in the liver of E4bp4 liver specific knockout mice.

overall_design: Microarray assay was performed with pooled RNA-samples from wildtype and E4bp4-LKO mice

first: Deqiang

last: Zhang

first: Xin

last: Tong


title: Impact of BMP and WNT signaling modulation on mesendoderm progenitor cells specification from hPSCs in 3D culture conditions

status: Public on Aug 01 2022

city: Lisbon

first: Mariana

middle: A.

last: Branco

state: Porto Salvo

address: Av. Prof. Doutor Cavaco Silva

department: Institute for Bioengineering and Biosciences

country: Portugal

institute: Instituto Superior Tecnico

summary: We report a bulk RNA sequencing analysis of a population containing different mesendoderm progenitor cells derived from hiPSCs in 3D environment. Specifically, 3D aggregates of hPSCs were differentiated into cardiac progenitor cells through WNT signaling activation from day 0 to day 1 and WNT signaling inhibition from day 3 to day 5 of differentiation, which allowed further efficient and reproducible specification into hiPSC-derived CMs. This represents the control protocol from which samples from D3 (D3N) and D5 (D5N) were collected. Additionally, adaptation of this control protocol by performing WNT and BMP signalling pathways activation from day 3 to day 5 of differentiation, allowed the modulation of the progenitor cells population to a more posterior splanchnic mesoderm which favours further specification of those progenitors into hiPSC-derived pro-epicardium/septum transversum cells. This represents the CB protocol from where samples from D3 (D3CB) and D5 (D5CB) were collected.

overall_design: Samples were collected from mesendoderm progenitor cell populations derived from hiPSC at day 3 (D3) and day 5 (D5) of differentiation, for the control (N) and for the adpted (CB) protocol, for bulk RNA-seq analysis. These samples were entitled D3N, D5N, D3CB and D5CB. Three biological replicates were obtained for each time point. Deep sequencing was performed in the Illumina platform.

first: Maria

last: Diogo


title: Biasing the conformation of Elmo2 reveals that the myoblast fusion process can be exploited for regenerative therapy

status: Public on Jul 25 2022

city: Montréal

first: Sophie

last: Ehresmann

state: Quebec

address: 110 Avenue des pins

country: Canada

institute: IRCM

summary: Myoblast fusion is fundamental for the development of multinucleated myofibers. Evolutionarily conserved proteins required for myoblast fusion include Rac1 and its activator Dock1. Here, we tested the functions of Elmo proteins, Dock1-interacting scaffolds, on myoblast fusion. When Elmo1-/- mice underwent muscle-specific Elmo2 genetic ablation, they exhibited severe myoblast fusion defects. A mutation in the Elmo2 gene that reduced signaling resulted in a decrease in myoblast fusion. Conversely, a mutation in Elmo2 promoting its open conformation increased myoblast fusion during development and in muscle regeneration. Finally, we showed that the dystrophic features of the Dysferlin-null mice, a model of limb-girdle muscular dystrophy type 2B, were reversed when expressing Elmo2 in an open conformation. These data provide direct evidence that the myoblast fusion process could be exploited for regenerative and therapeutic purposes.

overall_design: Gene expression profiling by RNAseq for differentiated primary myoblasts isolated from wildtype (WT, N=3) and Elmo EID/EID (EID, N=2) mice.

first: Jean

last: Côté


title: Single cell transcriptomic analysis of P8 and P15 mouse cochlea (control and three overexpression conditions) and simultaneous single cell transcriptomic and accessible chromatin analysis of P1 and P8 mouse cochlea (wildtype)

city: Houston

last: K Groves

state: Texas

address: One Baylor Plaza, Baylor College of Medicine

institute: Baylor College of Medicine

summary:
Purpose - To determine transcriptomic variations in the mouse cochlea in response to three different transcription factor overexpression conditions and no induction control and to determine transcriptomic and accessible chromatin variations in the mouse cochlea between postnatal day 1 (P1) and postnatal day 8 (P8) stages of development.
Methods - SC RNA seq performed on FACS enriched cells obtained from experimental animals (Sox9CreER; Rosa26A/GA/GAP/+; Rosa26 tdtomato). Same samples at two timepoints 1 week (P8) and 2 week (P15) ages. scMultiome ATAC + Gene Expression (10x Genomics) experiments on enzymatically dissociated and unenriched cochlear nuclei from wildtype mice in a mixed background of CD1 and FVB/NJ, and C57BL/6. Samples were collected at P1 and P8. Gene expression data was used to annotate clusters. Chromatin accessibility determined by ATAC was compared between P1 and P8 stages.
Results - The SC RNA seq highlighted differential transcriptomic changes between the two ages and the three overexpression conditions. Hair cell loci become less epigenetically accessible in supporting cells and GER cells between P1 and P8.
Conclusions - Our study highlights the variability in transcriptomic response to three transcription factor combination mediated reprogramming cues at two different ages. The SC RNA seq confirmed a variety of our biological observations with regard to the hair cell reprogramming process in the mouse cochlea. We also demonstrate variability in chromatin accessibility between P1 and P8, which may explain why GER and supporting cells of the cochlea become more resistant to transcription factor reprogramming into hair cells during the first postnatal week.

overall_design: Examination of transcriptome via single cell RNA seq of FACS purified mouse cochlear cells at P8 and P15 induced with transcription factor combinations. scMultiome ATAC + Gene Expression (10x Genomics) experiments on P1 and P8 wildtype cochlea sensory epithelium.

middle: K

last: Groves

first: Neil

last: Segil

first: Amrita

last: Iyer

first: Ishwar

last: Hosamani

first: John

last: Nguyen


title: Single-cell sequencing data for circulating CAR T cells in lymphoma patients

status: Public on Jul 28 2022

first: Zinaida

last: Good

state: California

address: 265 Campus Drive, Room G2105

department: Stanford Cancer Institute, Department of Biomedical Data Science

institute: Stanford University School of Medicine

summary:
Purpose: To compare cell states amoung three populations of interest among circulating CAR T cells in patients with lymphoma.
Methods: Nine patients with large B-cell lymphoma (LBCL) were treated with axicabtagene ciloleucel (axi-cel), a commercial CD19-targeted CAR T-cell therapy. On day 7, fresh peripheral blood mononuclear cells were stained with an antibody panel for fluorescence-activated cell sorting (FACS), a panel for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), and a viability dye. Single live CAR+ T cells were sorted from each patient, counted, processed for 5' single-cell RNA-sequencing with feature barcoding and TCR clonotype analysis on the 10X Genomics platform, and sequenced by the Stanford Genomics Facility (HighSeq 4000) or Novogene (NovaSeq 6000).
Results: We found that circulating CD4+ and CD8+ CAR T cells that express CD57 and T-bet are clonally expanded and display features of effector T cells. In contrast, CD4+ CD57- CAR T cells that express Helios expand polyclonally and display features of T regulatory cells.
Conclusions: This study provides insights into cell states of circulating CAR T cells on day 7 that associate with clinical response or toxicity in LBCL patients treated with axi-cel.

overall_design: CAR T cells were sorted from blood of nine LBCL patients on day 7 following axi-cel infusion. Three populations of interest were identified within each CAR T-cell sample.

first: Crystal

last: Mackall


title: A cohesin traffic pattern genetically linked to gene regulation

first: Anne-Laure

last: Valton


title: A cohesin traffic pattern genetically linked to gene regulation [CRISPR screens]

summary: Cohesin-mediated loop extrusion is blocked at specific cis-elements, including CTCF sites, producing patterns of loops and domain boundaries along chromosomes. Here, we explore such cis-elements, and their role in gene regulation. We find that transcription termination sites of active genes form cohesin- and RNA polymerase II-dependent domain boundaries that do not accumulate cohesin. At these sites, cohesin is first stalled and then rapidly unloaded. Start sites of transcriptionally active genes form cohesin-bound boundaries, as shown before, but are cohesin-independent. Together with cohesin loading possibly at enhancers, these sites create a pattern of cohesin traffic that guides enhancer-promoter interactions. Disturbing this traffic pattern, by removing CTCF, renders cells sensitive to knock-out of genes involved in transcription initiation, such as the SAGA complexes, and RNA processing such DEAD/H-Box RNA helicases. Without CTCF, these factors are less efficiently recruited to active promoters.

overall_design: We engineered a HAP1-derived human cell line in which CTCF could efficiently be removed using an auxin-inducible degron system. We performed genome-wide CRISPR screens in HAP1-CTCFdegron-Tir1 cells (that expressed reduced levels of CTCF) and compared the results to similar screens performed in HAP1-CTCF-degron cells (that express higher levels of CTCF). We also performed screens in the presence of different concentrations of auxin to further reduce the CTCF protein level (NT, 25uM and 500uM auxin). The screens were performed in three replicates.

first: Sergey

last: Venev

first: Barbara

last: Mair

first: Eraj

last: Khokhar

first: Amy

first: Matej

last: Usaj

first: Katherine

last: Chan

first: Athma

last: Pai

first: Jason

last: Moffat

first: Job

last: Dekker


title: The injury-induced transcription factor SOX9 alters the expression of LBR, HMGA2, and HIPK3 in human kidney

status: Public on Jul 08 2022

city: Gothenburg

first: Martin

middle: E

last: Johansson

address: Medicinaregatan 1G

country: Sweden

institute: University of Gothenburg

summary: Induction of SRY box transcription factor 9 (SOX9) has been shown to occur in response to kidney injury in rodents, where SOX9-positive cells proliferate and regenerate the proximal tubules of injured kidneys. Additionally, SOX9-positive cells demonstrate a capacity to differentiate toward other nephron segments. Here, we characterized the role of SOX9 in normal and injured human kidneys. SOX9 expression was found to colocalize with a proportion of so-called scattered tubular cells in the uninjured kidney, a cell population previously shown to be involved in kidney injury and regeneration. Following injury and in areas adjacent to inflammatory cell infiltrates, SOX9-positive cells were increased in number. With the use of primary tubular epithelial cells (PTECs) obtained from human kidney tissue, SOX9 expression was spontaneously induced in culture and further increased by TGF-β1, whereas it was suppressed by IFN-γ. siRNA-mediated knockdown of SOX9 in PTECs followed by analysis of differential gene expression, immunohistochemical expression, and luciferase promoter assays suggested lamin B receptor (LBR), high mobility group AT-hook 2 (HMGA2), and homeodomain interacting protein kinase 3 (HIPK3) as possible target genes of SOX9. Moreover, a kidney explant model was used to demonstrate that only SOX9-positive cells survive the massive injury associated with kidney ischemia and that the surviving SOX9-positive cells spread and repopulate the tubules. Using a wound healing assay, we also showed that SOX9 positively regulated the migratory capacity of PTECs. These findings shed light on the functional and regulatory aspects of SOX9 activation in the human kidney during injury and regeneration.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human primary tubular epithelial cells after siRNA-mediated knockdown of SOX9 versus siSCR and ctrl including three biological replicates.

first: Michelle

last: Kha

first: Helén

last: Nilsson


title: Astrocytic dysfunction induced by ABCA1 deficiency causes optic neuropathy

status: Public on Jul 11 2022

city: London

first: Alex

last: Leung

state: London

address: 11-43 Bath Street

institute: UCL Institute Of Ophthalmology


title: Expression of immune response and tissue repair genes in human colonic CD4s upon cytokine or TCR stimulation.

status: Public on Jul 02 2022

city: Oxford

first: Carl-Philipp

last: Hackstein

address: 3 South Parks Road

department: NDM Experimental Medicine

institute: University of Oxford

summary: Human Colonic CD4 T cells consist of several subsets differing in their expression of CD161. We exposed these cells to either cytokine, TCR or combined stimulation and assessed the subsequent changes in gene and protein expression with an emphasis on cytokine receptors and gene associated with tissue repair.

overall_design: Lamina propria mononuclear cells (LPMCs) from three donors (141, 194 and 267) were isolated and stimulated tih IL12/18 (C), plate-bound aCD3 (T) or a combination of both (TC) overnight. Cells were stained with BD Abseq antibodies and BD Sample Tags, CD4+ T cells were sorted, pooled and loaded onto a BD Rhapsody cartidge for single cell capture followed by cDNA cythesis and library preparation.


title: Spatiotemporal transcriptome analysis reveals critical roles for mechano-sensing genes at the border zone in remodeling after myocardial infarction

city: Tokyo

first: Shintaro

last: Yamada

address: 7-3-1, Hongo, Bunkyo-ku

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

summary: The underlying mechanisms of ventricular remodeling after myocardial infarction (MI) remain largely unknown. Here, we performed an integrative analysis of spatial transcriptomics and single-nucleus RNA-seq in a murine MI model and found that mechanical stress-response genes are expressed at the border zone and play a critical role in left ventricular remodeling following MI. An integrative analysis of single-nucleus RNA-seq and spatial transcriptome of the heart tissue after MI identified the unique cluster that appeared at the border zone in an early stage, highly expressing mechano-sensing genes such as Csrp3. AAV9-mediated gene silencing and overexpression of Csrp3 demonstrated that upregulation of Csrp3 plays critical roles in preventing cardiac remodeling after MI via regulation of genes associated with mechano-sensing. Overall, our study not only provides an insight into spatiotemporal molecular changes following MI but also highlights that the mechano-sensing genes at the border zone act as adaptive regulators of left ventricular remodeling.

overall_design: Integrative analysis of single-cardimyocyte analysis and spatial transcriptomics after myocardial infarction in mouse

first: Tohiyuki

last: Ko

first: Satoshi

last: Hatsuse

first: Seitaro

last: Nomura

first: Hiroyuki

last: Aburatani

first: Issei

last: Komuro


title: Role of Bcl3 in Dendritic cell function in the context of Toxoplasma gondii infection

city: Bethesda

first: Neelam

last: Redekar

state: MD

address: 9000 rockville pike

department: NIAID

institute: NIH

summary: This experiment contains two mice genotypes – WT and Bcl3 flx/flx Zbtb46 cre knockouts (both C57BL/6 background). These mice were either infected with 15 cysts of Toxoplasma gondii (ME49 strain) or kept uninfected. Spleens were harvested from mice 7 days post infection and splenocytes were isolated. With four experimental groups (KO/WT and infected/uninfected) and two biological replicate mice per group, we have a total of 8 biological samples comprising of single cell suspensions of splenocytes enriched for CD11c. Single cell RNA-seq libraries were prepared from CD11c-enriched single cells using the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics; Pleasanton, CA, USA). Eight sample libraries were multiplexed and sequenced 100bp paired end in four different runs of Illumina NextSeq2000, followed by demultiplexing that resulted in multiple raw FASTQ files corresponding to paired reads (R1 and R2), index barcodes (I1) and four sequencing runs (Seq1 - Seq4). The main goal of this project was to define Bcl3-associated transcriptional responses in dendritic cells during T. gondii infection.

overall_design: Single-cell mRNA profiles of splenocytes from Bcl3 flx/flx Zbtb46 cre KO and WT mice that were either infected with Toxoplasma gondii or kept uninfected.

first: June

last: Guha

first: Byunghyun

last: Kang

first: Philip

last: Murphy

first: Tiago

middle: R

last: Ferreira

first: Michael

last: Kelly


title: Astrocytic dysfunction induced by ABCA1 deficiency causes optic neuropathy [scRNA-seq]

summary: Glaucoma is an optic neuropathy characterized by progressive degeneration of retinal ganglion cells (RGCs) and visual loss. Previous studies have reported that the variation of the ATP-binding cassette transporter 1 (ABCA1) gene is linked to a higher risk of glaucoma in humans, but the pathological mechanisms remain unknown. Here we report that ABCA1 loss, especially in astrocytes, causes optic neuropathy. ABCA1 was mainly expressed in astrocytes rather than neurons, and that knockout of Abca1 gene under GFAP promoter (Glia-KO) caused age-associated RGC degeneration and ocular dysfunction without affecting intraocular pressure, a major risk factor for glaucoma. Glia-KO mice showed age-associated changes in astrocyte reactivity accompanied by the accumulation of cholesterol, a major substrate of ABCA1. Single-cell RNA sequencing revealed that Abca1 deficiency causes astrocyte-triggered inflammation and increased sensitivity of RGCs against excitotoxicity. Altogether, these findings suggest that astrocytic dysfunction caused by ABCA1 loss triggers age-associated optic neuropathy-like pathology.

overall_design: Single-cell expression profiling of mouse retinal tissue, with comparison between control and ABCA1 knockout samples

first: Youichi

last: Shinozaki

first: Kazuhiko

last: Namekata

first: Sei

last: Saitoh

first: Huy

middle: B

last: Nguyen

first: Akiko

last: Takeda

first: Yosuke

last: Danjo

last: Morizawa

first: Eiji

last: Shigetomi

first: Fumikazu

last: Sano

first: Nozomu

last: Yoshioka

first: Hirohide

last: Takebayashi

first: Nobuhiko

last: Ohno

first: Takahiro

last: Segawa

first: Kunio

last: Miyake

first: Kenji

last: Kashiwagi

first: Takayuki

last: Harada

first: Shin-ichi

last: Ohnuma

first: Schuichi

last: Koizumi


title: Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

status: Public on Aug 05 2022

city: New York

first: Dalia

last: Barkley

state: NY

address: 435 E 30th st

department: Institute for Computational Medicine

institute: NYU Langone Health

summary: Transcriptional heterogeneity among malignant cells of a tumor has been studied in individual cancer types and shown to be organized into cancer cell states; however, it remains unclear to what extent these states span tumor types, constituting general features of cancer. Here, we perform a pan-cancer single-cell RNA-Seq analysis across 15 cancer types and identify a catalog of gene modules whose expression defines recurrent cancer cell states including ‘stress’, ‘interferon response’, ‘epithelial-mesenchymal transition’, ‘metal response’, ‘basal’ and ‘ciliated’. Spatial transcriptomic analysis linked the interferon response in cancer cells to T cells and macrophages in the tumor microenvironment. Using mouse models, we further found that induction of the interferon response module varies by tumor location and is diminished upon elimination of lymphocytes. Our work provides a framework for studying how cancer cell states interact with the tumor microenvironment to form organized systems capable of immune evasion, drug resistance, and metastasis.

first: Itai

last: Yanai


title: The effects of environmental enrichment on maternal nurturance, lactation quality, and offspring social behavior

status: Public on Jul 01 2022

first: Jordan

last: Marrocco

address: 1230 York Ave

institute: The Rockefeller University

summary: It was our goal to discern the effects of environemental enrichement on quality of mRNA in milk from Sprague-Dawley rat mothers.

overall_design: Sprague-Dawley rats were housed and bred in either enriched environment or standard-housed conditions. Litters were standardized and cross-fostered across groups, and  maternal milk samples were then collected on P10 for analysis.

first: Salvatore

middle: G

last: Caradonna

first: Holly

last: DeRosa

first: Amanda

middle: C

last: Kentner


title: Bulk RNA-sequencing in Ldlr-/- or Ch25h-/-;Ldlr-/- peritoneal macrophages treated with LPS

first: Alberto

last: Canfran-Duque

state: New York

address: 550 1st Avenue

institute: NYU Langone

summary: Here we study the effect of LPS in the transcriptome of thioglycollate-elicited peritoneal macrophages isolated from Ldlr knock out and Ch25h;Ldlr double knock out mice

overall_design: mRNA profiles from thioglycollated-elicited peritoneal macrophages isoaltes from LDLR KO CH25H;LDLR DKO mice

last: Canfrán-Duque

first: Yajaira

last: Suárez

first: Carlos

last: Fernandez-Hernando


title: Ezh2 WT, Het, and Null Mouse Organoid Transcriptome

status: Public on Jun 30 2022

city: LEXINGTON

first: Aria

last: Byrd

state: Kentucky

address: 2865 Middlesex Way

institute: University of Kentucky

summary: We report the transcriptomics of Ezh2-/-, Ezh2+/-, and Ezh2+/+ mouse organoids

overall_design: In order to understand how Ezh2 expression influences lung stem cell fate in vivo, we compared transcriptional profiles of mouse lung organoids that were wild-type, heterozygous or homozygous for the Ezh2 floxed excised allele.

first: Christine

last: Brainson

first: Jinze

last: Liu

first: Xufeng

last: Qu


title: Maternal immune activation during the mid-lactational period affects nutritional milk quality and adolescent offspring sensory processing in male and female rats

summary: It was our goal to discern the effects of maternal immune activation on quality of mRNA in milk from Sprague-Dawley rat mothers.

overall_design: Sprague-Dawley rats mothers were injected with either lipolysaccharide to induce an immune response or a saline vehicle on postnatal day 10. Maternal milk samples were collected 2- and 24-hours post-injection to assess mRNA quality.


title: Single-cell RNA-Seq reveals changes in immune landscape in post-traumatic osteoarthritis

status: Public on Jul 18 2022

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

address: 7000 East Ave

department: BBTD

institute: LLNL

summary: Osteoarthritis (OA) is the most common joint disease, affecting over 300 million people world-wide. Accumulating evidence attests to the important roles of immune system in OA pathogenesis. Understanding the role of various immune cells in joint degeneration or joint repair after injury is helpful for improving therapeutic strategies for treating OA. Post-traumatic osteoarthritis (PTOA) develops in ~50% of individuals who have experienced an articular trauma like an anterior cruciate ligament (ACL) rupture. Here, using highly sensitive single-cell RNA sequencing technology, we delineated the temporal dynamics of immune cell accumulation in the mouse knee joint after ACL rupture.

overall_design: Right knee joints of 10-week-old C57Bl/6J mice were injured using a tibial compression injury model. Uninjured joints and injured joints from 1-, 3-, 7-, 15- and 30 days post-injury (n=5/group) were collected and immune (Cd45+) cells were analyzed using scRNA-seq. Non-immune (Cd45-) cells from D0 were also profiled using scRNA-seq to determine immune stromal interactions.

first: Aimy

last: Sebastian

first: Gabriela

last: Loots


title: NXN suppresses metastasis of hepatocellular carcinoma by promoting degradation of Snail through binding to DUB3

status: Public on Jul 26 2022

city: Guangzhou

first: Yuanping

last: Zhang

state: None Selected

address: 651 Dongfeng Road East

summary:
To investigate the function of NXN in the regulation of metastasis in hepatocellular carcinoma cells, we established NXN knock down Hep-3B cells by shRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at three time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Hep-3B cells and its KD derivatives (shNXN).

first: Binkui

last: Li

first: Yunfei

last: Yuan


title: Monoclonal Antibody to Marinobufagenin Downregulates TGFβ Profibrotic Signaling in Left Ventricle and Kidney and Reduces Tissue Remodeling in Salt‐Sensitive Hypertension [LV_Kidney]

status: Public on Jul 12 2022

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Elevated levels of an endogenous Na/K‐ATPase inhibitor marinobufagenin accompany salt‐sensitive hypertension and are implicated in cardiac fibrosis. Immunoneutralization of marinobufagenin reduces blood pressure in Dahl salt‐sensitive (Dahl‐S) rats. The effect of the anti‐marinobufagenin monoclonal antibody on blood pressure, left ventricular (LV) and renal remodeling, and LV gene expression were investigated in hypertensive Dahl‐S rats.

overall_design: Fifteen-week old Dahl salt‐sensitive (Dahl‐S, SS/JrHsd) male rats were given low or high salt diets (ls and hs, respectively) and treated once with control antibody (lsc and hsc, respectively) or a monoclonal antibody to  the endogenous Na/K‐ATPase inhibitor marinobufagenin (lsab abd hsab, respectively), and left ventricular gene expression changes were examined after one week  in six animals per group.

first: Yongqing

first: Wen

last: Wei

first: Victoria

last: Shilova

first: Natalia

middle: N

last: Petrashevskaya

first: Valentina

middle: I

last: Zernetkina

first: Yulia

last: Grigorova

first: Courtney

middle: A

last: Marshall

first: Rachel

last: Fenner

first: Elin

last: Lehrmann

first: William

last: Wood III

first: Kevin

last: Becker

first: Edward

last: Lakatta

first: Alexei

middle: Y

last: Bagrov

first: Olga

middle: V

last: Fedorova


title: Single cell transcriptome landscape of primary and metastatic tumor in colon cancer

city: Beijing

first: Rui

last: WANG

address: No.5 Yiheyuan Road, Haidian District

department: Biodynamics Optical Imaging Center (BIOPIC)

institute: Peking University

type: Genome variation profiling by high throughput sequencing

summary: Colorectal Cancer ranks as the second-leading cause of cancer-related death worldwide. Recent progress in colon cancer research has vastly expanded our understanding of colon cancer on the cellular and molecular levels and have improved the survival of CRC patients considerably. However, most of these genomic and gene expression profiling were usually characterized by bulk tumor tissue. In order to further understanding colon cancer, knowledge at the single cell level is urgently needed and expected to have clinical utility in cancer treatment. Single-cell transcriptome profiling of tumor tissues allows the characterization of heterogeneous tumor cells with neighbor microenvironment cell components and investigation of underlying mechanism of tumorigenesis and metastasis. Here, we adopt single cell RNA-Seq to colon cancer and analyze 3,585 cells from 6 patients with matching adjacent normal tissues, primary tumors and metastatic tumors. Most of tumor cells exhibit copy number variations and diverse CNV patterns existed. Novel markers have been identified to distinguish tumour from normal cells and even work for cancer cells that did not have CNVs. Compared with adjacent normal tissue, the number of stem cell and Paneth cell increased and the surrounding cancer-association cells like immune cells in microenvironment increased in tumour region. Moreover, the interaction of tumour cell and microenvironment cells have been elaborated. Our results demonstrate that colon cancer transcriptome has a wide range of intratumoral heterogeneity, which is shaped by tumor cells and cancer associated cells in the surrounding microenvironment.

overall_design: Single cell transcriptome profiles of six colon cancer patients were generated by next-generation sequencing using Illumina HiSeq 4000. In order to confirm the copy number variants inferred by single cell RNA-seq data, bulk whole genome sequencing were performed on normal tissue and tumor regions.

last: Wang

first: Jingyun


title: Astrocytic dysfunction induced by ABCA1 deficiency causes optic neuropathy [bulkRNA-seq]

first: Alex

last: Leung

overall_design: Comparison of expression profile of mouse retinal tissue between control and Glia-specific ABCA1 knockout

first: Youichi

last: Shinozaki

first: Kazuhiko

last: Namekata

first: Sei

last: Saitoh

first: Huy

last: Nguyen

first: Akiko

last: Takeda

first: Yosuke

last: Danjo

last: Morizawa

first: Eiji

last: Shigetomi

first: Fumikazu

last: Sano

first: Nozomu

last: Yoshioka

first: Hirohide

last: Takebayashi

first: Nobuhiko

last: Ohno

first: Takahiro

last: Segawa

first: Kunio

last: Miyake

first: Kenji

last: Kashiwagi

first: Takayuki

last: Harada

first: Shin-ichi

last: Ohnuma

first: Schuichi

last: Koizumi


title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification.

status: Public on Jun 22 2022

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

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

overall_design: Refer to individual Series


title: PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma [Human]

status: Public on Jun 18 2022

city: Richardson

first: Zhenyu

last: Xuan

state: TX

address: 800 West Campbell

institute: UT Dallas

summary: Intratumor epigenetic heterogeneity is emerging as a key mechanism underlying tumor evolution and drug resistance. Epigenetic abnormalities frequently occur in medulloblastoma, the most common childhood malignant brain tumor. Medulloblastoma is classified into four subtypes including SHH medulloblastoma, which is characterized by elevated SHH signaling and a cerebellum granule neuron precursor (CGNP) cell-of-origin. Here we report that the histone H3K27 methyltransferase polycomb repressor complex 2 (PRC2) is often heterogeneous within individual SHH medulloblastoma tumors. In mouse models, complete deletion of the PRC2 core subunit EED inhibited medulloblastoma growth, while a mosaic deletion of EED significantly enhanced tumor growth. EED is intrinsically required for CGNP maintenance by inhibiting both neural differentiation and cell death. Complete deletion of EED led to CGNP depletion and reduced occurrence of medulloblastoma. Surprisingly, medulloblastomas with mosaic EED levels grew faster than control wildtype tumors and expressed increased levels of oncogenes such as Igf2, which is directly repressed by PRC2 and has been demonstrated to be both necessary and sufficient for SHH medulloblastoma progression. IGF2 mediated the oncogenic effects of PRC2 heterogeneity in tumor growth. Assessing clones of a human medulloblastoma cell line with different EED levels confirmed that EEDlow cells can stimulate the growth of EEDhigh cells through paracrine IGF2 signaling. Thus, PRC2 heterogeneity plays an oncogenic role in medulloblastoma through both intrinsic growth competence and non-cell autonomous mechanisms in distinct tumor subclones.

overall_design: Total RNAs were extracted from human Daoy cells with wildtype or mutant EED.  Gene expression profiles were examined uisng RNA-seq.

first: Jiaqing

last: Yi

first: Jiang

last: Wu


title: Next Generation Sequencing-based Quantitative Analysis of female whole body transcriptomes from w1118 (control) and foxo mutant flies exposed to normoxia or hypoxia for 16 hrs

status: Public on Jun 17 2022

city: Calgary

first: Savraj

last: Grewal

state: Alberta

address: 3330 Hospital Drive

institute: University of Calgary

summary:
Purpose: The goal of this RNA-Seq is to analyze the whole-body transcriptomes from normoxia vs hypoxia exposed flies to identify differentially expressed genes and to identify which differentially gene expression changes require the FOXO transcription factor
Abstract from associated manuscript: When exposed to low oxygen or hypoxia, animals must alter their metabolism and physiology to ensure proper cell-, tissue- and whole-body level adaptations to their hypoxic environment. These alterations often involve changes in gene expression. While extensive work has emphasized the importance of the HIF-1 alpha transcription factor on controlling hypoxia gene expression, less is known about other transcriptional mechanisms. We previously identified the transcription factor FOXO as a regulator of hypoxia tolerance in Drosophila larvae and adults. Here we use an RNA sequencing approach to identify FOXO-dependent changes in gene expression that are associated with these tolerance effects. We found that hypoxia altered the expression of over 2000 genes and that approximately 40% of these gene expression changes required FOXO. We discovered that hypoxia exposure led to a FOXO-dependent increase in genes involved in cell signaling, such as kinases, GTPase regulators, and regulators of the Hippo/Yorkie pathway. Among these, we identified homeodomain-interacting protein kinase (Hipk) as being required for hypoxia survival. We also found that hypoxia suppresses the expression of genes involved in ribosome synthesis and egg production, and we showed that hypoxia suppresses tRNA synthesis and mRNA translation and reduces female fecundity. Among the downregulated genes, we discovered that FOXO was required for suppression of many ribosomal protein genes and genes involved in oxidative phosphorylation, pointing to a role for FOXO in limiting energetically costly processes such as protein synthesis and mitochondrial activity upon hypoxic stress. This work uncovers a widespread role for FOXO in mediating hypoxia changes in gene expression.
Results: RNA Seq differential expression analysis identified a significant (p<0.05,> 1.5 fold expression) change in 2835 transcripts, with 1602 transcripts showing reduced expression levels and 1233 transcripts with elevated expression levels.

overall_design: For each condition (normoxia vs hypoxia, w111w vs foxo mutant ) there were 3-4 independent biological samples, each consisting of total RNA extracted from 5 adult female flies.

middle: S


title: Cefazolin and Imipenem Enhance AmpC Expression and Resistance in NagZ-dependent manner in Enterobacter cloacae complex

city: Chenggu

first: Xianggui

last: Yang

state: 四川省

address: 278 Baoguang Road, Xindu

institute: Clinical Medical College

summary:
Background: Enterobacter cloacae complex (ECC) is a common opportunistic pathogen and is responsible for causing various infections in humans. Owing to its inducible chromosomal AmpC β-lactamase (AmpC), ECC is inherently resistant to the 1st- and 2nd- generation cephalosporins. However, whether β-lactams antibiotics enhance ECC resistance remains unclear.
Results: In this study, we found that subinhibitory concentrations (SICs) of cefazolin (CFZ) and imipenem (IMP) can advance the expression of AmpC and enhance its resistance towards β-lactams through NagZ in Enterobacter cloacae (EC). Further, AmpC manifested a substantial upregulation in EC in response to SICs of CFZ and IMP. In nagZ knockout EC (ΔnagZ), the resistance to β-lactam antibiotics was rather weakened and the effect of CFZ and IMP on AmpC induction was completely abrogated. NagZ ectopic expression can rescue the induction effects of CFZ and IMP on AmpC and increase ΔnagZ resistance. More importantly, CFZ and IMP have the potential to induce the expression of AmpR's target genes in a NagZ-dependent manner.
Conclusions: Our findings suggest that NagZ is a critical determinant for CFZ and IMP to promote AmpC expression and resistance and that CFZ and IMP should be used with caution since they may aggravate ECC resistance. At the same time, this study further improves our understanding of resistance mechanisms in ECC.

overall_design: Wild type Enterobacter cloacae (WT) and nagZ knock out Enterobacter cloacae (NagZ) were sequenced to analyze the gene expression

first: zhenguo

last: Wang


title: Hypertrophic cardiomyopathy: data of transcriptome profiling and epigenome-wide DNA methylation analysis

city: Moscow

first: Maxim

last: Kozin

address: Ostrovitanova 1

country: Russia

institute: Pirogov Russian National Research Medical University

summary: Hypertrophic cardiomyopathy (HCM) is the most common inherited heart disease, and its pathogenesis is still being intensively studied to explain the reasons of significant genetic and phenotypic heterogeneity of the disease. To search for possible HCM modifier genes involved in the HCM development we first attempted to analyze gene expression profile coupled with DNA methylation profile in the hypertrophied myocardium of HCM patients; the control group consisted of patients with aortic stenosis. The transcriptome analysis identified significant differences in levels of 193 genes, most of which were underexpressed in HCM. The methylome analysis revealed 1755 nominally significant differentially methylated positions (DMPs), mostly hypomethylated in HCM. The clear differences in DNA methylation profiles between the studied groups indicate the involvement of this process in the formation of primary left ventricle hypertrophy in HCM. Based on gene ontology enrichment analysis, the majority of biological processes, overrepresented by both differentially expressed genes (DEGs) and DMP-containing genes, are involved in the regulation of locomotion and muscle structure development. The intersection of 193 DEGs and 978 DMP-containing genes pinpointed eight genes, expression of which differed between studied groups and correlated with methylation levels of the neighboring DMPs. Half of these genes (AUTS2, GIGYF1, PRRT1, and SLC17A7) were found underexpressed in HCM and involved in neurogenesis and synapse functioning. Our data suggesting the possible involvement of innervation-associated genes in HCM provide additional insights in the disease pathogenesis and expand the field of further research.

overall_design: We performed RNA-seq analysis of the heart left ventricle samples obtained from 8 patients with hypertrophic cardiomyopathy and 5 samples from patients with aortic stenosis.

first: Ivan

last: Kiselev

first: Natalia

last: Baulina

first: Maria

last: Pisklova


title: Transcriptomics, Regulatory Syntax, and Enhancer Identification in Heterogenous Populations of Mesoderm-Induced ESCs at Single-Cell Resolution

city: Bethsda

first: Vittorio

last: Sartorelli

address: 50 South Dr.

department: NIAMS

summary: ESCs  can  adopt  lineage-specific  gene  expression  programs  by  stepwise  exposure  to  defined factors, resulting in the generation of functional cell types. Bulk and single cell-based assays were employed  to  catalogue  gene  expression,  histone  modifications,  chromatin  conformation  and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further lineage specification. These assays identified cis-regulatory regions and transcription factors presiding gene expression programs occurring at defined ESC transitions and revealed the presence of heterogenous cell populations within discrete ESC developmental stages.  The  datasets  were  employed  to identify  previously  unappreciated genomic  elements directing the initial activation of Pax7 and myogenic and neurogenic gene expression programs. This  study  provides  a  resource  for  the  discovery  of  genomic  and  transcriptional  features  of pluripotent, mesoderm-induced ESCs, and ESCs-derived cell lineages.

overall_design:
To  catalogue gene expression, histone modifications, chromatin conformation and accessibility transitions in ESC populations and individual cells undergoing lineage specification. we induced ESCs differentiation and characterized their transcriptome and epigenome at specific developmental junctures. we examined genome wide , chromatin accessibilty and gene expression in both bulk and single cell in Naive ESC (Naive) (three replicates) and instructed ESC (Instructed),  (two replicates). We characterized regulatory regions with active (H3K4me1 and H3K27ac, two replicates)  epigenetic marks in Naive and instructed ESC.  To gain insite on how chromatin accessibility remodelled and the transcriptionally heterogeneity of differntiated ESCs, we performed scATAC-seq and scRNAseq in ES-derived aPSM (aPSM) and multiomics in ES-derived HIFLR (HIFLR) . We then leveraged these datasets and, by combining chromatin accessibility, in situ Hi-C chromatin conformation in aPSM and HIFLR cells, genome editing, and reporter assays have identified regulatory regions directing initial Pax7 expression and activation of the myogenic and neurogenic programs.

Please note that 'HIFLR_snATAC_fragments.tsv.gz' file was included on Dec 6, 2022.

first: Mamduh

last: Khateb

first: Jelena

last: Perovanovic

first: Kyung

middle: D

last: Ko

first: Kan

last: Jiang

first: Xuesong

last: Feng

middle: a

last: Luna

first: Jérome

last: Chal

first: Veronica

last: Ciuffoli

first: Pavol

last: Genzor

first: Astrid

last: Haase

first: James

last: Simone

first: Olivier

last: Pourquie

first: Stefania

last: Dell'Orso


title: Cystathionine beta synthase (CBS) Over expression vs PLenti6 Expression Vector Human Bronchial Epithelial Cells (HBEC)

first: Aria

last: Byrd

summary: Cystathionine Beta Synthase (CBS), an enzyme that utilizes a methionine precursor to generate glutathione (GSSH), has been implicated in the mitigation of ROS production in COPD lung. Additionally, post-translational modification analysis on mouse and human cells treated with cigarette smoke showed the unique presence of mono- and di-methylated histone H3 lysine 27 that was not seen in controls, suggesting that cigarette smoke could lead to loss of Polycomb Repressive Complex 2 (PRC2) activity.  To elucidate CBS as a potential upstream target for PRC2 inhibition,  we overexpressed CBS in Human Bronchial Epithelial Cells (HBECs), grew them as 2D cultures, then conducted bulk RNA seq analysis.

overall_design: In order to understand how CBS expression influences PRC2 function in vitro, we compared transcriptional profiles of HBECs over expressing human CBS and HBECs that did not.

first: Christine

middle: F

last: Brainson

first: Chi

last: Wang

first: Jinpeng

last: Liu

middle: L


title: Selective PROTAC-mediated degradation and shRNA-driven knockdown of SMARCA2 in HCC2302 lung adenocarcinoma cells

status: Public on Jun 13 2022

city: South San Francisco

first: Matthew

last: Grimmer

state: CA

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

summary: SMARCA2 and SMARCA4 are mutually-exclusive, core catalytic subunits for the chromatin remodeling SWI/SNF complex. Mutations in SMARCA4 are common in lung adenocarcinoma and have shown synthetic lethality with loss of SMARCA2 loss of function. The purpose of this project is to answer questions related to the in vivo [mouse xenograft] efficacy of A947, a SMARCA2 degrader. The study involves in vitro versus in vivo comparisons of drug activity, in addition to genetic manipulation of the target. Model system: HCC2302 (RRID:CVCL_V636); Model origin: Lung Adenocarcinoma; Perturbation: A947 (VHL-PROTAC-based degrader)

overall_design: in vitro samples are treated with either a non-targeting shRNA (in vitro HCC2302-shNTC) or a SMARCA2-targeting shRNA (in vitro HCC2302-shSMARCA2-dual62 cl2), both of which are doxycycline-inducible. Vehicle (non-induced) samples are labeled as "Veh" and doxycycline-induced samples are labeled as "Dox." in vivo mouse xenograft samples (in vivo mouse xenograft HCC2302) are treated with either vehicle (Veh) or A947 (A947). There are 3 replicates per in vitro condition and 5 replicates per in vivo condition.

first: Bob

last: Yauch

first: Xiaofen

last: Ye


title: Nanostring nCounter Immunology Panel between WT and DRA KO mice Colonic Mucosa

status: Public on Jun 29 2022

city: Chicago

first: Dulari

last: Jayawardena

state: Illinois

address: 820 S Damen Avenue, Rm 7221

department: Medicine

institute: University of Illinois at Chicago

summary: Signifiacntly altered genes releated to immunologfy was compared between DRA KO  mice and their WT littermates at baseline in the distal colonic mucosal RNA

first: D


title: Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas

status: Public on Jun 08 2022

city: Rehovot

first: Efrat

last: Shema

address: Herzl St 234

department: Biological Information

country: Israel

institute: Weizmann Institute of Science

summary: We identified two epigenetically distinct subpopulations in DIGP, reflecting inherent heterogeneity in the expression levels of the mutant histone.

overall_design: Examination of different cell lines expressing the H3-K27M mutant histone

first: Nofar

last: Harpaz

first: Tamir

last: Mittelman

first: Olga

last: Beresh

first: Ofir

last: Griess

first: Noa

last: Furth

first: Tomer-Meir

last: Salame

first: Roni

last: Oren

first: Liat

last: Fellus-Alyagor

first: Alon

last: Harmelin

first: Sanda

last: Alexandrescu

first: Joana

last: Marques

first: Mariella

last: Filbin

first: Guy

last: Ron


title: Nicotinamide mononucleotide administration triggers macrophages reprogramming and alleviates inflammation during sepsis induced by experimental peritonitis

city: Nyon

first: Nicolas

last: Hulo

address: Avenue Reverdil 4

country: Switzerland

institute: Nuvamid SA

summary:
Peritonitis and subsequent sepsis lead to high morbidity and mortality in response to uncontrolled systemic inflammation primarily mediated by macrophages. We investigated whether the administration of a natural biosynthetic precursor of NAD+,  β-nicotinamide mononucleotide (β‐NMN), could prevent clinical deterioration effects of sepsis. To this purpose, C57BL6 mice were subjected to the cecal ligation and puncture (CLP) model to provoke sepsis or were injected with thioglycolate (TGC) to induce a sterile peritonitis with recruitment and differentiation of macrophages into the inflamed peritoneal cavity.
β-NMN was administered for 4 days after CLP and for 3 days post TGC treatment.
Administration of β‐NMN decreased bacterial load in blood and reduced clinical signs of distress and mortality during sepsis. Transcriptomic analysis of hearts and lungs 24 hours post CLP-induction, revealed that β-NMN downregulated genes controlling immuno-inflammatory response and upregulated genes involved in bioenergetic metabolism, mitochondria biogenesis, and autophagy.
In the thioglycolate model, β‐NMN treatment significantly reduced phagolysosomes acidification and inflammatory mediators secretion from bacteria-stimulated peritoneal macrophages. Transcriptomic signature of these macrophages showed that β‐NMN administration limited the pro-inflammatory M1 phenotype, induced the expression of specific markers of M2 type macrophages and significantly impacted gens involved in NAD+ metabolism.

overall_design: Animals treated with either β-NMN (185 mg/kg/day) or vehicle (saline, 0.9% NaCl) were subjected to CLP-induced sepsis or TGC-induced peritonitis. Subsequently, mRNA profiles were established from hearts, lungs of mice with sepsis and from peritoneal cells of mice with peritonitis.

first: Matthias

last: Canault


title: Oncofusion driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1

status: Public on Jun 04 2022

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania


title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. [HiC]

first: Rachel

last: McCord

summary: We investigate the 3D genome alterations in early and late passage progeria (HGPS) using two different patient cell lines and two different healthy adult cell lines.

overall_design: Primary skin fibroblast cells from Progeria patients and healthy parents of progeria patients were grown to confluency and crosslinked with 1% formaldehyde.  Hi-C was performed according to protocol specified and paired end reads were sequenced and mapped to the genome to create chromosome contact matrices.

first: Rebeca

last: San Martin

first: Priyojit

last: Das

first: Jacob

middle: T

last: Sanders

first: Ashtyn

last: Hill

middle: P


title: Oncofusion driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1 [ChIP-seq]

summary: Ewing Sarcoma (EwS) is a highly aggressive tumor of bone and soft tissues that mostly affects children and adolescents. The pathognomonic oncofusion EWSR1-ETS (EWS-FLI1/EWSR1-ERG) transcription factors drive EwS by orchestrating an oncogenic transcription program through de novo enhancers. Pharmacological targeting of these oncofusions has been challenged by unstructured prion-like domains and common DNA binding motifs in the EWSR1 and ETS protein, respectively. Alternatively, identification and characterization of mediators and downstream targets of EWS-FLI1 dependent or independent function could offer novel therapeutic options. By integrative analysis of thousands of transcriptome datasets representing pan-cancer cell lines, primary cancer, metastasis, and normal tissues, we have identified a 32 gene signature (ESS32) that could stratify EwS from pan-cancer. Of the ESS32 (Ewing Sarcoma Specific 32), LOXHD1 - coding for a stereociliary protein was the most exquisite gene expressed in EwS. CRISPR-Cas9 mediated deletion or silencing of EWS-FLI1 bound upstream de novo enhancer elements in EwS cells led to the loss of LOXHD1 expression and altered the EWS-FLI1, MYC, and HIF1 pathway genes, resulting in decreased proliferation and invasion in vitro and in vivo. These observations open up new avenues for developing LOXHD1-targeted drugs or cellular therapies for this deadly disease.

overall_design: Histone mark occupancy analysis using ChIP-seq analysis in RD-ES and SK-N-MC cell lines

first: Qu

last: Deng

first: Ram

last: Natesan


title: PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma

first: Zhenyu

last: Xuan


title: PRC2 Heterogeneity Drives Tumor Growth in Medulloblastoma [mouse]

overall_design: Total RNAs were extracted from mouse medulloblastoma samples with different Eed genotypes .  Gene expression profiles were examined uisng RNA-seq.

first: Jiaqing

last: Yi

first: Jiang

last: Wu


title: The metabolic regulator USF1 is involved in the control of affective behaviour in mice

status: Public on May 27 2022

city: Vienna

first: Spyridon

last: Sideromenos

address: Schwarzspanierstrasse 17

department: Center for Physiology and Pharmacology

country: Austria

institute: Medical University of Vienna

summary: Epidemiological studies indicate a bidirectional association between metabolic disturbances, including obesity and related pathological states, and mood disorders, most prominently major depression. However, the biological mechanisms mediating the comorbid relationship between the deranged metabolic and mood states remain incompletely understood.   Here we tested the hypothesis that the enhanced activation of brown fat tissue (BAT), known to beneficially regulate obesity and accompanying dysfunctional metabolic states is also paralleled by an alteration of affective behaviour. We used upstream stimulatory factor 1 (USF1) knock-out mice as a genetic model of constitutively activated BAT with a positive cardiometabolic profile and find a reduction of depression- and anxiety-like behaviour associated with USF1 deficiency. Surgical removal of interscapular BAT did not impact the behavioural phenotype of USF1 KO mice which was not accompanied by alterations of neural progenitor cell proliferation, differentiation or survival in the hippocampal dentate gyrus. RNAseq analysis characterized the molecular signature of USF1 deficiency in the hippocampus and revealed a significant increase in the expression of several members of the X-linked lymphocyte-regulated (xlr) genes, including xlr3b and xlr4b, implicated in the regulation of dendritic branching, dendritic spine number and morphology. These molecular changes were accompanied by morphological alterations in hippocampal neurons, manifested reduced dendritic length and complexity.  Collectively these data suggest that the metabolic regulator USF1 is involved in the control of affective behaviour in mice and that this modulation of mood states is unrelated to USF1-dependent BAT activation, but instead associates with structural changes in the brain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in hippocampal tissue of Wild-Type and USF-1 KO mice

first: Spyros

first: Maria

last: Nikou

first: Barbara

last: Czuczu

first: Nikolas

last: Thalheimer

first: Anna

last: Gundacker

first: Orsolya

last: Horvath

first: Laura

last: Rico

first: Marco

last: Niello

first: Timo

last: Partonen

first: Daniela

last: Pollak


title: Effect of circRNA on barrier function and the potential value as a biomarker in sepsis

status: Public on May 28 2022

first: Haiyan

last: Liao

state: Beijing

address: 168 Litang Road Changping District, Beijing, China

institute: Tsinghua University

summary:
Sepsis is one of the main causes of death in critically ill patients with high morbidity and mortality. Circular RNAs (CircRNAs) is aberrantly expressed in many diseases and exhibit roles. However, the expression profiles and functions of circRNAs in sepsis have not yet been fully understood.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells at the same time point.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for lipopolysaccharide (LPS) induced sepsis  human umbilical vein endothelial cells (HUVECs)  and normal HUVECs.


title: Real-time quantitative PCR analysis of gene expression in human colon cancer cells treated with cottonseed-derived gossypol

city: New Orleans

first: Heping

last: Cao

state: LA

address: 1100 Robert E. Lee Blvd

department: Southern Regional Research Center

institute: USDA-ARS

summary: Relative mRNA levels of 55 genes were evaluated with the SYBR Green qPCR assays after gossypol treatment for 8 h.

overall_design: Human colon cancer cells (COLO 225) were purchased from ATCC. The  cells in triplicate were treated with various concentrations of gossypol for 8 h. RNA isolation and cDNA synthesis were performed as described previously. Relative mRNA levels were evaluated with the SYBR Green qPCR assays using Bio-Rad reagents. BCL2 mRNA was selected as the internal reference for qPCR analysis for this cell type. 1% DMSO treatment was the sample control. The 2-ΔCT and 2-ΔΔCT method of relative quantification was used to determine the fold change in expression.

first: Cao

last: Heping


title: Gene activation guided by nascent RNA-bound transcriptional factors

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

summary:
Purpose: To identify differential expressed genes after Narta activation
Methods: cell lines with gene of interest  inserted with TriTag were activated by Narta  and then collected for RNA sequencing at 48 hpf (hours post Narta activation)
Results: We found 1 and 2 (overlapped) up-regulated genes in HSPB8 and LMNA respectivelly at 48 hpf  (FDR < 0.05, log2 fold change > 2)
Conclusions: Narta is an activation system with high specificity

overall_design: comparison of tanscriptome between control and activation group at 48 hpf

last: Cheng

first: Ying

last: Liang


title: The human ion channel TRPM2 modulates migration and invasion in neuroblastoma through regulation of integrin expression

city: Hershey

first: Fernanda

last: Festa

address: 500 University Dr BMR C7846

department: Pediatrics

institute: Penn State University

summary: Transient receptor potential channel TRPM2 is highly expressed in many cancers and involved in regulation of key physiological processes including mitochondrial function, bioenergetics, and oxidative stress. In Stage 4 non-MYCN amplified neuroblastoma patients, high TRPM2 expression is associated with worse outcome. Here, neuroblastoma cells with high TRPM2 expression demonstrated increased migration and invasion capability. RNA sequencing, RT-qPCR, and Western blotting demonstrated that the mechanism involved significantly greater expression of integrins α1, αv, β1, and β5 in cells with high TRPM2 expression. Transcription factors HIF-1α, E2F1, and FOXM1, which bind promoter/enhancer regions of these integrins, were increased in cells with high TRPM2 expression. Subcellular fractionation confirmed high levels of α1, αv, and β1 membrane localization and co-immunoprecipitation confirmed the presence of α1β1, αvβ1, and αvβ5 complexes. Inhibitors of α1β1, αvβ1, and αvβ5 complexes significantly reduced migration and invasion in cells highly expressing TRPM2, confirming their functional role. Increased pAktSer473 and pERKThr202/Tyr204, which promote migration through mechanisms including integrin activation, were found in cells highly expressing TRPM2. TRPM2 promotes migration and invasion in neuroblastoma cells highly expressing TRPM2 through modulation of integrins together with enhancing cell survival, negatively affecting patient outcome and providing the rationale for TRPM2 inhibition in anti-neoplastic therapy.

overall_design: Two samples were analyzed in duplicate: SHSY5Y KO+V5 and SHSY5Y KO+M2

first: Lei

last: Bao

first: Iwona

last: Hirschler-Laszkiewicz

first: Kerry

last: Keefer

first: Hong-Gang

last: Wang

first: Joseph

last: Cheung

last: Miller


title: Effect of long-term adaptation of an acetogenic bacterium Clostridium sp. AWRP under acetate stress

status: Public on Jun 26 2022

city: Busan

first: Soo Jae

last: Kwon

address: KIOST, 385, Haeyang-ro, Yeongdo-gu, Busan Metropolitan City, KOREA

institute: KIOST

summary:
Acetate is a simple carboxylic acid that is synthesized in various microorganisms. Although acetate toxicity and tolerance have been studied in many microorganisms, little is known about the effects of exogenous acetate on the cell growth of acetogenic bacteria. In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution under acetate challenge. When compared with the wild-type strain, the acetate-adapted strain displayed a tolerance to acetate up to 10 g L-1 and higher biomass yields in batch cultures, although the metabolite profiles greatly varied depending on culture conditions. Interestingly, genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase, which is crucial to its autotrophic growth on CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed the global change in the gene expression profile of the acetate-adapted strain. Strikingly, most genes involved in CO2-fixing Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated. In addition, we observed that a couple of metabolic pathways associated with dissimilation of nucleosides and carbohydrates were significantly up-regulated in the acetate-adapted strain as well as several amino acid biosynthetic pathways, indicating that the strain might increase its fitness by utilizing organic substrates in response to the down-regulation of carbon fixation. Further investigation into the carbon fixation degeneration of the acetate-adapted strain will provide practical implications in CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation.
The transcriptome profiles of the wild-type Clostridium sp. AWRP and its acetate-tolerant derivative 46T-a were compared.

overall_design: Two strains were cultivated using bioreactors with continous gas flow. The samples were taken at exponential and stationary phases and subjected to transcriptome analysis.

first: HyunSook

last: Lee

first: Joungmin

first: SooJae


title: Effect of methyl jasmonate treatment on rice leaves of wild-type and rice COI mutatns

status: Public on Jun 11 2022

city: Utsunomiya

first: Koji

last: Miyamoto

state: Tochigi

address: 1-1 Toyosatodai

department: Department of Biosciences

institute: Teikyo University

summary: Analysis of leaves of wild-type and rice COI mutants treated with methyl jasmonate (MeJA). Results provide the role of rice COI on response to jasmonic acid.

overall_design: Expression profiling in wild-type and COI mutatns leaves treated with or without 0.5 mM methy jasmonate was analyzed using one-color method with three biological replicates.

first: Hideo

last: Inagaki

first: Hisakazu

last: Yamane


title: Mechanical Unloading of Engineered Human Meniscus Models Under Simulated Microgravity

status: Public on May 20 2022

city: Edmonton

first: Zhiyao

last: Ma

institute: University of Alberta

summary: The aim of this study is to demonstrate that mechanical unloading via SMG will induce a higher osteoarthritic-like gene profile in bioengineered meniscal cartilage from healthy female MFC versus healthy male MFC. This would serve as the molecular basis for early onset of knee osteoarthritis in females

overall_design: Meniscus models were generated from healthy human meniscus fibrochondrocytes (MFC) of 6 males and 6 females seeded onto a type I collagen scaffold and cultured under simulated microgravity (SMG) conditions in rotatory wall vessel bioreactor with static normal gravity as controls. The response to SMG was evaluated by biochemical assays, gene expression, and mechanical testing

first: David

last: LI

first: Ryan

middle: K

last: Chee

first: Melanie

last: Kunze

first: Aillette

last: Mulet-Sierra

first: Mark

last: Sommerfeldt

first: Lindsey

last: Westover

first: Daniel

last: Graft

first: Adetola

last: Adesida


title: Oncofusion driven de novo enhancer assembly promotes malignancy in Ewing sarcoma via aberrant expression of the stereociliary protein LOXHD1 [hypoxia]

first: Irfan

last: Asangani

overall_design: Gene expression analysis in normoxia and hypoxia in control and LOXHD1 enhancer knockdown (eKD1 and eKD2) SKNMC cell lines.

first: Qu

last: Deng

first: Ram

last: Natesan


title: Naturally-aged microglia exhibit phagocytic dysfunction accompanied by gene expression changes reflective of underlying neurologic disease

status: Public on Jun 10 2022

city: Cincinnati

first: Alyssa

last: Thomas

state: Ohio

address: 250 Albert Sabin Way

department: Immunobiology

institute: Cincinnati Children's Hospital Medical Center

summary: Age-associated microglial dysfunction contributes to the accumulation of amyloid-b (Ab) plaques in Alzheimer’s disease. Although several studies have shown age-related declines in the phagocytic capacity of myeloid cells, relatively few have examined phagocytosis of normally aged microglia. Furthermore, much of the existing data on aging microglial function have been generated in accelerated genetic models of Alzheimer’s disease. Here we found that naturally aged microglia phagocytosed less Ab over time. To gain a better understanding of such dysfunction, we assessed differences in gene expression between young and old microglia that either did or did not phagocytose Ab. Young microglia had both phagocytic and neuronal maintenance signatures indicative of normal microglial responses, whereas, old microglia, regardless of phagocytic status, exhibit signs of broad dysfunction reflective of underlying neurologic disease states. We also found downregulation of many phagocytic receptors on old microglia, including TREM2, an Ab phagocytic receptor. TREM2 protein expression was diminished in old microglia and loss of TREM2+ microglia was correlated with impaired Ab uptake, suggesting a mechanism for phagocytic dysfunction in old microglia. Combined, our work reveals that normally aged microglia have broad changes in gene expression, including defects in Ab phagocytosis that likely underlies the progression to neurologic disease.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of young and aged microglia that have and have not phagocytosed amyloid beta

first: Maria

last: Lehn

first: Edith

middle: M

last: Janssen

last: Hildeman

first: Claire

last: Chougnet


title: CD11c+ myeloid cell exosomes regulate intestinal inflammation

city: Salt Lake City

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

summary: Intercellular communication is critical for maintaining homeostasis in mammalian organ systems, including the gastrointestinal (GI) tract. Exosomes are small nanoscale lipid extracellular vesicles that mediate communication between a wide variety of cell types. Notably, the roles played by immune cell exosomes in regulating homeostasis and inflammation in the GI tract are largely uncharacterized. By generating novel mouse strains deficient in cell-specific exosome production, we demonstrate that specific disruption of exosome signaling via the deletion of Rab27a in myeloid cells exacerbates colitis, which is reversed through administration of dendritic cell (DC)-derived exosomes. Profiling small, non-coding RNAs within exosomes from colonic tissues revealed a distinct subset of microRNAs (miRNAs) carried by both colon- and DC-derived exosomes. Among the DC-enriched exosomal miRNAs, miR-146a was transferred from gut immune cells to myeloid and T cells through a Rab27-dependent mechanism to regulate macrophage phenotypes during colitis. Upon assessing clinical samples, RAB27A was also expressed at lower levels in a cohort of ulcerative colitis patients. Together, this work reveals an exosome-mediated regulatory mechanism underlying gut inflammation, and paves the way for potential use of exosomes containing miRNA cargo as a novel therapeutic for inflammatory bowel disease.

overall_design: miRNA-sequencing of colon explant EVs and bone marrow dendritic cell EVs

first: Kaylyn

last: Bauer