title: Single-cell bottlenecks and dead-ends during glioma premalignancy

first: Kevin

middle: A.

last: Janes

address: Box 800759 Health System

department: Department of Biomedical Engineering

summary: Glial brain tumors are composed of diverse cell types whose origins are just beginning to be unraveled.  The final cellular composition of a fulminant glioma could be very different from the regulatory adaptations needed, or attempted, to establish the tumor ecosystem from an originating mutant.  Using a genetically engineered mouse model that combines inducible Nf1?Trp53 loss with lineage tracing, we measured bulk and subpopulation transcriptomes during early gliomagenesis in oligodendrocyte precursor cells (OPCs).  Large populations or small pools of labeled OPCs were isolated directly from their niches by laser-capture microdissection and profiled by RNA sequencing.  The bulk transcriptomes of frank gliomas had relatively little in common with age-matched OPCs, but we detected generic adaptations to tumor-suppressor loss shortly after induced Nf1?Trp53 deletion.  The diversity of OPCs targeted for deletion was uncovered by a stochasticprofiling fluctuation analysis of 10-cell measurements that revealed a spectrum of stem-progenitor, proneural, and mesenchymal states.  Months after Nf1?Trp53 deletion, bulk differences were difficult to detect reliably, as the 10-cell data indicated several mixed-lineage states, including those not previously documented in glioma that likely marked dead-end niches.  In addition, we identified a group of mutant cells devoid of conventional lineage markers, which abundantly expressed key effectors of nonsense-mediated decay and homologydependent DNA repair.  In Trp53-null OPCs driven to proliferate by Nf1 deletion, ?productive? (i.e., tumorigenic) niche formation and resolution of replication stress stand out as predicted bottlenecks for glioma initiation.

overall_design: Bulk samples and 10-cell samples of oligodendrocyte precursor cells from mouse brain tissue were collected by laser capture microdissection.

middle: A

first: Matthew

last: Sutcliffe


title: Profiling of melocular mechanism of SOX17 effect during hematopoieisis of human ES cells

status: Public on Jan 06 2021

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

country: USA

institute: University of Wisconsin

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Here, using SOX17-knockout and SOX17-inducible human PSCs, paired with cell biology and molecular profiling studies, we revealed that SOX17 represents a critical upstream factor that is required for activation and linkage of HOXA and arterial programs in hemogenic endothelium and establishing definitive lympho-myeloid hematopoiesis. These SOX17 effects are mediated through activation of NOTCH, CDX2 and retinoic acid signaling.  Collectively, these findings are important to design strategies for direct HSC fate programming from hPSCs.

overall_design: For ATAC-seq, DNA profiles of overexpression of SOX17 and non-overexpressed SOX17 were prepared in duplicate.  For ChIP-seq, SOX17 and IgG antibodies in PHE.  For RNA-seq, mRNA profiles of overexpression of SOX17 and non-overexpressed SOX17 were generated by sequencing, in triplicate.

first: Ho

middle: S

last: Jung

first: Peng

last: Liu

first: Irene

middle: M

last: Ong

middle: I


title: Occupancy of Integrator subunits on DNA after hyperosmotic stress

status: Public on Jan 04 2021

city: New Haven

first: Nicolle

last: Rosa-Mercado

state: CT

address: 295 Congress Avenue

department: Molecular Biophysics and Biochemistry

institute: Yale University

summary: ChIP-seq was performed using antibodies against Integrator subunits 11 or 3 to measure the occupancy of these proteins on DNA after hyperosmotic stress.

overall_design: HEK-293T cells were treated with 80 mM KCl to induce hyperosmotic stress. Cells were crosslinked during the last 10 minutes of stress inductions using 1% formaldehyde. Chromatin immunoprecipitations were performed as described in Bieberstein et al. 2014 using 25 µL of anti-Int11 antibody or 30 µL of anti-Int3 antibody.

first: Joshua

middle: T

last: Zimmer

first: Maria

last: Apostolidi

first: Jesse

last: Rinehart

middle: D

last: Simon

first: Joan

last: Steitz


title: Synergistic action of estradiol and PGE2 on endometrial transcriptome in vivo resembles pregnancy effects better than estradiol alone

city: Olsztyn

first: Piotr

last: Kaczynski

address: Tuwima 10

department: Department of Hormonal Action Mechanisms

country: Poland

institute: Institute of Animal Reproduction and Food Research of Polish Academy of Sciences

summary: Porcine endometrial transcriptome has been profiled using expression micrarrays to determine the effect of PGE2 administered together with E2 on global gene expression profile.

overall_design: Crossbred gilts at the same age and genetic background, after second natural estrous cycle underwent estrus synchronization according to the procedure. On day 8-9 of the third natural estrous cycle animals underwent surgery during which both uterine horns has been cannulated. Animals were then divided in 2 groups. In the control group, each horn received intrauterine Placebo (vehicle; 5 mL of 1% v/v ethanol saline) infusions. In the experimental group randomly selected horns within each gilt received hormonal infusions: PGE2 (200 µg/infusion) with E2 (33.3 µg/infusion). The contralateral horn received vehicle infusions. Treatments were administered every 4 h for 24 h on days 11-12 after the onset of estrus.

first: Agnieszka

last: Waclawik

first: Stefan

last: Bauersachs


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [CUT&RUN]

city: Chapel Hill

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

summary: Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovarian cancer. SCCOHT tumors have inactivating mutations in SMARCA4 (BRG1), one of the two mutually exclusive ATPases of the SWI/SNF chromatin remodeling complex. To address the role that BRG1 loss plays in SCCOHT tumorigenesis, we performed integrative multi-omic analyses in a SCCOHT cell line +/- BRG1 re-expression. BRG1 re-expression induced a gene and protein signature similar to an epithelial cell and gained chromatin accessibility sites correlated with other epithelial originating TCGA tumors. Gained chromatin accessibility and BRG1 recruited sites were strongly enriched for transcription factor binding motifs of AP-1 family members. Furthermore, AP-1 motifs were enriched at the promoters of highly upregulated epithelial genes. Using a dominant negative AP-1 cell line, we found that both AP-1 DNA binding activity and BRG1 re-expression are necessary for the gene and protein expression of epithelial genes. Our study demonstrates that the BRG1 re-expression drives an epithelial-like gene and protein signature in SCCOHT cells that depends upon by AP-1 activity.

overall_design: Two biological replicates of BIN67 and SCCOHT-1 cells were co-transfected (FuGENE 6, Promega #E269A) with either control (pCMV-neo or pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2 µg/ml puromycin for 3 days and then harvested for CUT&RUN analysis

first: Krystal

last: Orlando

first: Bernard

middle: E

last: Weissman

middle: R


title: The effect of CDDP and iron chelators for squamous cell carcinoma

status: Public on Jan 05 2021

city: Okayama

first: Toshiaki

last: Ohara

state: Okayama

address: 2-5-1 Shikata-cho

department: Pathology & Experimental Medicine

country: Japan

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

summary: The aim is to find a cue about iron controlled cancer therapy.

overall_design: Total 8 Samples, 8 groups, 6 Comparisons. (test vs. control)


title: Mapping the transcriptional response to auxin in differentiated endodermal cells

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

summary: Here we show that differntiated endodermal cells have a distinct transcriptional response to auxin treatment. We perform a time serie of 10µM NAA treatment and sample at t=0, 2, 4, 8, 16 and 24hrs after NAA treatment. For the time series we compared roots of the solitairy root 1 (slr-1) mutant to the CASP1::shy2-2/slr-1 double mutant. We also provide RNAseq data of slr-1, CASP1::shy2-2 and CASP1::shy2-2/slr-1 at t=0

overall_design: Examination of transcriptional changes in slr-1  and CASP1::shy2-2/slr-1 mutants after NAA (10µM) treatment.

first: Robertas

last: Ursache

first: Emanuel

last: Schmid-Siegert

first: Sandra

last: Calderon Copete

first: Niko

last: Geldner

first: Joop

last: Vermeer


title: RNA Polymerase II binding profiles of HEK-293T cells exposed to hyperosmotic stress

first: Nicolle

last: Rosa-Mercado

summary: Anti-Pol II ChIP-seq was performed to assess the redistribution of RNA Polymerase (Pol) II after hyperosmotic stress.

overall_design: HEK-293T cells were treated with 80 mM KCl to induce hyperosmotic stress. Cells were crosslinked during the last 10 minutes of stress inductions using 1% formaldehyde. Chromatin immunoprecipitations were performed as described in Bieberstein et al. 2014 using 30 µL of anti-Pol II antibody (Cell Signaling D8L4Y).

last: Zimmer

last: Apostolidi

first: Matthew


title: Stepwise chromatin and transcriptional acquisition of an intraepithelial lymphocyte program

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

summary: Mesenteric lymph node (mLN) T cells undergo tissue adaptation upon migrating to intestinal lamina propria (LP) and intraepithelial (IE) compartments, ensuring appropriate balance between tolerance and resistance. By combining mouse genetics with single-cell and chromatin analyses, we addressed the molecular imprinting of gut epithelium on T cells. Transcriptionally, conventional and regulatory (Treg) CD4+ T cells from mLN, LP and IE segregate based on the gut layer they occupy; trajectory analysis suggests a stepwise loss of CD4-programming and acquisition of an intraepithelial profile. Treg fate–mapping coupled with RNA– and ATAC–sequencing revealed that the Treg program shuts down before an intraepithelial program becomes fully accessible at the epithelium. Ablation of CD4 lineage–defining transcription factor ThPOK results in premature acquisition of an IEL profile by mLN Tregs, partially recapitulating epithelium imprinting. Thus, coordinated replacement of circulating lymphocyte program with site–specific transcriptional and chromatin changes is necessary for tissue imprinting.

overall_design:
Atac-Seq: ATAC-Seq was performed on 5,000-40,000 FACS-purified cells from 2-9 mice. In brief, cells were lysed in lysis buffer for 1 minute and transposed with Tagment DNA Enzyme 1 (Illumina) for 30 minutes. DNA was cleaned up using a MinElute DNA purification Kit (Qiagen), followed by barcoding and library preparation by the Nextera DNA Library preparation kit (Illumina) according to manufacturer’s guidelines and sequenced on an Illumina Illumina NextSeq 500.

ChIP-Seq: Cells were fixed in 1% formaldehyde for 20min, quenched with 0.15M glycine and washed in PBS. 2x106 were then sorted and lysed for 30min at 4ºC. Cells were then sonicated for 22 minutes at 30 seconds on/off using the Bioruptor sonicator (Diagenode) and spun down. 10% was frozen for input, the remaining 90% was incubated with anti-ThPOK antibody bound to goat anti-rabbit M280 magnetic beads (Invitrogen) overnight at 4ºC prior to washing with RIPA buffer and overnight decrosslinking at 65ºC. DNA was then eluted off beads into TE buffer and, along with input, purified using the Zymogen DNA clean & concentrator kit. DNA was sequenced using NextSeq2500. To obtain Tregs, Foxp3RFP reporter mice were injected with IL-2/aIL-2 complex as previously described for 3 consecutive days for Treg expansion. CD4+ T cells were isolated from the spleen and mLNs and sorted as Thy1+TCRb+CD4+CD8a–RFP+.

RNA-Seq: Sorted cells (300-800) were lysed in TCL buffer (Qiagen, 1031576) supplemented with 1% βmercaptoethanol. RNA was isolated using RNAClean XP beads (Agentcourt, A63987), reversibly transcribed, and amplified. Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 550.

Single Cell Sequencing: Lymphocytes were sorted, counted for viability and immediately subjected to library preparation. The scRNA-Seq library was prepared using the 10x Single Cell Chromium system, according to the manufacturer’s instructions at the Genomics core of Rockefeller University and was sequenced on an Illumina NextSeq 550 to a minimum sequencing depth of 50,000 reads per cell using read lengths of 26 bp read 1, 8 bp i7 index, 98 bp read 2.

Please note that the processed data generated from both replicates is linked to the corresponding rep1 sample (with the lower GSM accn number).

first: Mariya

last: London

first: Angelina

last: Bilate

middle: B

first: Daniel

last: Mucida


title: TT-TL-seq reveals transcriptional profiles that accompany DoG induction after hyperosmotic stress.

summary: TT-TimeLapse-seq was used to investigate the nascent transcription profiles that accompany the induction of downstream-of-gene (DoG) containing transcripts in human cell lines. Data from HEK-293T cells exposed to hyperosmotic stress and cells transfected with siRNAs against Integrator subunit 11 are included.

overall_design: Samples were treated with 80 mM KCl for 1 hour or with siRNAs for 48 hours. During the last 5 minutes of treatment, nascent RNAs were labeled with 1 mM s4U. After RNA extractions using TRIzol, 4% RNA from Drosophila S2 cells was added to each sample. TT-TL-seq preparations were done as described in Schofield et al. 2018.

first: Joshua

first: Maria

first: Jesse

last: Rinehart

last: Simon

first: Joan

last: Steitz


title: Transcriptome Analysis of Differential Genes Related to Anthocyanin Synthesis in Red and Green Walnut

city: Zhengzhou

first: wu

last: guoliang

address: Nongye Road num 63

country: China

institute: Henan Agricultural University

summary: We report the application of high-throughput analysis of genes related to anthocyanin synthesis in red and green walnuts based on transcriptome sequencing technology. By obtaining a sequence of more than 3 billion bases from mRNA, we found genes that are differentially expressed with anthocyanin synthesis in 4 leaf growth stages and 3 peel growth stages of red and green walnuts.

overall_design: Transcriptome Analysis of Differential Genes in Four Growth Stages of Red and Green Walnut Leaves and Three Growth Stages in the Peel under the Same Growth State

first: Guoliang

last: Wu

first: Yongzhou

last: Li


title: Single-cell transcriptome and 3D genome atlas of the developing mouse brain

status: Public on Jan 07 2021

city: Cambridge

first: Longzhi

last: Tan

state: MA

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Integrated differential DNA methylation and gene expression of formalin-fixed paraffin-embedded uveal melanoma specimens identifies genes associated with early metastasis and poor prognosis

city: OSLO

first: Agate

last: Noer

address: Kirkeveien 166

department: Ophthalmology

country: Norway

institute: Oslo University Hospital, Ullevaal

type:
Methylation profiling by array
Expression profiling by array


title: Genom-wide expression study of cMoP and iMoP from murine bone marrow

city: Freiburg

first: Anne

last: Loesslein

address: Breisacherstr. 115

department: CCI

country: Germany

institute: Universität Freiburg

summary: We defined iMoP as a new precursor subset in murine bone marrow. The aim of this expression analysis was the identification of transcriptional differences between iMoP and their progeny cMoP.

overall_design: cMoP and iMoP were collected from the bone marrow of 2 pooled Cx3cr1+/GFP C57Bl/6 mice by fluorescence-activated cell sorting. For each subset, two replicates were purified from 2 independent litters.

last: Lösslein

first: Philipp

last: Henneke


title: Expression data from rat NSCs co-cultured with green fluorescence protein (GFP)-ectodermal mesenchymal stem cells (EMSCs) versus mono-cultured rat NSCs

status: Public on Jan 03 2021

city: Zhenjiang

first: Wenwen

last: Deng

state: Jiangsu

address: 301 Xuefu Road, Jingkou District

department: School of Pharmacy

institute: Jiangsu University

summary:
Rat NSCs  were isolated from developing whole brian of the SD rat embryos at day 13.5. In the NSC/GFP-EMSC co-culture system, the NSCs showed significantly enhanced neuronal differentiation rather than astrocytic commitment, in comparison with the mono-cultured NSCs.
In order to reveal the gene expression profiles of NSCs under these two diffferent culture conditions, we used microassrays to examine the global programme of gene expression of NSCs under these two diffferent culture conditions.

overall_design: These NSCs were co-cultured with GFP-EMSCs or mono-cultured for 14 days. The co-cultured NSCs were the expeimental group, while the mono-cultured ones were the control.


title: Evolution of conserved noncoding sequences (CNS) in Arabidopsis thaliana

city: East Lansing

first: Alan

last: Yocca

state: MI

address: 1066 Bogue St. Room A317

institute: Michigan State University

summary: We report ATAC-seq for several A. thaliana accessions in healthy leaf tissue. As part of an investigation into the evolution of conserved noncoding sequences, our goal was to identify overlaps between regions of accessible chromatin and CNS. Manuscript in review. Biorxiv preprint doi: https://doi.org/10.1101/727669

overall_design: ATAC-seq in diverse A. thaliana accessions

first: Zefu

last: Lu

first: Robert

middle: J

last: Schmitz


title: Diploid chromatin conformation capture (Dip-C) of single cells from the developing visual cortex of dark-reared and control mice

summary: To study the effect of sensory experience on 3D genome structure of the mouse brain, we performed Dip-C on 1,692 single cells from the visual cortex of dark-reared and control mice at different ages throughout the first postnatal month.

overall_design: We performed Dip-C on 1,692 single cells and analyzed them with dip-c and hickit packages.


title: Multi-Omics Analysis of Brain Metastasis Outcomes Following Craniotomy

city: Indianapolis

first: Jing

last: Su

state: Indiana

address: 410 W. 10th Street, HITS 3000

department: Department of Biostatistics

institute: Indiana University School of Medicine

summary:
Purpose: To reveal multi-omics features and disease subtypes associated with brain metastasis outcomes following craniotomy
Methods: We executed a single institution retrospective collection of brain metastasis from patients who were diagnosed with lung, breast, and other primary tumors. The brain metastatic samples were sent for RNA sequencing, proteomic and metabolomic analysis of brain metastasis. The primary outcome was distant brain failure after definitive therapies that included craniotomy resection and radiation to surgical bed. Novel prognostic subtypes were discovered using transcriptomic data and sparse non-negative matrix factorization.
Results: We discovered two molecular subtypes showing statistically significant differential prognosis irrespective of tumor subtype. The median survival time of the good and the poor prognostic subtypes were 7.89 and 42.27 months, respectively. Further integrated characterization and analysis of these two distinctive prognostic subtypes using transcriptomic, proteomic, and metabolomic molecular profiles of patients identified key pathways and metabolites. The analysis suggested that immune microenvironment landscape as well as proliferation and migration signaling pathways may be responsible to the observed survival difference.
Conclusions: A multi-omics approach to characterization of brain metastasis provides an opportunity to identify clinically impactful biomarkers and associated prognostic subtypes and generate provocative integrative understanding of disease.

first: J

first: Jimmy

last: Ruiz


title: Gene exprssion profile of gestational trophoblastic neoplasms

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

summary: Gene expressions obtained from the total RNA sequencing of 2 choriocarcinomas, 4 epithelioid trophoblastic tumors, and 4 placental site trophoblastic tumors were evaluated for differential gene expression, pathway alteration, fusion gene, infiltrating immune cell type, and PD-L1 expression level, and mutation analysis was performed using the RNA sequencing data.

overall_design:
Gene expression profiling using total RNA sequenicng in 10 gestational trophoblastic neoplasms (GTN) including 2 choriocarcinomas (CC), 4 epithelioid trophoblastic tumors (ETT), and 4 placental site trophoblastic tumors (PSTT).
submitter states "We will submit the raw data to dbGap because of patient privacy concerns"

first: EunJeong

last: Cho

first: Sung-Min

last: Chun

first: ChangOhk

first: Kyu-Rae

last: Kim


title: Spatiotemporal Analysis of Human Intestinal Development at Single Cell Resolution - Spatial Transcriptomics

city: Oxford

first: Alison

last: Simmons

address: John Radcliffe Hospital/Headley Way

department: The MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

summary: Development of the human intestine is not well understood. Here we link single-cell RNA sequencing and spatial transcriptomics to characterize intestinal morphogenesis through time. We identify 101 cell states including novel epithelial and mesenchymal progenitor populations and programs linked to key morphogenetic milestones. We describe principles of crypt-villus axis formation; neural, vascular, mesenchymal morphogenesis and immune population of the developing gut. We identify the differentiation hierarchies of developing fibroblast and myofibroblast subtypes and describe new functions for these including as vascular niche cells.  We pinpoint the origins of Peyer’s patches and gut-associated lymphoid tissue (GALT) and describe location specific immune programs. We use our resource to present an unbiased analysis of morphogen gradients that direct sequential waves of cellular differentiation and define cells and locations linked to rare developmental intestinal disorders.

overall_design: Colon and terminal ileum tissue sections from adult and fetal (12 and 19 post-conceptual weeks) were subject to spatial transcriptomics analysis

first: David

last: Fawkner-Corbett

first: Agne

last: Antanaviciute

first: Kaushal

last: Parikh

first: Marta

last: Jagielowicz

first: Ana

last: Gerós

first: Tarun

last: Gupta

first: Neil

last: Ashley

first: Hashem

last: Koohy


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [COV434_RNA-seq]

status: Public on Jan 01 2021

first: Bernard

middle: E.

last: Weissman

state: NC

address: 450 West Drive

department: Pathology and Laboratory Medicine

institute: University of North Carolina at Chapel Hill

summary: COV434 cells +/- BRG1 re-expression - RNA-seq

overall_design: Three biological replicates of COV434 cells were co-transfected (FuGENE 6, Promega #E269A) with control (pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 10-6.25:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 2-3 µg/ml puromycin for 3 days and then cell pellets were harvested for RNA-seq.

first: Krystal

last: Orlando

first: Jesse

last: Raab


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [CCOHT1_RNA-seq]

summary: SCCOHT-1 cells +/- BRG1 re-expression - RNA-seq

overall_design: Three biological replicates of SCCOHT-1 cells were co-transfected (FuGENE 6, Promega #E269A) with control (pCDNA3-neo) or BRG1 (PBJ5-BRG1) plasmids at a 6.25:1 ratio to a plasmid containing puromycin resistance (pBABE-puro). Twenty-four hours after transfection, cells were placed on 0.5 µg/ml puromycin for 3 days and then cell pellets were harvested for RNA-seq.


title: Epithelial miR-141 regulates IL-13-induced airway mucus production  [miRNA-seq]

city: San Francisco

first: Srilaxmi

last: Nerella

state: CA

address: HSE1355A, 513 Parnassus ave

department: Department of Medicine

institute: UCSF

type: Non-coding RNA profiling by high throughput sequencing

summary: We performed small RNA sequencing (TruSeq) of gene expression on bronchial cells from human bronchial epithelial brushings from 16 independent subjects whose samples were classified as either healthy controls (with no asthma or lung disease) or steroid-naive asthmatics (subjects with asthma not using inhaled corticosteroids (ICS) for 6 weeks before enrollment that were studied at baseline ('Steroid-naive asthma - Baseline') or after 8 weeks of treatment with budesonide, 200 μg twice a day, ('Steroid-naive asthma - Post-ICS treatment')). The goal was to assess abundance of miRNAs in all the samples collectively.

overall_design: Small RNA sequencing (TruSeq) was performed on a total of 20 samples of epithelial brushings from subjects (n=16); healthy controls (n=7), 2 subjects of which had a repeated sample, and from steroid-naive asthmatic subjects (n=9), all of which have baseline samples before the initiation of 8 weeks of treatment using inhaled budesonide (200 micrograms twice per day) included while 2 of those 9 subjects have additional samples included after the budesonide treatment. The goal was to assess abundance of various miRNAs in all the samples collectively.

first: Prescott

middle: G

last: Woodruff

first: Sana

last: Siddiqui


title: Effects of in utero and lactational exposure to low-dose neonicotinoid clothianidin on the gene expression profiles of the ovary in 3 weeks old mice

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
Neonicotinoid pesticides which were developed newly since the 1980s are chemically similar to nicotine. Prenatal and lactational exposure to neonicotinoid pesticides has been shown to cause reproductive toxicity in males, but not yet in female mice.
We investigated effects of in utero and lactational exposure to a neonicotinoid pesticide, clothianidin (CLO) on gene expression profiles of the ovary in 3 weeks old mice.

overall_design: Pregnant mice were administrated 65 mg/kg/day of CLO or vehicle (1%DMSO) from gestational day 1.5 to postnatal day 21 of age of the litter.

first: Sayaka

last: Kitauchi

first: Nobuhiko

last: Hoshi

first: Yoshiaki

last: Tabuchi


title: Impact of short- and long-term extracellular acidosis on gene expression of tumors in vitro and in vivo

status: Public on Jan 02 2021

city: Halle/S.

first: Oliver

last: Thews

address: Magdeburger Str. 6

department: Institute of Physiology

institute: University of Halle

summary:
Purpose: The aim of the study was to analyze the impact of acidic pHe on gene expression in two experimental tumor lines of the rat in vitro and in vivo. The results of short-term incubation (24 h) were compared to chronically acidosis-adapted cells (5 weeks).
Methods: Gene expression was analyzed in AT1 prostate and Walker-256 mammary carcinoma of the rat. Cells were exposed to pH 7.4 and 6.6 for 24 h or 5 weeks. Experimental tumors were implanted in rats and control tumors were compared to tumors in which the glycolytic metabolism was intensified.
Results: The analyses revealed that 147 genes were uniformly regulated in both cell lines (in vitro) and 79 genes in both experimental tumors after 24 h at low pH. 265 genes were uniformly regulated during long- and short-term exposure to low pH.

overall_design:
Exposure of two different tumor cell lines to pH 7.4 and 6.6 in cell culture and solid experimental tumors.
Adaptation of one tumor cell line to pH 6.6 of 11 passages (=5 weeks).

first: Mandy

last: Rauschner

first: Anne

last: Riemann

first: Sarah

last: Reime

first: Alexander

last: Nolze


title: Gene expression signatures to the radiation attenuated Schistosome Vaccine

city: Salvador

first: Leonardo

middle: Paiva

last: Farias

state: Bahia

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz-Fiocruz

summary: The radiation-attenuated (RA) cercarial vaccine is still the best model eliciting high protection levels, although the immune mechanisms have not yet been fully characterized. In order to identify genes and pathways underlying protection we investigated patterns of gene expression in PBMC and skin draining Lymph Nodes (LN) from mice using two exposure comparisons: vaccination with 500 attenuated cercariae versus infection with 500 normal cercariae; one versus three doses. Vaccinated mice were challenged with 120 normal parasites. Integration of PBMC and LN data from the infected group revealed early up-regulation of pathways associated with Th2 skewing and polarization of IgG antibody profiles. Additionally, hemostasis pathways were downregulated in infected mice, correlating with platelet reduction, potentially a mechanism to assist parasite migration through capillary beds. Conversely, up regulation of such mechanisms after vaccination may explain parasite blockade in the lungs. In contrast, a single exposure to attenuated parasites revealed early establishment of a Th1 bias (signaling of IL-1, IFN-γ; and Leishmania infection). Genes encoding chemokines and their receptors were more prominent in vaccinated mice, indicating an enhanced capacity for inflammation, potentially augmenting the inhibition of intravascular migration. Increasing the vaccinations from one to three did not dramatically elevate protection, but there was a clear shift towards antibody-mediated effectors. However, elements of the Th1 bias were still evident. Notable features after three vaccinations were markers of cytotoxicity (including IL-6 and NK cells) together with growth factors and their receptors (FGFR/VEGF/EGF) and the apoptosis pathway. Indeed, there is evidence for the development of anergy after three vaccinations, borne out by the limited responses detected in samples after challenge. We infer that persistence of a Th1 response puts a limit on expression of antibody-mediated mechanisms. This feature may explain the failure of multiple doses to drive protection towards sterile immunity. We suggest that the secretions of lung stage parasites would make a novel cohort of antigens for testing in protection experiments.

overall_design: Mice were vaccinated with one dose (V1) or three doses (V3) of 500 attenuated cercariae, or infected (VC) with 500 normal ceracriae. Then, gene expression in mice PBMC was measured in a time course manner at days 7 (7dpi) and 17 (17dpi) after vacination or infection. In addition, the vaccine groups (V1 and V3) and a challenge control (Chc) were challenge with 120 normal cercariae and PBMC gene expression was measured 7 days post-challenge (7dpc). PBMC from control (C) non-treated mice was used to generate the baseline of gene expression. Four to five independent biological replicates were assessed per group (V1, V3, VC and Chc) per time point, and 16 biological replicates from control group (C) were used to generate the baseline of expression for PBMC microarray analysis. All biological replicate consisted of a pool of PBMCs (containing equal amounts of total RNA) from three mice. Data is derived from one independent experiment.  Gene expression in mice skin draining lymph nodes (sdLN) was measured in an independent assay 5 days (5dpi) after one vaccine dose (V1) or three vaccine doses (V3) of 500 attenuated cercariae, or after infection (VC) with 500 normal ceracriae. Three independent biological replicates were assessed per group for sdLN microarray analysis, in which each biological replicate consisted of a pool of sdLNs from three mice. Data is derived from one independent experiment.

middle: P

first: Juliana

last: Vitoriano-Souza

first: Lucas

last: Cardozo

last: Gama

first: Giulliana

last: Almeida

first: Sergio

last: Verjovski-Almeida

first: Helder

last: Nakaya

first: Luciana

middle: C

last: Leite


title: Coordination of Mediator Complex and Histone Acetyltransferase CBP/p300 in Transcriptional Regulation [RNA-seq]

city: Beijing

first: xinjian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: CBP/p300 is one group of histone acetyltransferases, which catalyze the acetylation of histone lysine in order to loosen the chromatin structure and promote transcription. The multiple-subunits complex MEDIATOR is important for the transcription initiation through participating in the assembly of transcriptional pre-initiation complex (PIC). Our study identified that MEDIATOR interacts with HAC1 and HAC5, and participate in the regulation of transcription coordinately, thereby regulating the development of Arabidopsis. Besides, MEDIATOR, HAC1, and HAC5 may be organized together by the LLPS to regulate transcription.

overall_design: Examination of the mRNA expression of wild type and hac1hac5, med8med25 mutants.

first: Xin


title: Coordination of Mediator Complex and Histone Acetyltransferase CBP/p300 in Transcriptional Regulation


title: Coordination of Mediator Complex and Histone Acetyltransferase CBP/p300 in Transcriptional Regulation [ChIP-seq]

overall_design: Examination of H3Ac levels in wild type and hac1hac5, med8med25 mutants.


title: Transcriptomic profiles of Streptococcus mutans UA159 grown in the presence or absence of mucins or mucin glycans

first: Katharina

last: Ribbeck

state: Massachusetts

address: 77 Massachusetts Ave

department: Biological Engineering

institute: Massachusetts Institute of Technology

summary: We use high-throughput sequencing to profile the response of oral commensal pathogen Streptococcus mutans to mucins protein polymers (human MUC5B mucins) and soluble mucin glycans (human MUC5B glycans and porcine MUC5AC glycans). We find that mucins and their glycans alter the regulation of dozens of S. mutans genes, specifically downregulating competence-associated quorum sensing genes. The transcriptional responses induced by MUC5B mucins, MUC5B glycans, and MUC5AC glycans are highly correlated.

overall_design: Examination of differential gene expression in Streptococcus mutans UA159 in response to MUC5B mucins, MUC5B glycans in solution, and MUC5AC glycans in solution

first: Caroline

last: Werlang


title: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [A427_RNA-seq]

city: Chapel Hill

first: Bernard

last: Weissman

summary: A427 (NSCLC - Non-Small Cell Lung Cancer) cells +/- BRG1 re-expression - RNA-seq

overall_design: AA427 pINDUCER20-BRG1 cell lines were generated by lentiviral infection of the pINDUCER20-BRG1 construct (Gateway Cloning) and subsequently selected in G418 containing medium +selecting in 400 µg/ml G418 to create a mass population. Following selection, the mass population was single cell cloned and screened for BRG1 expression after DOX (1 µg/µl) induction for 48 hours by western blotting. Clones that were able to induce BRG1 were pooled to create a mass pool. A427 pIND20-BRG1 cells were induced with DOX (1 µg/µl) for 48 hours and cell pellets were harvested for RNA-seq.

first: Krystal

last: Orlando

first: Jesse

last: Raab

first: Vinh

last: Nguyen

first: Rayvon

last: Moore


title: Genom-wide expression study of cMoP and monocytes from murine bone marrow compared to their differentiated descendants

first: Anne

last: Loesslein

summary: cMoP and monocytes differ in their potential to form multinucleated giant cells (MGC) in reaction to mycobacterial ligands. The aim of this expression analysis was the identification of transcriptional differences undelying the mechanisms of MGC formation.

overall_design: cMoP and monocytes were collected from the bone marrow of 3 pooled Cx3cr1+/GFP C57Bl/6 mice by fluorescence-activated cell sorting. The subsets were collected directly or cultured either with M-CSF alone or additionally with lipomannan from M. smegmatis. For each subset, two replicates were purified from 2 independent litters.

last: Lösslein

first: Philipp

last: Henneke


title: White Button Mushroom (Agaricus bisporus) Disrupts Androgen Receptor Signaling in Human Prostate Cancer Cells (LNCaP)

city: Duarte

first: Hsun

middle: Teresa

last: Ku

address: 1500 E. Duarte Road

department: Translational Research and Cellular Therapeutics

institute: City of Hope

summary:
Purpose: To evalute the antagonistic effects of White Button Mushroom/WBM extract on AR signaling in human prostate cance cells.
Methods: LNCaP cells were treated with 1 nM DHT, with or without WBM extract (3 μL/mL), for 48h, in triplicates, and total RNA was isolated and sequenced.
Results: We identified 155 up-regulated genes (Fold-change ≥ 2, p<0.05) versus 185 down-regulated genes (Fold-change ≤ 0.5, p<0.05).
Conclusion: White Button Mushroom suppressed androgen respsonive genens and cell cycle division genes Collectively, these results suggest that WBM extract affects prostate cancer by interrupting AR-dependent cell cycle division and DNA replication.

first: Shiuan

last: Chen

first: Xiaoqiang

last: Wang


title: Single cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL [PDX_ETPs_scRNA-seq]

city: Boston

first: Birgit

last: Knoechel

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

summary: Lineage plasticity and stemness have been invoked as the cause of therapy resistance in cancer, as these flexible states allow cancer cells to de-differentiate and alter their dependencies. We investigated such resistance mechanisms in relapsed / refractory early T-cell progenitor acute lymphoblastic leukemia carrying activating NOTCH1 mutations, by full-length single cell RNA sequencing of malignant and microenvironmental cells. We identified two highly distinct stem-like states that critically differ in their cell-cycle and oncogenic signaling. Fast-cycling stem-like leukemia cells demonstrate Notch activation and are effectively eliminated in patients by Notch inhibition, while slow cycling stem-like cells are Notch-independent but rather rely on PI3K signaling, likely explaining the poor efficacy of Notch inhibition in this disease. Remarkably, we find that both stem-like states can differentiate into a more mature leukemia state with prominent immune-modulatory functions, including high expression of the LGALS9 checkpoint molecule. These cells promote an immunosuppressive leukemia ecosystem with clonal accumulation of dysfunctional CD8+ T cells that express HAVCR2, the cognate receptor for LGALS9. Our study identifies complex interactions between signaling programs, cellular plasticity and immune programs that characterize T-ALL and illustrates the multi-dimensionality of tumor heterogeneity. In this scenario, combination therapies targeting diverse oncogenic states and the immune ecosystem appear most promising to successfully eliminate tumor cells that escape treatment through co-existing transcriptional programs.

overall_design: Single cell expression profiles of seven ETP-ALL PDX models and five T-ALL PDX models.

first: Praveen

last: Anand

first: Amy

last: Guillaumet-Adkins

first: Valeriya

last: Dimitrova

first: Huiyoung

last: Yun

first: Yotam

last: Drier

first: Noori

last: Sotudeh

first: Anna

last: Rogers

first: Madhu

last: Ouseph

first: Monica

last: Nair

first: Sayalee

last: Potdar

first: Randi

last: Isenhart

first: Jake

middle: A

last: Kloeber

first: Tushara

last: Vijaykumar

first: Leili

last: Niu

first: Tiffaney

last: Vincent

first: Guangwu

last: Guo

first: Julia

last: Frede

first: Marian

middle: H

last: Harris

first: Andrew

last: Place

first: Lewis

last: Silverman

first: David

last: Teachey

last: Lane

first: Daniel

last: DeAngelo

first: Jon

last: Aster

first: Bradley

last: Bernstein

first: Jens

last: Lohr


title: Kap1 ChIP-seq Analysis of Wild Type(WT) and Dcaf11 overexpresion(OE) ESCs

city: Shanghai

first: Yixin

last: Huang

address: Siping Road

institute: Tongji University

summary: ESC Kap1 profiles of WT and Dcaf11 OE were generated by deep sequencing, using Illumina GAIIx.

first: Rongrong

last: Le

first: Yanping

last: Zhang


title: GFRAL-expressing Neurons Suppress Food Intake via Aversive Pathways

city: Ann Arbor

first: Martin

last: Myers Jr

address: 1000 Wall St

institute: University of Michigan

summary: The TGFβ cytokine family member, GDF15, reduces food intake and body weight and represents a potential treatment for obesity.  Because the brain stem-restricted expression pattern of its receptor, GDNF Family Receptor α–like (GFRAL), presents an exciting opportunity to understand mechanisms of action for area postrema neurons in food intake, we generated GfralCre and conditional GfralCreERT mice to visualize and manipulate GFRAL neurons. We found infection or pathophysiologic states (rather than meal ingestion) stimulate GFRAL neurons. TRAP-Seq analysis of GFRAL neurons revealed their expression of a wide range of neurotransmitters and neuropeptides. Artificially activating GfralCre-expressing neurons inhibited feeding, decreased gastric emptying, and promoted a conditioned taste aversion (CTA). GFRAL neurons most strongly innervate the parabrachial nucleus (PBN), where they target CGRP-expressing (CGRPPBN) neurons.  Silencing CGRPPBN neurons abrogated the aversive and anorexic effects of GDF-15. These findings suggest that GFRAL neurons link non-meal-associated, pathophysiologic signals to suppress nutrient uptake and absorption.

overall_design: 5 bead and 5 paired supernatant samples

first: Alan

last: Rupp

last: Myers

first: Randy

last: Seeley


title: Protective role of HMGB1 in keratinocytes in skin inflammation

city: Meguro-ku

first: Hideyuki

last: Yanai

state: Tokyo

address: Komaba 4-6-1

institute: University of Tokyo

summary:
Dysregulation and abnormal expression of inflammatory mediators by keratinocytes promote the pathogenesis of the skin inflammation such as allergic contact dermatitis (ACD). High-mobility group box 1 (HMGB1) protein, a prototypical damage-associated molecular pattern (DAMP), that is expressed in the nucleus but released extracellularly upon inflammation has gained attention as an accelerator for skin inflammation. However, in vivo role of HMGB1 in ACD and other skin disorders remains to be elusive. In this study, we generated conditional knockout mice in which HMGB1 is deleted in keratinocytes and examined its role in skin inflammation models including 2,4-dinitrofluorobenezene (DNFB)-induced ACD. Unexpectedly, deletion of HMGB1 in keratinocytes exacerbated skin inflammation, accompanied by increased ear thickening.
Elevated mRNA expression of interleukin-24 (IL-24), a known cytokine which promotes the pathogenesis of ACD, was also observed in the skin lesion of the mice. In accordance with above observations, both constitutive and IL-4-induced Il24 mRNA expression in vitro was augmented in hmgb1-deficient primary mouse keratinocytes and keratinocyte cell line PAM212 cells. Chromatin immunoprecipitation (ChIP) analysis revealed increased binding of tri-methyl histone H3 (lys4) (H3K4me3), a well-known histone mark for transcription active genes, to the promoter region of the Il24 gene in the hmgb1-deficient cells. ChIP-sequencing data also showed broad changes of H3K4me3 mark in the cells. Thus, HMGB1 in the nucleus dictates histone modifications. In conclusion, our study demonstrated a key role for HMGB1 in keratinocytes in the maintenance of chromatin modification status to protect from exuberant skin inflammation.

overall_design: We analyzed keratinocytes from WT and K5-HMGB1 male mice. Keratinocytes were left untreated or treated with rIL-4 for 12 hours. Total RNA was extracted and analyzed by the Affymetrix Clariom S Array, Mouse. Array data was processed by Affymetrix Exon Array Computational Tool. No technical replicates were performed.

first: Naoyuki

last: Senda


title: ULI-NChIP-seq Analysis of Wild Type(WT) and Dcaf11 overexpresion(OE) ESCs [ChIP-seq]

summary: Our study demonstrates that Dcaf11 plays important roles in telomere elongation in early embryos and ESCs through activating Zscan4.

overall_design: ESC histone profiles of WT and Dcaf11 OEs were generated by deep sequencing, using Illumina GAIIx.


title: Treg Cell TGF-β1 Regulates Distinct Checkpoints Governing Allergy and Autoimmunity

first: Talal

last: Chatila

address: 1 Blackfan Circle

department: Division of Immunology

institute: Boston Children’s Hospital

summary: The mechanisms by which regulatory T (Treg) cells differentially control allergic and  autoimmune responses remain unclear. We show that Treg cells in food allergy (FA) have  decreased expression of transforming growth factor beta 1 (TGF-b1) due to IL-4 and  STAT6-dependent inhibition of Tgfb1 transcription. These changes were modelled by  Treg cell-specific Tgfb1 monoallelic inactivation, which induced allergic dysregulation by  impairing microbiota-dependent ROR-gt+ Treg cell differentiation. This dysregulation was  rescued by treatment with Clostridiales species, which upregulated Tgfb1 expression in  Treg cells. Biallelic deficiency precipitated fatal autoimmunity, with intense autoantibody  production and dysregulated T follicular helper and B cell responses. These results  identify a privileged role for Treg cell-derived TGF-b1 in regulating allergy and  autoimmunity at distinct checkpoints in a Tgfb1 gene dose and microbiota-dependent  manner.

overall_design: We employed FA-prone mice that carry a gain of function  mutation in the IL-4Ra chain gene (Il4raF709) to investigate the mechanisms by which FA  develops in these mice. Epigenetic analysis of mesenteric lymph node Treg cells isolated from Il4raF709 mice using Assay for  Transposase-Accessible Chromatin using sequencing (ATAC-seq) revealed decreased  access at the Tgfb1 locus, which was reversed by deletion of Stat6.

first: Chatila

last: Talal


title: Asah2 represses the p53-Hmox1 axis to protect myeloid-derived suppressive cells from ferroptosis

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

summary: Myeloid-derived suppressor cells (MDSCs) are immune suppressive cells that massively accumulate under pathological conditions to suppress T cell immune response. Dysregulated cell death contributes to MDSC accumulation, but the molecular mechanism underlying this cell death dysregulation is not fully understood. We report here that neutral ceramidase (N-acylsphingosine amidohydrolase, ASAH2) is highly expressed in tumor-infiltrating MDSCs in colon carcinoma and acts as a MDSC survival factor. To target ASAH2, we performed molecular docking based on human ASAH2 protein structure. Enzymatic inhibition analysis of identified hits determined NC06 as an ASAH2 inhibitor. Chemical and NMR analysis determined NC06 as 7-chloro-2-(3-chloroanilino)pyrano[3,4-e][1,3]oxazine-4,5-dione. NC06 inhibits ceramidase activity with IC50 of 10.16-25.91 M for human ASAH2 and 18.6-30.2 uM for mouse Asah2 proteins. NC06 induces MDSC death in a dose-dependent manner and inhibition of ferroptosis decreased NC06-induced MDSC death. NC06 increases glutathione synthesis and decrease lipid ROS to suppress ferroptosis in MDSCs. Gene expression profiling identified p53 pathway as the Asah2 target in MDSCs. Inhibition of Asah2 increased p53 protein stability to up-regulate Hmox1 expression to suppress lipid ROS production to suppress ferroptosis in MDSCs. NC06 therapy increases MDSC death and reduces MDSC accumulation in tumor-bearing mice, resulting in increased activation of tumor-infiltrating CTLs and suppression of tumor growth in vivo. Our data indicate that ASAH2 protects MDSCs from ferroptosis through destabilizing p53 protein to suppress the p53 pathway in MDSCs in the tumor microenvironment. Targeting ASAH2 with NC06 to induce MDSC ferroptosis is potentially an effective therapy to suppress MDSC accumulation in cancer immunotherapy.

overall_design: MDSC-like J774M cells were treated with neutral ceramidase inhibitor NC06 and then analyzed for gene expression changes

first: Huabin

last: Zhu

first: John

last: Klement

first: Chunwan

last: Lu

first: Priscilla

middle: S

last: Redd

first: Dafeng

last: Yang

first: Alyssa

last: Smith

first: Dakota

last: Poschel

first: Juan

last: Zou

first: Ding

first: Peng

last: Wang

last: Ostrov

first: Nicolas

last: Coant

first: Yusuf

last: Hannun

first: Aaron

last: Colby

first: Mark

middle: W

last: Grinstaff


title: Expression data from mouse wild type and Trp53-/- Cdkn2a-/- mammary epithelial basal cells

city: Stanford

first: Michael

middle: F.

last: Clarke

address: 265 Campus Dr

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: Three well-known tumor suppressors, TRP53, p16INK4a, and p19ARF (p16INK4a and p19ARF are both coded by the gene Cdkn2a) have been connected to the limiting of stem cell self-renewal and proliferation in some tissues. Here we deposit RNA microarray expression data of sorted mouse Krt14-cre mT/mG Trp53f/f Cdkn2a-/- mammary epithelial basal cells and their wild type control cells (Krt14-cre mT/mG).

overall_design: Basal cells of freshly isolated mammary epithelial cells from 8-14-week-old virgin female mice were sorted by FACS before analyzed by RNA microarray.

first: Linda

last: van Weele

middle: F


title: A single cell view of the transcriptome during lateral root initiation

city: Seattle

first: Christine

last: Queitsch

state: WA

address: 3720 15th Ave NE, Foege Hall

department: Genome Sciences

institute: University of Washington

summary: Plant root architecture is a major determinant of fitness, and is under constant modification in response to favorable and unfavorable environmental stimuli. Beyond impacts on the primary root, the environment can also alter the position, spacing, density, and length of secondary or lateral roots. Lateral root development is among the best-studied developmental processes in Arabidopsis thaliana, yet the earliest steps of organogenesis remain elusive. Among the challenges faced in capturing these early molecular events is the fact that this process occurs in a small number of cells with unpredictable timing. The advent of single-cell sequencing affords the opportunity to isolate cells undergoing this fate transition and examine their transcriptomes independently. Using this approach, we successfully captured the transcriptomes of lateral root primordia and discovered many previously unreported upregulated genes. To further study this process, we developed a method to selectively repress genes in the xylem pole pericycle cells where lateral roots originate. We found that expression of several of the upregulated genes was required for normal root development. In addition, we discovered a subpopulation of cells in the endodermal cell file that respond to lateral root initiation, further highlighting the benefits of the single cell approach.

overall_design:
Using the 10X single cell transcriptomics platform, we isolated cells from Arabidopsis roots to study lateral root formation. To stimulate lateral root formation, Arabidopsis seedlings were rotated 90 degrees and cells from the root bend were captured 08 hours, and 20 hours after the stimulus. Cells from a no bend control, 00 hours, were collected as well.

The RDS files (included on Jan 25, 2021) are the processed Monocle 3 cell data structures, which can be loaded directly into R, to help those trying to reproduce analysis results or those who want to use the UMAPs for further analysis.

first: Josh

middle: T

last: Cuperus

first: Jennifer

middle: L

last: Nemhauser


title: Genome-wide DNA methylation and expression patterns of microRNAs in relation to breast cancer subtypes among American women of African and European ancestry [methylation array]

city: Buffalo

first: Yao

last: Song

state: NY

address: Carlton House - A349, Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

type: Methylation profiling by genome tiling array

summary: We reAggressive high-grade, estrogen receptor negative (ER-) breast cancer is more common among American women of African ancestry (AA) than those of European ancestry (EA). The reasons remain largely unknown. Epigenetic mechanisms, particularly DNA methylation and altered microRNA (miRNA) expression, may contribute to racial differences in breast cancer. However, the characterization of this epigenetic modification in relation to ER+ and ER- breast cancer, and its functional role in the regulation of miRNA expression remains to be investigated, especially among high risk AA women. In this study, we evaluated methylation patterns of miRNA genes and their effect on miRNA expression in breast tumors from both AA and EA women. The genome-wide methylation screen identified a number of differentially methylated loci (DML) between ER- and ER+ tumor subtypes in tumors from both races, or specific to AA or EA women. Integrated analysis of DNA methylation and miRNA expression further identified certain DMLs whose methylation levels were significantly correlated with the expression of relevant miRNAs, such as multiple CpGs highly correlated with miR-190b and miR-135b. In summary, our results suggest that DNA methylation patterns in miRNA encoding genes differ between breast cancers according to cancer subtype and race, and that this altered methylation may affect miRNA expression. Further pathway analysis identified their potential role in modulating cancer-related key biological processes. These findings shed light on the epigenetic regulation of miRNA expression and provide insights into the relations of clinical-relevant miRNAs to their target genes and to serve as potential preventative and therapeutic targets. port the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.

overall_design: Geome-wide methylation assay on HM450 Bead Chip using genomic DNA extracted from flash frozen human breast tumor tissue

first: Zhihong

last: Gong

first: Jianhong

last: Chen

first: Jie

first: Song

last: Liu

last: Ambrosone

last: Higgins


title: Genome-wide DNA methylation and expression patterns of microRNAs in relation to breast cancer subtypes among American women of African and European ancestry [miRNA-seq]

overall_design: Integrative analysis of miRNA expression and methylation

last: Wang


title: Genome-wide DNA methylation and expression patterns of microRNAs in relation to breast cancer subtypes among American women of African and European ancestry

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

overall_design: Refer to individual Series


title: Autosomal dominant VCP hypomorph mutation impairs disaggregation of PHF-tau

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

summary: RNA-seq analysis of wild-type, heterozygous, and homozygous mice with p.Asp395Gly mutation in VCP

overall_design: Anterior cortex RNA profiles of 15 month old WT, DG/+, and DG/DG mice

first: Nabil

last: Darwich


title: Cystic fibrosis Airway primary epithelial cells in air-liquid interrface culture show abnormal inflammation and lipid metabolism related RNA expresssion compared to non-CF

city: Rotterdam

first: Rutger

last: Brouwer

address: Wytemaweg 80

department: Center for Biomics

country: Netherlands

institute: Erasmus MC

summary: A deficiency in cystic fibrosis transmembrane conductance regulator (CFTR) function in cystic fibrosis (CF) leads to chronic lung disease. However, the molecular mechanisms are not well understood and therapies that can help all patients remain elusive. CF is associated with abnormalities in fatty acids, ceramides and cholesterol, therefore we examined the impact of CFTR deficiency on lipid metabolism and pro-inflammatory signaling in airway epithelium using mass spectrometric, protein array and RNAseq analyses. We observed a striking imbalance in fatty acid and ceramide metabolism, associated with chronic oxidative stress under basal conditions in CF mouse lung  and well differentiated bronchial epithelial cell cultures of CFTR knock out pig and CF patients. Cell autonomous features of all three CF models included high ratios of ω-6- to ω-3-polyunsaturated fatty acids and long- to very long- chain ceramide species (LCC/VLCC). The anti-oxidants glutathione (GSH) and deferoxamine partially corrected the lipid profile indicating that oxidative stress may promote the lipid abnormalities. CFTR-targeted modulators reduced the lipid imbalance and apparent oxidative stress, confirming the CFTR dependence of lipid ratios. RNA sequencing and protein array analysis revealed higher expression and shedding of cytokines and growth factors from CF epithelial cells compared to non-CF cells, consistent with sterile inflammation and tissue remodeling under basal conditions. Treatment with antioxidants or CFTR modulators that mimic the approved combination therapies, Orkambi and Trikafta, did not suppress the inflammatory phenotype. These results suggest that anti-inflammatory therapies may provide additional benefit for CF patients taking CFTR modulator drugs.

overall_design: Here we report analysis of nine samples, three  of Cf patient (BCF000174), homozygous for F508del CFTR, compared to two non-CF in triplicate each (P21, P11, ErasmusMC, Rotterdam, compared pairwise)

first: B

last: Scholte

first: R

first: J

last: Hanrahan


title: Temporally integrated single cell RNA sequencing analysis of controlled and natural DENV-1 infections

city: Syracuse

first: Adam

middle: Tully

last: Waickman

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: Controlled dengue human challenge studies present a unique opportunity to address many longstanding questions in the field of flavivirus biology. These fundamental questions include defining the early immunological signatures of infection, the host/environmental factors that impact disease severity, and the role of preexisting immunity on the development of symptomatic viral infection. However, while several controlled dengue human challenge studies have been performed and appear to clinically recapitulate may features of mild natural DENV infection, limited data are available on how the immunological and transcriptional response elicited by these attenuated challenge viruses compares to the profile associated with a natural, unattenuated DENV infection. To bridge this knowledge gap, we performed scRNAseq analysis on longitudinally collected PBMC samples obtained from 3 individuals (8 time points per subject) enrolled in the SUNY/WRAIR DENV-1 controlled human challenge study. In addition, 3 time points (two acute infection time points, one control time point) from two individuals experiencing a natural DENV-1 infection were analyzed and computationally integrated with the challenge model dataset. This temporally integrated dataset contains a total of 171,208 cells and 22 statistically distinct populations corresponding to all major anticipated leukocyte subsets. While all identified cell populations demonstrated significant and consistant perturbations in their transcriptional profile in response to either natural or experimental DENV infection, conventional monocytes respond most robustly to infection across all subjects and study groups from an unbiased transcriptional perspective. Using these data, core sets of genes that were consistently induced by either natural or experimental DENV were identified, and the overlap between the two arms of the study assessed.

overall_design: scRNAseq (10xGenomics Single Cell 5' v2 Reagents Kit) analysis was performed on unfractionated PBMC obtained from three DHIM-1 subjects (8 time points per subject), and two subjects with natural DENV-1 infections (3 time points per subject).

first: Jeffrey

last: Currier


title: High-fiber diet mitigates maternal obesity-induced cognitive and social dysfunction in the offspring via gut-brain axis

city: Shenzhen

first: Jin

last: Xin

state: Guangdong

address: Beishan road

institute: BGI

summary: We sought to examine whether directly dietary fiber application to offspring could also reverse the behavioral and neurobiological deficits characteristic of MHFD offspring. RNA-sequencing (RNA-seq) on mice hippocampus were performed in order to identify the key biological processes and pathways regulated by dietary fiber.

overall_design: 8 CD-C mice,8 CD-F mice,8 FD-C mice, 8 FFD-C mice, 9 HFD-C mice, 8 HFD-F mice

first: Xiaoning

first: Xin

last: Jin


title: tRNA-seq and YAMAT-seq profiling the expressions of tRNA-derived fragments and tRNAs in plants

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

department: College of Life Sciences

institute: Tianjin Normal University

summary: Here, we apply tRNA-seq and YAMAT-seq to profile the expressions of tRFs and tRNAs in plants. We provide a high-quality expression atlas of tRFs and tRNAs in Arabidopsis and rice, and uncover complex tRF population and the dynamic expressions of tRNA genes in plants.

sample_organism:
Arabidopsis thaliana
Glycine max
Hordeum vulgare
Setaria italica
Sorghum bicolor
Triticum aestivum
Zea mays

overall_design: We constructed tRNA-seq and YAMAT-seq libraries from various plants. The tRNA-seq and YAMAT-seq methods were described previously (Cozen et al. 2015 Nat Methods; Zheng et al. 2015 Nat Methods; Shigematsu et al. Nucleic Acids Res.).

first: Weijiang

last: Luan


title: Regnase-1 overexpression/knockdown effect on primary mouse articular chondrocytes

city: Gwangju

first: Jeong-In

last: Yang

address: 123 Cheomdangwagiro

institute: Gwangju Institute of Science and Technology

summary:
Gene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expression mouse Regnase-1 or recombinant adenovirus expressing mouse small hairpin RNA of Regnase-1.
In this study, we have attempted to explore the effects of Regnase-1 overexpression or knockdown on mouse transcriptome and have identified numerous genes which are involved in osteoarthritis pathogenesis.

overall_design: Primary mouse articular chondrocytes were isolated from mouse femoral condyles and tibial plateaus cartilage tissue and were infected with null(control) or recombinant adenovirus expressing Regnase-1 (Ad-Regnase-1) or small hairpin RNA of Regnase-1 (Ad-shRegnase-1) for 36 hours. At 36 hours post-infection, total RNA was extracted and subjected to microarray analysis.

first: Jang-Soo

last: Chun


title: Translatome of aged mouse NEBD – stage oocytes determined using a new polysomal profiling method

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

summary: We provide complete translatome of mouse oocytes from aged females after the breakdown of nuclear envelope (NEBD). RNAseq of polysomal and non-polysomal RNA was determined by using a novel approach combining polysomal fractionation of 200 NEBD-staged oocytes in small SW55Ti centrifugation tubes in the absence of any external spike and qRT-PCR analysis of ribosomal RNA in collected fractions. We compared these data to the translatome of same stage oocytes from young females (GSE121358). We report that genome-wide translatome profiling reveals considerable numbers of transcripts that are differentially translated in oocytes obtained from aged compared to young females. Additionally, we show the majority of aberrantly translated mRNAs in older oocytes have roles associated with cell cycle regulation. Indeed, we demonstrate the differential translation rates of four specific maternal age related transcripts (Sgk1, Castor1, Aire and Eg5) are associated with distinct localization patterns around the newly forming meiotic spindle.

overall_design: 3 replicates of RNAseq datasets from polysomal (P) and non-polysomal (NP) fractions

first: Tomas

last: Masek

first: Andrej

last: Susor

first: Edgar

last: del Llano

first: Michal

last: Kubelka

first: Martin

last: Pospisek


title: Epithelial response to IFN-γ promotes SARS-CoV-2 infection

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

summary: SARS-CoV-2, the agent causing COVID-19, invades epithelial cells, including those of the respiratory and gastrointestinal mucosa, using angiotensin-converting enzyme-2 (ACE2) as a receptor. Subsequent inflammation can promote rapid virus clearance. However, severe cases of COVID-19 are characterized by an inefficient immune response that fails to clear infection.  Using primary epithelial organoids from the colon, we explored how IFN-γ, a central antiviral mediator elevated in COVID-19, affects differentiation, ACE2 expression, and infectivity with SARS-CoV-2. ACE2 is mainly expressed by surface enterocytes of mouse and human colon. Inducing enterocyte differentiation in organoid culture resulted in increased ACE2 production. IFN-γ treatment promoted differentiation into mature KRT20+ enterocytes expressing high levels of ACE2. Similarly, IFN-γ promoted expression of ACE2 in human primary lung cells. IFN-y driven differentiation increased susceptibility to SARS-CoV-2 infection and electron microscopy revealed that the virus can efficiently complete its full life cycle in IFN-γ-treated enterocytes. Furthermore, infection-induced epithelial interferon signaling promoted enterocyte maturation and enhanced ACE2 expression. We reveal a mechanism by which IFN-y-driven inflammatory responses may increase susceptibility to SARS-CoV-2 and promote its replication.

overall_design: Microarray experiments were performed as dual-color hybridizations on custom whole genome human 8 × 60K multipack microarrays (Agilent-048908). To compensate for dye-specific effects, a dye-reversal color-swap was applied.

first: Michael

last: Sigal

first: Julian

last: Heuberger

first: Jakob

last: Trimpert

first: Nikolaus

last: Osterrieder

first: Thomas

last: Meyer


title: Exon microarray expression data of CSMN from ALS and control mice at P30

city: Chicago

first: Hande

last: Ozdinler

state: Illinois

address: 4141 N. Lawndale Ave

department: Neurology

institute: Northwestern University

summary: Brain is complex and heterogeneous.  Even though numerous independent studies indicate cortical hyperexcitability as a potential contributor to amyotrophic lateral sclerosis (ALS) pathology, the mechanisms that are responsible for upper motor neuron (UMN) vulnerability remain elusive. In an effort to reveal the electrophysiological determinants of corticospinal motor neuron (CSMN, a.k.a UMN in mice) vulnerability, we investigated the motor cortex of hSOD1G93A mice at P30 (postnatal day 30), ¬a presymptomatic time point. Glutamate uncaging by laser scanning photostimulation revealed altered dynamics especially within the inhibitory circuitry and more specifically in L2/3 of the cortex, whereas the excitatory microcircuits were unchanged. Observed microcircuitry changes were specific to CSMN in the motor column. Electrophysiological evaluation of the intrinsic properties in response to the microcircuit changes, as well as the exon microarray expression profiles of CSMN isolated from hSOD1G93A and healthy mice at P30 revealed the presence of a very dynamic set of events, ultimately directed to establish, maintain and retain the balance at this early stage. In addition, the expression profile of key voltage gated potassium and sodium channel subunits as well as of the inhibitory GABA receptor subunits and modulatory proteins began to suggest the challenges CSMN face at this early stage. Since neurodegeneration is initiated when neurons can no longer maintain balance, the complex cellular events that occur at this critical time point help reveal how CSMN try cope with challenges of disease manifestation. This information is critically important for proper modulation of upper motor neurons and for developing effective treatment strategies in the near future.

overall_design:
The exon microarray analyses were performed 3 independent times and the averages of exon readings were determined during data analyses.
*** Raw data are no longer available.

first: P


city: Hannover

first: Janin

last: Bublitz

address: Carl-Neuberg-Str. 1

department: Human Genetics

institute: Medizinische Hochschule Hannover

summary:
CN profiles of microglandular adenosis and adjacent breast cancer
Affymetrix Oncoscan arrays were performed according to the manufacturer's directions on DNA extracted from FFPE-breast tumor tissues.

overall_design: Copy number analysis using Oncoscan (Thermoscientific) arrays was performed for 6 microglandular adenosis and 4 adjacent breast cancers

first: Doris

last: Steinemann

first: Jana

last: van Luttikhuizen

last: Radner

first: Matthias

last: Christgen

first: Hans

last: Kreipe


title: Correlating functional heterogeneity of human dermal fibroblasts with differences in gene expression

city: London

first: Oliver

last: Culley

address: Floor 28, Tower Wing, Guy’s Hospital, Great Maze Pond

department: Centre for Stem Cells and Regenerative Medicine

institute: King’s College London

summary: Recent work has identified markers of fibroblast heterogeneity in human dermis. Transforming growth factor-β1 (TGF-β1) promotes fibroblast-to-myofibroblast differentiation, characterised by the expression of α-smooth muscle actin (α-SMA). Human dermal fibroblasts (hDF), treated with TGF-β1, were assayed for differentiation, proliferation and cell shape using the Operetta imaging system. One donor hDF, derived from female 64-year-old breast skin, expressed decreased levels of α-SMA protein. The gene expression profile of this donor hDF was determined using the Agilent microarray system. Four gene candidates (Asporin, ASPN; C-X-C motif chemokine ligand 1, CXCL1; Insulin-like growth factor 1, IGF1; and Wnt family member 4, WNT4) were chosen based on expression values and validated by TaqMan qPCR. Successful knockdown of IGF1 and WNT4 was achieved using MISSION shRNA-based lentiviral treatment. Fibroblast IGF1 knockdown (shIGF1) increased α-SMA mRNA and protein expression; no effect was seen with fibroblast WNT4 knockdown (shWNT4). Here I have characterised hDF phenotype and gene expression with regard to population heterogeneity. This work highlights the role of IGF-1 signalling on α-SMA expression and dermal fibroblast fate. Targeting IGF-1 signalling could provide therapeutic benefit for skin disorders involving aberrant wound healing and excessive fibrosis.

overall_design: Enzyme-derived, human dermal fibroblasts from four adult donors. Treated with/without TGF-β1 for 12h/24h and used for Agilent one colour microarray.

first: Fiona

middle: M

last: Watt


title: A Light-Inducible Strain for Genome-Wide Histone Turnover Profiling in Neurospora crassa

city: Eugene

first: Eric

middle: U

last: Selker

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

summary: Histones are not statically embedded, but are constantly exchanged outside of DNA replication. This study reports the characterization and validation of a histone turnover reporter strain of Neurospora crassa, and the method employed. This strain utilizes FLAG-tagged histone H3 under the control of a light-inducible promoter. This study also preliminarily explores histone turnover defects at constitutive heterochromatin with the loss of the heterochromatin proteins DIM-2, HDA-1, DIM-5, and HPO.

overall_design: ChIP-seq: We analyzed incorporated FLAG-tagged histone H3 in Neurospora crassa strains in wild-type, ∆dim-2, ∆hda-1, ∆dim-5, and ∆hpo backgrounds by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced.

first: William

middle: K

last: Storck

first: Vincent

last: Bicocca

last: Rountree


title: Enhancer landscape of meningioma

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic


title: Single cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute


title: Enhancer landscape of meningioma [RNA-seq]

summary: Meningiomas are the most common primary intracranial tumor. However, surgical resection and radiation frequently fail to eliminate high grade tumors, leading to significant morbidity and mortality. Predicting which tumors will recur rapidly is critical to effective treatment strategies. To address the prognostic challenges and dearth of therapeutic targets, we interrogated the enhancer landscape of a diverse cohort of meningiomas. Enhancers robustly stratified meningiomas into three biologically distinct groups and identified a subset of tumors with a poor prognosis, independent of histological grading. Integrating enhancer networks with transcriptional profiles revealed unique lineage transcriptional regulators associated with each subgroup. A strong hormonal epidemiologic association is well-characterized in meningiomas, but mechanistic insight remains lacking. We identified differential hormonal regulators that stratified between subgroups, and implicated progesterone receptor in maintaining the super enhancer network of a subset of tumors. Super enhancers marked critical and druggable dependencies across a panel of meningioma models.

overall_design: 13 RNA-seq samples (with matching ChIP-seq samples in GSE139650)

first: Jeremy

last: Rich


title: Single cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL [Patients_TALLs_scRNA-seq]

summary: Lineage plasticity and stemness have been invoked as the cause of therapy resistance in cancer, as these flexible states allow cancer cells to de-differentiate and alter their dependencies. We investigated such resistance mechanisms in relapsed / refractory early T-cell progenitor acute lymphoblastic leukemia carrying activating NOTCH1 mutations, by full-length single cell RNA sequencing of malignant and microenvironmental cells. We identified two highly distinct stem-like states that critically differ in their cell-cycle and oncogenic signaling. Fast-cycling stem-like leukemia cells demonstrate Notch activation and are effectively eliminated in patients by Notch inhibition, while slow cycling stem-like cells are Notch-independent but rather rely on PI3K signaling, likely explaining the poor efficacy of Notch inhibition in this disease. Remarkably, we find that both stem-like states can differentiate into a more mature leukemia state with prominent immune-modulatory functions, including high expression of the LGALS9 checkpoint molecule. These cells promote an immunosuppressive leukemia ecosystem with clonal accumulation of dysfunctional CD8+ T cells that express HAVCR2, the cognate receptor for LGALS9. Our study identifies complex interactions between signaling programs, cellular plasticity and immune programs that characterize T-ALL and illustrates the multi-dimensionality of tumor heterogeneity. In this scenario, combination therapies targeting diverse oncogenic states and the immune ecosystem appear most promising to successfully eliminate tumor cells that escape treatment through co-existing transcriptional programs.

overall_design:
Single cell expression profiles of five patients with relapsed/refractory ETP-ALL and five normal donors.

**Raw data not provided due to patient privacy concerns**

first: Praveen

last: Anand

first: Amy

last: Guillaumet-Adkins

first: Valeriya

last: Dimitrova

first: Huiyoung

last: Yun

first: Yotam

last: Drier

first: Noori

last: Sotudeh

first: Anna

last: Rogers

first: Madhu

last: Ouseph

first: Monica

last: Nair

first: Sayalee

last: Potdar

first: Randi

last: Isenhart

first: Jake

last: Kloeber

first: Tushara

last: Vijaykumar

first: Leili

last: Niu

first: Tiffaney

last: Vincent

first: Guangwu

last: Guo

first: Julia

last: Frede

first: Marian

last: Harris

first: Andrew

middle: E

last: Place

first: Lewis

middle: B

last: Silverman

first: David

last: Teachey

last: Lane

first: Daniel

middle: J

last: DeAngelo

first: Jon

last: Aster

first: Bradley

last: Bernstein

first: Jens

middle: G

last: Lohr


title: Enhancer landscape of meningioma [ChIP-seq]

first: Briana

last: Prager

overall_design: 33 samples from snap frozen meningioma tissue and 3 arachnoid granulation models were analyzed with H3K27ac ChIP-seq with matching input sequencing. 13 samples have matched RNA-seq.

first: Jeremy

last: Rich


title: Single cell RNA-seq Analysis of Wild Type(WT), Dcaf11 knockout(KO) and Dcaf11 knockdown(KD) embryos

city: Shanghai

first: Yixin

last: Huang

address: Siping Road

institute: Tongji University

summary: Telomeres play vital roles in ensuring chromosome stability and are thus closely linked with the onset of aging and human disease. Telomeres undergo extensive lengthening during early embryogenesis through the so-called alternative lengthening of telomere (ALT) mechanism. However, the detailed molecular mechanism of telomere resetting in early embryos remains unknown. Here, we showed that Dcaf11 participates in telomere elongation in early embryos and 2-cell-like embryonic stem cells (ESCs) in a telomerase-independent manner. The deletion of Dcaf11 in embryos and ESCs leads to reduced telomere sister-chromatid exchange (T-SCE) and impairs telomere lengthening. Importantly, Dcaf11-deficient mice exhibit gradual telomere erosion with successive generations, and hematopoietic stem cell (HSC) activity is greatly compromised. Mechanistically, DCAF11 reactivates Zscan4 and facilitates the removal of heterochromatic H3K9me3 at telomere/subtelomere regions through targeting TRIM28 for ubiquitination-mediated degradation. Our study therefore demonstrates that the ALT factor Dcaf11 plays important roles in telomere elongation in early embryos and ESCs.

overall_design:
We tested the transcriptome of ESC of WT and Dcaf11 KD ESC , and late 2-cell (hCG 36hr) embryos from WT and Dcaf11 KO mice  using the Covaris DNA shearing protocol for Smart-seq sequence library generation. We found that the activation of Dux is important but not essential for ZGA, but the silencing and elimination of Dux is strictly necessary for early embryonic development.
Embryos mRNA profiles of WT, Dcaf11 KO and Dcaf11 KD were generated by deep sequencing.

first: Rongrong

last: Le

first: Yanping

last: Zhang


title: miRNA expression profiling of HCT116 cell after dichloroacetate treatment

first: Yu

last: Liang

address: No. 639 Zhizaoju Road, Shanghai 200011, China

institute: Department of Gastroenterology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Using the highly sensitive miRNA array, we screened  out different microRNAs regulated by different concertration of dichloroacetate for different time. Among them 119 microRNAs were obvious
Metabolic abnormality is one of the hallmarks of cancer and has been shown to be involved in chemoresistance. In this context, targeting the abnormal metabolism of cancer cells has been an intense avenue of research aiming at    asphyxiating the tumor   . DCA inhibits the enzymatic activity of Pyruvate Dehydrogenase Kinases (PDK 1 to 4), which are enzymes critical for the activation of the pyruvate dehydrogenase necessary to transform pyruvate into acetyl-CoA, linking the glycolytic metabolism to the citric acid cycle. DCA is primarily used to treat lactic acidosis and hereditary mitochondrial disease, which has been also reported to have anti-cancer effect . However, the mechanism underlying the effect of DCA on CRC treatment remain unsettled. Multiple and complex mechanisms have been described that control the metabolic shift in cancer cells, including microRNAs (miRNAs). MicroRNAs represents a class of small endogenous noncoding RNAs that regulate translation and degradation of mRNAs. Besides controlling the metabolism, miRNAs participate in many more biological processes including cell proliferation, migration, apoptosis    , self-renewal, initiation and development of cancers, and chemoresistance.Here we explore the molecular mechanism involved in regulating glucose metabolism and associated chemotherapy resistance in CRC. By exploiting DCA, pyruvate dehydrogenase kinase (PDK) inhibitor, in CRC cells, trying to elucidate the roles of related miRNAs and thereby outlining a signaling pathway.

overall_design: In this study, HCT116 cell was treated with different contrations of dichloroacetate (5mM, 10mM, 20mM) for different times (12h, 24h,48h)

first: Meng

last: Xiangjun


title: Integrated analysis of lncRNA and mRNA expression profiles in the submandibular glands of DIO mice

status: Public on Dec 31 2020

city: Beijing

first: huimin

last: liu

state: Beijing

address: 38 Xueyuan Rd , Haidian District

department: Peking University Health Science Center

institute: Peking University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Objective: Obesity contributes to the dysfunction of salivary gland. To explore the specific underlying mechanism for obesity-induced hyposalivation, a model for high-fat diet-induced obese (DIO) mice were constructed to analyze long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) expression profiles.
Methods: The DIO group and control group were fed a diet containing 60 kcal% fat and a normal chow diet for 16 weeks respectively. Microarray analyses were performed to detect the expression profiles of lncRNA and mRNA in submandibular gland tissues from control group mice and DIO mice. Gene ontology, kyoto encyclopedia of genes and genomes, protein-protein interaction, coding-non-coding gene co-expression, transcription factors and competing endogenous RNA analyses were performed to examine the function of differential expressed genes.
Results: The microarray identified that 624 lncRNAs, along with 297 mRNAs were differentially expressed. Bioinformatic analyses revealed that “complement and coagulation cascades”, “glutathione metabolism”, “cysteine and methionine metabolism”, and “estrogen signaling pathway” were significantly associated with candidate lncRNAs, transcription factors analysis on candidate lncRNAs reveled several genes such as tribbles pseudokinase 3 may play regulatory roles.
Conclusions: Our results revealed the expression profiles of lncRNAs and mRNAs and provided new insights into the mechanism of obesity-induced hyposalivation using bioinformatic analyses.

overall_design: Huimin, Liu

first: Ruolan

last: Xiang


title: Tumor and gut biopsies from refractory metastatic melanoma patients before and after treatment with fecal microbiota transplantation (FMT) and anti-PD-1 re-induction (Baruch et al, Science 2020)

city: Houston

first: Moran

last: Amit

state: TX

address: 1515 Holcombe Blvd

department: Head & Neck Surgery - Research

institute: The University of Texas MD Anderson Cancer Center

summary: We performed a phase I clinical trial to assess the safety and feasibility of fecal microbiota transplantation (FMT) and re-induction of anti-PD-1 immunotherapy in patients with anti-PD-1-refractory metastatic melanoma. FMT donors were two metastatic melanoma patients who achieved a durable complete response. FMT recipient patients were metastatic melanoma patients who failed at least one anti-PD-1 line of treatment. Each recipient patient received FMT implants from only one of the two donors. FMT was conducted by both colonoscopy and oral ingestion of stool capsules, followed by anti-PD-1 re-treatment (Nivolumab, BMS). Recipient patients underwent pre- and post-treatment stool sampling, tissue biopsy of both gut and tumor, and total body imaging. Clinical responses were observed in three patients, including two partial responses and one complete response.  Notably, treatment with FMT was associated with favorable changes in immune cell infiltrates and gene expression profiles in both the gut lamina propria and the tumor microenvironment.

overall_design: Biopsies from the sigmoid colon (large bowel, gut) and from remote (non-GI) tumor metastasis were collected from available treatment recipient patient (n=9) before initiation of treatment (day 0). Repeated sigmoid colon biopsies were collected on day 31 of treatment. Repeated tumor biopsies, either from the same metastasis as the baseline sample or an adjunct metastasis in a same organ, were collected on day 65. Overall, each patient had two gut biopsies and two tumor biopsies. All biopsies underwent RNA sequencing to assess for potential dynamics of the immune system in response to treatment

first: Erez

middle: N

last: Baruch

first: Katerina

last: Adler

first: Gal

last: Markel


title: Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO [ChIP-seq and CUT&RUN]

city: Nashville

first: Scott

last: Hiebert

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

summary: Transcription factors regulate gene networks controlling normal hematopoiesis and are frequently deregulated in acute myeloid leukemia (AML). Critical to our understanding of the mechanism of cellular transformation by oncogenic transcription factors is the ability to define their direct gene targets. However, gene network cascades can change within minutes to hours, making it difficult to distinguish direct from secondary or compensatory transcriptional changes by traditional methodologies. Utilizing CRISPR-based genome editing, we inserted a degron tag into the endogenous AML1-ETO locus of Kasumi-1 cells, as well as overexpressed a degradable AML1-ETO protein in CD34+ human cord blood cells. This allowed rapid AML1-ETO protein degradation upon addition of a proteolysis targeting chimera (PROTAC). Furthermore, by combining rapid degradation with nascent transcript analysis (PRO-seq), RNA-seq and Cut&Run, we have defined the core AML1-ETO regulatory network. De-repression of this small set of genes set off a cascade of transcriptional events resulting in myeloid differentiation.

overall_design: ChIP-seq and CUT&RUN were used to characterize histone modifications and transcription factor binding in the presence and absence of AML1-ETO in both Kasumi-1 cells and CD34+ HSPC cell cultures

first: Kristy

middle: R

last: Stengel

first: Clare

last: Spielman

first: Monica

last: Bomber


title: Tumor immunological phenotype signature-based high-throughput screening for the discovery of combination immunotherapy compounds

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

summary: Immune checkpoint blockade (ICB) therapy intends to only benefit a fraction of cancer patients, and combination immunotherapy with a compound is a promising treatment to overcome this limitation. Here, a tumor immunological phenotype (TIP) gene signature and high throughput sequencing-based high throughput screening (HTS2) were combined to identify combination immunotherapy compounds. We firstly defined a TIP gene signature, which expression pattern distinguishes “cold” tumors from “hot” tumors, and predicts ICB response in cancer patients. Then, after screening thousands of compounds, we identified that aurora kinase inhibitors, including ENMD-2076 and TAK-901, could reprogram the expression pattern of TIP genes from “cold” tumor to “hot” tumor in triple negative breast cancer (TNBC) cells. The treatment of aurora kinase inhibitors on TNBC cells dramatically up-regulates expression of Th1 type chemokine genes CXCL10 and CXCL11, which promotes effective T cells infiltrating into tumor microenvironment and significantly improves anti-PD-1 efficacy in inhibiting the tumor growth of TNBC in preclinical models. Mechanistically, these aurora kinase inhibitors are mainly through inhibiting AURKA-STAT3 signaling pathway to stimulate the expression of CXCL10 and CXCL11. Our study established a high throughput strategy to discover candidate compounds for combination immunotherapy, and suggested the therapeutic potential of combining aurora kinase inhibitors with checkpoint blockade immunotherapy for the treatment of TNBC.

overall_design: 2×10e5 MDA-MB-231 cells were plated in a 6-well plate for 24 h and then treated with ENMD-2076 at 2.5 or 5 µmol/L (or TAK901 at 1 or 2 µmol/L) for 24 h. 1×10e5 4T1 cells were plated in a 6-well plate for 24 h and then treated with ENMD-2076 at 1.25 or 2.5 µmol/L (or TAK901 at 1 or 2 µmol/L) for 24 h. Cells were harvested, and RNA was isolated using TRIzol (Invitrogen). The libraries were constructed by using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on HiSeq 2500 sequencing system (Illumina).

first: Haiyan

last: Wang

first: Qianyu

first: Dong


title: Prox1 inhibits axon outgrowth during central nervous system development

city: Athens

first: Panagiotis

last: Politis

address: Soranou Efessiou 4

country: Greece

institute: Biomedical Research Foundation, Academy of Athens (BRFAA)

summary: During central nervous system (CNS) development, proper and timely induction of axon elongation is critical for generating functional, mature neurons and neuronal networks. Despite the wealth of information on the action of extracellular cues, little is known about the intrinsic gene regulatory factors that control this developmental decision. Here we report the identification of Prox1, a homeobox transcription factor, as a key player in inhibiting axon elongation. Although Prox1 promotes acquisition of early neuronal identity and is expressed in nascent post-mitotic neurons, it is heavily down-regulated in the majority of terminally differentiated neurons, indicating a regulatory role in delaying axon outgrowth in newly formed neurons. Consistently, we show that Prox1 is sufficient to inhibit neurite extension in neuroblastoma cell lines. Furthermore, shRNA-mediated knock-down of Prox1 in Neuro2A cells induces the extension of neurites. More importantly, Prox1 overexpression suppresses axon elongation in primary neuronal cultures as well as in the developing mouse brain, while Prox1 knock-down promotes axon outgrowth. Mechanistically, RNA-Seq analysis reveals that Prox1 affects critical pathways for neuronal maturation and neurite extension. Interestingly, Prox1 strongly inhibits many components of Ca2+ signaling pathway, an important mediator of axon extension and neuronal maturation. In accordance, Prox1 represses Ca2+ entry upon KCl-mediated depolarization and reduce CREB phosphorylation. These observations suggest that Prox1 acts as a potent suppressor of axon elongation by inhibiting Ca2+ signaling pathway. This action may provide the appropriate time window for nascent neurons to find the correct position in the CNS prior to initiation of axon elongation.

overall_design: 3′mRNA-Seq (Quant-seq) of Neuro2A Prox1 and GFP overexpressing cells (GFP-Tet-On and Prox1-Tet-On Neuro2A cells)

first: V

last: Kaltezioti

first: I

middle: P

last: Foskolou

last: Lavigne

first: M

last: Fousteri

first: P


title: Low responders to endurance training exhibit impaired hypertrophy and divergent biological process responses in skeletal muscle

city: Gold Coast

first: Kevin

middle: John

last: Ashton

state: QLD

address: University Drive

department: Health Sciences & Medicine

country: Australia

institute: Bond University

summary: Divergent skeletal muscle phenotypes result from chronic resistance-type- versus endurance-type contraction, reflecting the principle of training specificity. However, it is unclear whether there is a common set of genetic factors that influence skeletal muscle adaptation to different modes of training. Female rats were obtained from out-bred lines selectively bred from high responders to endurance training (HRT) or low responders to endurance training (LRT; n=6/group; generation 19). Both groups underwent 14 d of synergist ablation to induce functional overload of the plantaris muscle prior to comparison to non-overload controls of the same genotype.  RNA sequencing was performed to identify Gene Ontology Biological Processes with differential (LRT vs HRT) gene set enrichment. Running distance, determined well in advance of synergist ablation, increased in response to aerobic training in HRT but not LRT (65 ±26% versus -6 ±18%, respectively, mean ±SD, p<0.0001). The hypertrophy response to functional overload was attenuated in LRT versus HRT (20.1 ±5.6% versus 41.6 ±16.1%, respectively, P = 0.015). There were between-group differences in the magnitude of response of 96 upregulated- and 101 downregulated pathways. A further 27 pathways showed contrasting upregulation or downregulation in LRT versus HRT in response to functional overload. In conclusion, low responders to aerobic endurance training were also low responders for compensatory hypertrophy, and attenuated hypertrophy was associated with differential gene expression. Thus, our findings suggest that genetic factors that underpin aerobic training maladaptation may also dysregulate the transcriptional activity of biological processes that contribute to adaptation to mechanical overload.

overall_design: RNA-seq of 14-month old female LRT/HRT rats (generation 19) following 14 days induced plantaris functional overload compared to controls (total=24 samples; n=6/group)

first: Vernon

last: Coffey

first: Daniel

last: West

first: Jamie-Lee

last: Thompson


title: Expression data from jejunum IEC deleted for both HDAC1 and HDAC2

city: Sherbrooke

first: Alexis

last: Gonneaud

state: QC

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

country: Canada

institute: Université de Sherbrooke

summary: Both HDAC1 and HDAC2 are epigenetic erasers that drive specific and redundant gene expression patterns, in part by removing acetyl groups on histones. Deletion of these Hdac in intestinal epithelial cell (IEC) in vivo alters intestinal homeostasis, dependent on the Hdac deleted and the level of expression of both. To determine the intrinsic specific IEC function of HDAC1 and HDAC2, we have performed transcriptomic and quantitative proteomic approaches on IEC-deficient for Hdac1 and Hdac2. We have defined changes in both mRNA and protein expression patterns affecting IEC differentiation. We have identified IEC Hdac1- and Hdac2-dependent common as well as specific pathways and biological processes. These findings uncover unrecognized similarities and differences between normal IEC and HDAC1/2 deleted jejunum IEC.

overall_design: Total RNAs from wild-type and HDAC1/2-deleted IEC were purified with the RNeasy mini kit (Qiagen), and quantified with a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

first: Claude

last: Asselin