title: Co-Administration of Propionate or Protocatechuic Acid Does Not Affect DHA-Specific Transcriptional Effects on Lipid Metabolism in Cultured Hepatic Cells

status: Public on Sep 30 2020

city: Bologna

first: Alessandra

last: Bordoni

address: Viale Fanin 44

department: Department of Biochemistry and Molecular BiologyDepartment of Agricoltural and Food Sciences

country: Italy

institute: Università di Bologna

summary: Long-chain n-3 polyunsaturated fatty acids (n-3 LC-PUFAs) are collectively recognized triglyceride-lowering agents, and their preventive action is likely mediated by changes in gene expression. However, as most studies employ fish oil, which contains a mixture of n-3 LC-PUFAs, the docosahexaenoic acid (DHA)-specific transcriptional effects on lipid metabolism are still unclear. The aim of the present study was to further elucidate the DHA-induced transcriptional effects on lipid metabolism in the liver, and to investigate the effects of co-administration with other bioactive compounds having effects on lipid metabolism. To this purpose, HepG2 cells were treated for 6 or 24 h with DHA, the short-chain fatty acid propionate (PRO), and protocatechuic acid (PCA), the main human metabolite of cyanidin-glucosides. Following supplementation, we mapped the global transcriptional changes. PRO and PCA alone had a very slight effect on the transcriptome; on the contrary, supplementation of DHA highly repressed the steroid and fatty acid biosynthesis pathways, this transcriptional modulation being not affected by co-supplementation. Our results confirm that DHA effect on lipid metabolism are mediated at least in part by modulation of the expression of specific genes. PRO and PCA could contribute to counteracting dyslipidemia through other mechanisms.

overall_design: Human liver-derived cell line HepG2 cells were stimulated with vehicle or bioactive compound for 6 hours or 24 hours, respectively, before RNA harvest and subsequent mRNA sequencing (RNA-seq). All samples were performed in biological triplicates.

first: Francesca

last: Danesi

first: Bjørk

middle: D

last: Larsen

first: Mattia

last: Di Nunzio

first: Ronni

last: Nielsen

first: Dario

last: de Biase

first: Veronica

last: Valli

first: Susanne

last: Mandrup


title: Mycobacteria excises DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair

status: Public on Oct 06 2020

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

country: USA

institute: University of North Carolina  at Chapel Hill

summary: In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers (CPDs) are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual incision patterns have been discovered: prokaryotic type which removes the damage in 11-13 nucleotide-long oligomers and eukaryotic type which removes the damage in 24-32 nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from incisions at 15 nucleotides from the 3’ end and 9 nucleotides from the 5’ end flanking the damage. To test this model we used the in vivo excision assay and the XR-seq genome-wide repair mapping method developed in our lab to determine the repair pattern and genome-wide repair map of M. smegmatis. We find that M. smegmatis, which possesses homologues of the E. coli UvrA, B, and C genes, removes CPDs from the genome in a manner identical to the prokaryotic pattern by incising 7 nucleotides 5’ and 3 or 4 nucleotides 3’ to the photoproduct.

overall_design: We apply XR-seq in Mycolicibacterium smegmatis MC2 155, the cells were grown with shaking at 37 °C in Luria Broth containing 0.5% (w/vol) Tween 80. Exponentially growing cells were transferred to R150 tissue culture dishes in volumes of 15 mL and were irradiated at an OD600 of ∼0.6 at room temperature with 100 J/m2. Dishes were then incubated for 10 min at room temperature, and then cells were harvested, chilled, and maintained on ice. Excision products were then isolated using a modified Hirt procedure that employs shearing to assist cell lysis.  Cells were pelleted at 4 °C, resuspended in ice-cold TE [Tris (10 mM)-EDTA (1 mM) (pH 8.0)], transferred to ice cold Eppendorf tubes, and pelleted at 4 °C, and the supernatants were removed. Pellets were then resuspended with 360 μL of ice-cold TE. Then, 50 μL of room temperature 10% (wt/vol) SDS was added, and cells were lysed by passage through a 26G needle 40 times followed by incubation at room temperature for 20 min. A 120-μL volume of room temperature NaCl (5 M) was then added, tubes were gently mixed, and suspensions were incubated at 4 °C overnight. After centrifuging at high speed for 1 h in a microfuge at 4 °C, supernatants (about 480 μL each) were taken, and each was mixed with and incubated with 12 μL of RNaseA (R4642; Sigma) for 1 h at 37 °C, and then with 12 μL of proteinase K (P8107S; NEB) for 1.5 h at 60 °C. Samples were then extracted twice with phenol/chloroform/isoamyl alcohol and precipitated with ethanol. Samples were immunoprecipitated with an anti-CPD antibody and then ligated to adapters and processed for sequencing (XR-seq). XR-seq libraries were pooled and then sequenced on the HiSeq 2500 Rapid Run platform at the UNC-Chapel Hill High-Throughput Sequencing Facility. Analysis pipeline is available on https://github.com/yanyanyangunc/DNA-Damage-Repair-Circadian-Clock/tree/master/Mycobacterium_smegmatis_str_mc2_155

first: Christopher

middle: P

last: Selby

first: Laura

middle: A

last: Lindsey-Boltz

first: Aziz

last: Sancar


title: Direct induction of retinal ganglion cell-like neurons

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

country: China

institute: Zhongshan Ophthalmic Center, SYSU

type: Expression profiling by high throughput sequencing

summary: Retinal ganglion cells (RGCs) are the projection neurons in the retina that connect the visual sensing tissue to the brain. We found that Ascl1/Brn3b/Isl1 transcription factor combination can quickly and efficiently reprogramming mouse embryonic fibroblasts (MEFs) into retinal ganglion cell-like neurons (iRGCs). Using RNA-seq, we analyzed the transcriptomes of MEFs infected with Ascl1/Brn3b/Isl1-overexpressing viruses on day 2 or day 7 of reprogramming, or the final iRGCs on day 13 of reprogramming.

overall_design: MEFs infected with Ascl1/Brn3b/Isl1-overexpressing lentiviruses were FACS sorted based on GFP expression (linked to the end of Ascl1/Brn3b/Isl1 through 2A peptides), and processed for RNA-seq library construction and sequencing.

first: Shuyi

last: Chen


title: RNA-seq analysis of  WT, CD5 KO, CD6 KO, CD5/CD6 double KO (I) and LAT KO naïve CD4+ T cells (II)

status: Public on Sep 29 2020

city: Marseille

first: Rudy

last: AUSSEL

address: Parc Scientifique et Technologique de Luminy

country: France

institute: CIML

summary: Transmembrane adaptors on T cells play crucial roles in TCR signal transduction. Although the TCR-LAT signal-transduction axis occupies a central place in T cell activation, it does not work in isolation and is tuned by other T-cell surface receptors among which stand the CD5 and CD6 receptors. Here we assessed the extent of transcriptional changes that initiated by TCR-CD28 pathways in the absence of CD5, of CD6, of both CD5 and CD6, or of LAT by RNA-seq analysis.

overall_design: RNA-seq analysis of untreated  and stimulated naïve CD4+ T cells of wild-type, CD5 KO, CD6 KO, CD5/CD6 double KO and LAT KO.  Purified T cells were stimulated with anti-CD3 plus anti-CD28 for 4 h and 20 h. WT (hDTR+) and Lat–/– (hDTR–) naïve CD4+ T cells were purified from pooled lymph nodes and spleens from Latfl-dtr maT-Cre mice using FACS AriaIII as described in Roncagalli et al (2014). There were 3 biological replicates for each conditions.

first: Daiki

last: Mori

last: Aussel

first: Bernard

last: Malissen


title: CD200 expression marks leukemia stem cell (LSC) in human AML part 3

status: Public on Oct 10 2020

city: Toronto

first: Jean

last: Wang

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

summary: The leukemia stem cell (LSC) populations of acute myeloid leukemia (AML) exhibit phenotypic, genetic and functional heterogeneity that contribute to therapy failure and relapse. Progress towards understanding the mechanistic basis for therapy resistance in LSCs has been hampered by difficulties in isolating cell fractions that enrich for the entire heterogeneous population of LSCs within individual AML samples. We previously reported that CD200 gene expression is upregulated in LSC-containing AML fractions. We demonstrate that CD200 is present on a greater proportion of CD45dim blasts compared to more differentiated CD45high cells in AML patient samples. In 75% of AML cases examined, CD200 was expressed on 10% of CD45dim blasts; of these, CD200 identified LSCs within the blast population in 90% of samples tested in xenotransplantation assays. Notably, CD200 expression captured both CD34- and CD34- LSCs within individual AML samples. Highly purified CD45dimCD200+ LSC-containing blasts were enriched in primitive HSC/progenitor-like signatures, while CD45dimCD200- nonengrafting blasts were enriched in myeloid-like signature. Moreover, analysis of CD45dimCD200+ blasts from NPM1-mutated AMLs also demonstrated an enrichment of primitive gene expression signatures compared to unfractionated (bulk) cells.

overall_design: CD45dim blasts were sorted into CD200+ and CD200- fractions from AML samples functionally validated to contain CD200+ LSCs (Metadata1) before RNA extraction and sequencing. RNA from unfractionated (bulk) cells was extracted and subjected to gene expression analysis using Illumina HumanHT-12 v4 microarrays (Ng et al. Nature. 2016;540:433-437) (Metadata2) or sequencing (Metadata3).

first: Liqing

last: Jin


title: Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq

status: Public on Oct 02 2020

city: Beijing

first: Xiaomeng

last: Zhao

address: No.1 Xiangshan Beigou, Haidian District

institute: Institute of Apicultural Research, Chinese Academy of Agricultural Sciences

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Bumblebees (Hymenoptera: Apidae) are important pollinating insects that play pivotal roles in crop production and natural ecosystem services. To achieve a comprehensive profile of accessible chromatin regions and provide clues for all possible regulatory elements in the bumblebee genome, we did ATAC-seq for Bombus terrestris samples derived from its four developmental stages: egg, larva, pupa, and adult, respectively. The sequencing reads of ATAC-seq were mapped to B. terrestris reference genome, and its accessible chromatin regions were identified and characterized using bioinformatic methods. Our study will provide important resources not only for uncovering regulatory elements in the bumblebee genome, but also for expanding our understanding of bumblebee biology.

overall_design: ATAC-seq was performed on Bombus terrestris samples derived from its four developmental stages (egg, larva, pupa, adult). Chromatin open regions were identified for each developmental stage with two biological replicates.

first: Long

last: Su

first: Weilin

last: Xu

first: Cheng

last: Sun


title: Quantitative and multiplexed chemical-genetic phenotyping in mammalian cells using QMAP-Seq

status: Public on Oct 01 2020

city: Chicago

first: Sonia

last: Brockway

state: IL

address: 303 E Superior St, SQBRC 7-500

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: Here, we develop Quantitative and Multiplexed Analysis of Phenotype by Sequencing (QMAP-Seq), which leverages next-generation sequencing for pooled high-throughput chemical-genetic profiling. We apply QMAP-Seq to investigate how cellular stress response factors affect therapeutic response in cancer. Using minimal automation, we treat pools of 60 cell types—comprising 12 genetic perturbations in five cell lines—with 1,440 compound-dose combinations, generating 86,400 chemical-genetic measurements.

overall_design: Targeted sequencing of sgRNAs and cell line barcodes from samples consisting of 5 cell lines x 12 sgRNAs + cell spike-in standards. Sequencing run was composed of 1,536 samples, each representing a unique compound-dose-replicate combination. 96 samples were DMSO-treated (control), and 1,440 samples were compound-treated.

first: Geng

first: Jasen

middle: M

last: Jackson

first: David

middle: R

last: Amici

first: Seesha

last: Takagishi

first: Matthew

last: Clutter

first: Elizabeth

middle: T

last: Bartom

first: Marc

middle: L

last: Mendillo


title: Human Keratinocyte Response to Superantigens

city: Iowa City

first: Aloysius

middle: John

last: Klingelhutz

state: IA

address: 3-604 BSB, 51 Newton Road

department: Microbiology and Immunology

institute: University of Iowa

summary: Purpose: The goal of this study was to determine what genes and canonical pathways are altered by exposure of human keratinocytes to S. aureus superantigens TSST-1 or SEB; Methods: Primary human keratinocytes were treated with 100 ug purified TSST-1, SEB, or vehicle for 6 hours. RNA was extracted with Trizol, DNase treated, and purifed using a Qiagen column.  RNAseq was used to assess gene expression. Bioinformatic analyses were used to determing differential gene expression between superantigen treated cells and controls. Validition of cytokine increases was performed using ELISAs.

overall_design: RNAseq profile of differential gene expression caused by treatment of human keratinocytes with S. aureus TSST-1 or SEB

middle: J

first: Patrick

last: Schlievert


title: Evaluation of the transcriptomic response to oxidative stress and melatonin treatment

city: Tarragona

first: Mercè

last: Sunyer-Figueres

state: Catalunya

address: C/ Marcel·lí Domingo, 1

department: Departament de Bioquímica i Biotecnologia

country: Spain

institute: Universitat Rovira i Virgili

summary: Melatonin (N-acetyl-5-methoxytryptamine) is a ubiquitous indolamine that plays important roles in biological processes in different organisms. Recently, it has been found to have a important role in the antioxidant response in yeast. In this study the transcriptomic response to mild oxidative stress driven by Saccharomyces cerevisiae strain QA23 supplemented to different concentrations of melatonin (5 and 25 µM) is assessed.

overall_design: One-color microarray experiment comparing gene expression of S. cerevisiae cells grown with and without melatonin supplementation (5 and 25 µM) until the cells reached the initial expeonential phase, when oxidative stress (2 mM H2O2) was induced during 1h, when all samples were taken. Three biological replicates were used.

first: Jennifer

last: Vázquez

last: Sunyer

first: Albert

last: Mas

first: Gemma

last: Beltran

first: María-Jesús

last: Torija


title: Egg-white proteins have a minor impact on the bactericidal action of egg white towards Salmonella Enteritidis at 45 °C

city: Rennes

first: Florence

last: Baron

address: 65 rue de Saint Brieuc

institute: Agrocampus Ouest

summary: Transcriptional profiling of Salmonella Enteritidis to egg-white filtrate  exposure at 45°C for  45 min

sample_organism: Salmonella enterica subsp. enterica serovar Enteritidis

overall_design: 3 biological replicates, 2 technical replicates and one or two probes / gene

first: F

first: M

middle: F

last: Cochet

last: Alabdeh

first: S

last: Bonnassie

last: Nau

first: C

last: GuÃ©rin-Dubiard

first: V

last: Lechevalier

last: Gautier

middle: C

last: Andrews

last: Jan


title: Identification of potential target genes of KRAB zinc-finger proteins in cancer cells

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

summary: KRAB zinc-finger proteins (KZFPs) are potent transcriptional suppressors and suspected to be associated with cancer progression. To identify the potential target genes of KZFPs in lung adenocarcinoma cells, we established a panel of A459 cell lines that over-express 30 types of KZFPs (A549/KZFP cells) and performed RNA-sequencing (RNA-Seq) analysis of these cells.

overall_design: The lentivirus vector expressing HA-tagged KZFP was transduced into A459 cells. The ectopic expression of KZFP in A549/KZFP cells was verified by Western blotting with an anti-HA antibody. Total RNA was extracted from the A549/KZFP cells by QIAamp RNA Blood Mini Kit (QIAGEN #52304) and treated with RNase-Free DNase Set (QIAGEN #79254). Quality check of the purified RNA, library construction, and sequencing were performed by Novogene (https://en.novogene.com). Pair-ended and 150bp read length sequencing was performed by Illumina Novaseq6000. Single-replicate experiment was performed for respective A549/KZFP cells, and triplicate experiment was performed for the empty vector-transduced A549 cells.

first: Izumi

last: Kimura

first: Naoko

last: Misawa

first: Jumpei

last: Ito


title: Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration

city: Durham

first: Anna Mae

last: Diehl

address: Research Drive

institute: Duke University

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

overall_design: Refer to individual Series


title: Beauveria bassiana Hapx (BbHapX) regulating genes involved in asexual development

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

summary: Gene BbHapX plays an essential role in maturation of conidia, a dorminant spore type for the biocontrol potential of entomopathogenic fungi. The genome-wide expression analysis involved in fungal development was analyzed by using high throughput sequencing (RNA-Seq). Our transcriptional profiles revealed that numerous differentially expressed genes (DEGs), of which involved in metabolism, cell transport and cell rescue, were significantly involved in asexual development of B. bassiana.

overall_design: Total RNA obtained from ∆BbHapX disruption mutant were compared to that of wild type strain (WT) grown under the indicated conditions.

first: Sheng

middle: H

first: Ming

middle: G

last: Feng


title: Impact of compound VU0026921 on S. aureus transcriptional profile

status: Public on Oct 07 2020

city: Nashville

first: Lillian

last: Juttukonda

state: TN

address: 1161 21st Avenue South

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

summary: Compound VU0026921 is antimicrobial to S. aureus in a manner modulated by Mn. To elucidate information regarding the mechanism of action of VU0026921, we performed RNA sequencing of S. aureus exposed to VU0026921 in the presence or absence of excess Mn

overall_design: Cultures of S. aureus were exposed to either 100 micromolar VU0026921, 100 micromolar VU0026921 + 1 mM MnCl2, 1 mM MnCl2 alone, or untreated media. The experiment was performed in biological triplicate for a total of 12 samples.  Note that the data for medium alone compared to 1 mM MnCl2 alone has been previously deposited at GEO: GSE124285

first: Eric

last: Skaar

first: Matthew

middle: B

last: Scholz


title: Targeting 14-3-3ζ overcomes resistance to EGFR-TKIs in lung adenocarcinoma via BMP2/Smad/ID1 signaling

city: Harbin

first: Hailing

last: Lu

address: 150 Haping Road

institute: Harbin Medical University Cancer Hospital

summary:
14-3-3ζ has been found to promote the proliferation, metastasis and chemoresistance of cancer cells in several cancers including lung adenocarcinoma; however, its significance in epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) resistance remains unknown. Our work uncovers a hitherto unappreciated role of 14-3-3ζ in EGFR-TKI resistance.
We determined global gene expression profiling in EGFR-TKI-resistant H1975 cells using microarray analysis.

overall_design: EGFR-TKI-resistant H1975 cells were infected with a lentivirus expressing either scrambled shRNA or 14-3-3ζ-shRNA

first: Li

last: Cai


title: Analysis of transcription profile for High Grade Serous Ovarian Cancer (HGSC) cell line panel and how it relates to chromosomal instability (CIN)

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Seven HGSC cancer cell lines were analysed with two immortalised Fallopian tube derived cell lines as controls. RNAseq was used to identify which genes showed transcript changes in cell lines showing particular phenotypes for chromosomal instability; enrichment of genes in particular pathways was used to identify possible mechanisms of CIN.

overall_design: RNA sequencing was performed on seven HGSC ovarian cancer cell lines. Three replicates were analysed per cell line. Two hTERT immortalised Fallopian tube cell lines were used as controls.

first: Nadeem

last: Shaikh

first: Jun

last: Wang

first: Sarah

last: McClelland


title: Single-cell omics analysis reveals functional diversification of hepatocytes during liver regeneration [ATAC-Seq]

summary: Adult liver has enormous regenerative capacity as it can regenerate after losing two-thirds of its mass while sustaining essential metabolic functions. How the liver balances dual demands for increased proliferative activity with maintenance of organ function is unknown, but essential to prevent liver failure. Using partial hepatectomy (PHx) in mice to model liver regeneration, we integrated single-cell RNA and ATAC sequencing to map state transitions in ~ 13,000 hepatocytes at single-cell resolution as livers regenerated, and validated key findings with immunohistochemistry, to uncover how the organ regenerates hepatocytes while simultaneously fulfilling its vital tissue-specific functions. After PHx, hepatocytes rapidly and transiently diversified into multiple distinct populations with distinct functional bifurcation: some retained the chromatin landscapes and transcriptomes of hepatocytes in undamaged adult livers while others transitioned to acquire chromatin landscapes and transcriptomes of fetal hepatocytes.  Injury-related signaling pathways known to be critical for regeneration were activated in transitioning hepatocytes and the most fetal-like hepatocytes exhibited chromatin landscapes that were enriched with transcription factors regulated by those pathways.

overall_design: Profiling of chromatin accessibility of liver hepatocytes by high throughput sequencing

first: Anna

first: Tianyi

last: Chen


title: RNA-Seq and ATAC-Seq of HEK239T cell line carrying different genotypes at rs4420550 by CRISPR/Cas9 editing

city: Kunming

last: Li

state: Yunnan

address: NO 32 Jiao-Chang Donglu

institute: Kunming Institute of Zoology, Chinese Academy of Sciences

summary: Background: Genome-wide association studies (GWAS) have reported hundreds of genomic loci associated with schizophrenia, yet identifying the functional risk variations is a key step in elucidating the underlying mechanisms. Methods: We applied multiple bioinformatics and molecular approaches, including expression quantitative trait loci (eQTL) analyses, epigenome signature identification, luciferase reporter assay, chromatin conformation capture (3C), homology-directed genome editing by CRISPR/Cas9, RNA-sequencing (RNA-Seq) and assay for transposase-accessible chromatin using sequencing (ATAC-Seq). Results: We found that the schizophrenia GWAS risk variations at 16p11.2 were significantly associated with mRNA levels of multiple genes in human brain, and one of the leading eQTL genes, MAPK3, located ~200-kb away from these risk variations in the genome. Further analyses based on the epigenome marks in human brain and cell lines suggested that a noncoding single nucleotide polymorphism (SNP) rs4420550 (p=2.36×10–9 in schizophrenia GWAS) was within a DNA enhancer region, which was validated via in vitro luciferase reporter assays. The 3C experiment showed that the rs4420550 region physically interacted with the MAPK3 promoter and TAOK2 promoter. Precise CRISPR/Cas9 editing of single base pair in cells followed by RNA-Seq further confirmed the regulatory effects of rs4420550 on the transcription of 16p11.2 genes, and ATAC-Seq demonstrated that rs4420550 affected chromatin accessibility at the 16p11.2 region. The rs4420550-[A/A] cells showed significantly higher proliferation rates compared with rs4420550-[G/G] cells. Conclusions: These results together suggest that rs4420550 is a functional risk variation, and this study illustrates an example of comprehensive functional characterization of schizophrenia GWAS risk loci.

overall_design: To understand if the different alleles of rs4420550 could affect nearby gene expressions and chromatin accessibility of the 16p11.2 region, we performed RNA-Seq and ATAC-Seq in four colonies carried the [A/A] genotype and the other four carried the [G/G] genotype at rs4420550.

first: Hong

last: Chang

first: Xin

first: Huijuan


title: Expression data of human melanoma cells plus/minus Androgen Receptor (AR) silencing by two independent shRNAs

city: Epalinges

first: Soumitra

last: Ghosh

state: Choose State/Province

address: Chemin des Boveresses 155

department: Biochemistry

country: Switzerland

institute: University of Lausanne, Switzerland

summary:
Cancer susceptibility of male versus female individuals is significantly different in melanoma, with females showing greater survival than males. Accrued information on the role fo sex hormones in melanoma is mostly limited to estrogen signaling, with only circumstantial evidence related to androgen receptor.
We used Clariom™ D GeneChip Assay to study the global gene expression changes upon silencing of AR by two independent shRNAs in three human melanoma cell lines.

overall_design: Three different human melanoma cells were infected with lentivirus containing either two independent shRNAs against AR or control shRNA. 48 hours after virus transfection, cells were selected for puromycin resistance for 3 days before RNA extraction.

first: Min

last: Ma

first: Daniele

last: Tavernari

first: Gian-Paolo

last: Dotto


title: Reconstitution of prospermatogonial specification in vitro from human induced pluripotent stem cells

status: Public on Sep 28 2020

city: Philadelphia

first: Youngsun

last: Hwang

state: PA

address: 3800 Spruce Street Old Vet Quad 220E

institute: University of Pennsylvania

summary: Establishment of spermatogonia throughout the fetal and postnatal period is essential for production of spermatozoa and male fertility. Here, we established a protocol for in vitro reconstitution of human prospermatogonial specification whereby human primordial germ cell (PGC)-like cells (hPGCLCs) differentiated from human induced pluripotent stem cells were further induced into M-prospermatogonia-like cells (MLCs) and T1 prospermatogonia-like cells (T1LCs) using long-term cultured xenogeneic reconstituted testes. Single cell RNA-sequencing was used to delineate the lineage trajectory leading to T1LCs, which closely resemble human T1-prospermatogonia in vivo and exhibited gene expression related to spermatogenesis and diminished proliferation, a hallmark of quiescent T1 prospermatogonia. Notably, this system enabled us to visualize the dynamic and stage-specific regulation of transposable elements during human prospermatogonial specification. Together, our findings pave the way for understanding and reconstructing human male germline development in vitro.

overall_design: hiPSCs, iMeLCs, hPGCLCs, and hPGCLC-derived cells from xrTestis were used in this study. Human fetal testicular cells are also used in this study.

first: Young

middle: S

first: Kotaro

last: Sasaki


title: The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s

first: Helen

middle: M.

last: Rowe

state: --- Select a state ---

address: 4 Newark St, Whitechapel

department: Blizard Institute, Barts and The London School of Medicine and Dentistry

summary: The Human Silencing Hub (HUSH) complex is necessary for epigenetic repression of LINE-1 elements. We found that depletion of HUSH components in human cell lines and primary fibroblasts leads to induction of interferon-stimulated genes (ISGs) through JAK/STAT signaling. This effect was mainly attributed to MDA5 and RIG-I sensing of double-stranded RNAs and coincided with upregulated LINE-1 RNAs. This included the human-specific family, L1HS, which produced bidirectional RNAs of around 6Kb, as well as ancient primate-conserved LINE-1s. LTRs nearby ISGs were derepressed likely rendering these genes more responsive to interferon. LINE-1 shRNAs could abrogate the HUSH-dependent response, while overexpression of an engineered LINE-1 construct could activate interferon signaling. Finally, we found that the HUSH component, MPP8 is frequently downregulated in diverse cancers and that its depletion leads to DNA damage. These results suggest that LINE-1s may drive physiological or autoinflammatory responses through RNA sensing and gene-regulatory roles and are controlled by the HUSH complex.

overall_design: Identification of repetitive elements controlled by the HUSH complex that are capable of inducing a type I interferon response.

first: Hale

last: Tunbak

first: Rocio

last: Enriquez-Gasca

first: Christopher

last: Tie

first: Poppy

last: Gould

first: Petra

last: Mlcochova

first: Ravi

last: Gupta

first: Liane

last: Fernandes

first: James

last: Holt

first: Annemarthe

last: van der Veen

first: Evangelos

last: Giampazolias

first: Kathleen

last: Burns

first: Pierre

middle: V

last: Maillard


title: Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea

status: Public on Sep 25 2020

city: Cambridge

first: Ya

last: Min

state: Massachusetts

address: 16 Divinity Ave.

institute: Harvard University

summary: The current experiment was designed to obtain a broad characterization of the genetic pathways acting in early Aquilegia coerulea floral meristem development. We conducted an in-depth transcriptome profiling of early floral development in A. coerulea at four finely dissected developmental stages, with eight biological replicates per stage. . The developmental window we sequenced sampled stages that started with a late phase of stamen initiation, covered the period of FM termination, and ended with the initial stage of morphogenesis of the floral organs.

overall_design:
Four developmental stages during early floral meristem development; Eight biological replicates per developomental stage.
developmental stage1: stamen primordia initiating
developmental stage2: staminode primordia finish initiating
developmental stage3: rims of carpel primordia elevated
developmental stage4: apex of floral bud consumed by developing carpel primordia

first: Elena

last: Kramer


title: Inhibitory effect of a human microRNA, miR-6133-5p, on the fibrotic activity of hepatic stellate cells in culture

city: Nagoya

first: masaya

last: onishi

address: Kawasumi, Mizuho

department: Virology & Liver unit

institute: Nagoya City University Graduate School of Medical Sciences

summary:
Purpose: We recently identified 39 human microRNAs, which effectively suppress hepatitis B virus (HBV) replication in hepatocytes. Because chronic HBV infection often results in active, hepatitis-related liver fibrosis, we assessed whether any of these microRNAs have anti-fibrotic potential and predicted that miR-6133-5p may target several fibrosis-related genes.
Methods:  The hepatic stellate cell line LX-2 was transfected with miR-6133-5p mimic and subsequently treated with TGF-β. mRNA and protein products of COL1A1, encoding collagen, and ACTA2, an activation marker of hepatic stellate cells, were quantified.
Results: Expression of COL1A1 and ACTA2 was markedly reduced in LX-2 cells treated with miR-6133-5p. Interestingly, phosphorylation of JNK also was significantly decreased by miR-6133-5p treatment. The expression of several predicted target genes of miR-6133-5p, including TGFBR2 and FGFR1, was also reduced in miR-6133-5p-treated cells. The knockdown of TGFBR2 by the corresponding small interfering RNA greatly suppressed the expression of COL1A1 and ACTA2. Treatment with the JNK inhibitor, SP600125, also suppressed COL1A1 and ACTA2 expression, indicating that TGFBR2 and JNK would mediate the anti-fibrotic effect of miR-6133-5p. Downregulation of FGFR1 may result in a decrease of phosphorylated AKT, ERK, and JNK.
Conclusions: miR-6133-5p has a strong anti-fibrotic effect, mediated by inactivation of TGFBR2, AKT and JNK.

overall_design: mRNA profiles of  the cells transfected with miR-6133-5p and those transfected with miControl, 24 hours after rhTGF-β treatment.

first: Susumu

last: Hamada-Tsutsumi

first: Masaya

last: Onishi

first: Yasuhito

last: Tanaka


title: Roles of human endogenous retroviruses and KRAB-zinc finger proteins in tumor progression

first: Kei

last: Sato


title: Single-cell RNA sequencing on EM-E6/E7/TERT-1 endometrial epithelial cells

city: San Antonio

first: Tim

middle: Hui-Ming

last: Huang

state: TX

address: 7703 Floyd Curl Dr

institute: University of Texas Health at San Antonio

summary: We report the single-cell high-throughput sequencing for non-tumorigenic EM-E6/E7/TERT-1(EME6/7t) endometrial epithelial cell line. EME6/7t cells were exposed to condition medium (CM) of adipose-derived stromal cells (ASCs) with or without tiplaxtinin (PAI-039). We employed unsupervised clustering analysis to characterize various PAI-1 related regulatory models in EME6/7t cells. This study provides a framework for exploring heterogeneous gene expression patterns caused by plasminogen activator inhibitor-1 (PAI-1) responses in the tumor microenvironment.

overall_design:
Single-cell mRNA profiles of 1,911 EME6/7t cells were used to study and analyze PAI-1 responses in the development of endometrial cancer

Please note that [1] the raw R1 reads was used to demultiplex row barcodes of column samples, and alignment was done on R2 reads. Therefore only R2 was provided and processed as single [2] the 'raw_to_processed_data_file.txt' contains the list of the raw data files associated with each processed data file.

first: Nameer

last: Kirma

first: Li-Ling

last: Lin

first: Chun-Lin


title: Single-Cell RNA-seq immune profile of normal and inflammed mouse skin

status: Public on Sep 26 2020

city: San Francisco

first: Jeffrey

last: Cheng

state: CALIFORNIA

address: 1701 Divisadero St, 4th floor

department: Dermatology

institute: UCSF

summary: Comparison of mouse immune cells from skin treated with oxazolone or imiquimod

overall_design: This data includes 18 samples (4 treatment groups, each with 3 replicates (12 mice total)). The treatment groups are: IMQ-C (no IMQ treatment negative control (Vanicream)),   IMQ (5% Imiquimod cream), OXA-C (no oxazolone challenge negative control),  OXA (oxalazone sensitization and challenge). IMQ-C serves as the negative control for the IMQ samples and OXA-C is the negative control for the OXA samples. OXA-C and OXA replicates contain transcript (scRNA-seq) data and epitope (CITE-seq) data which are listed as separate samples. However, the CITE-seq and scRNA-seq data for each replicate comes from the same mouse (for example: OXA-C Replicate 1 - RNAseq and OXA-C Replicate 1 - CITE-seq is from the same mouse). There is no CITE-seq data for IMQ-C and IMQ groups.

first: Raymond

last: Cho

first: Yale

last: Liu

first: Christopher

middle: P

last: Cook


title: YAP and TAZ protect against white adipocyte cell death during obesity

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Investigation of the effect of YAP/TAZ on white adipocyte survival during obesity

overall_design: Total RNA was prepared using isolated primary white adipocytes from epididymal  WAT of wild-type (WT) and Ad-Yap/Taz-KO mice (KO) fed normal chow (NC) or HFD for 4 weeks starting from the age of week 5.

first: Lei

last: Wang


title: Transcriptome-wide analysis of mRNA translation and associated post-transcriptional regulatory mechanisms following neuronal membrane depolarisation

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

type: Non-coding RNA profiling by high throughput sequencing

summary: Here, we employed ribosome profiling to explore global changes in mRNA translational status in neuronally differentiated neuroblast cultures at several time-points after whole cell depolarisation, and compared this to steady-state mRNA levels. Immediately after depolarisation, genes with known function at the synapse were subjected to a surge of translational activity without corresponding changes in mRNA levels. At later time-points, however, these changes became synchronised, suggesting there are different layers of post-transcriptional regulation which are temporally separated but become coordinated over time. Sequencing of small RNAs additionally revealed that changes in microRNA (miRNA) and tRNA-derived small RNA fragments (tRFs) coincided with this early post-transcriptional disparity, however these molecules exhibited strongest association with the remodelling of mRNA steady-state levels. Transcripts displaying high levels of translational dynamics relative to underlying mRNA levels were characterised by more intrinsic features, including mRNA length, GC content, secondary structure and motifs for RNA binding proteins. These data suggest that activity-associated neuronal translation is initially regulated independently of mRNA levels, wherein transcript features contribute to modulation of mRNA translatability, while miRNA and tRFs fine-tune mRNA levels.

overall_design: Examination of changes in mRNA translation, expression and small RNA expression in neuronally differentiated SH-SY5Y cells.

first: Murray

last: Cairns


title: microRNA expression analysis of metastatic adrenocortical tumors

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

summary:
Background: Adrenocortical carcinoma (ACC) is a rare, often-aggressive neoplasm of the adrenal cortex, with a 14.5-month median overall survival. We asked whether tumors from patients with advanced or metastatic ACC would offer clues as to putative genes that might have critical roles in disease progression or in more aggressive disease biology.   Methods: We conducted comprehensive genomic and expression analyses, including microRNA profiling, of 33 ACCs and 6 normal adrenals.  Results: Copy number gains and losses matched that previously reported. We identified a median mutation rate of 3.38 per megabase (Mb), somewhat higher than in a previous study possibly related to the more advanced disease. The mutational signature was characterized by a predominance of C>T, C>A and T>C transitions. As in previously reports, only cancer genes TP53 (26%) and beta-catenin (CTNNB1, 14%) were mutated in more than 10% of samples. The TCGA-identified putative cancer genes MEN1 and PRKAR1A were found in low frequency – 4.7% and 2.3%, respectively. Most of the mutations were in genes not implicated in the etiology or maintenance of cancer. Specifically, amongst the 38 genes that were mutated in more than 9% of samples, only four were represented in Tier 1 of the 576 COSMIC Cancer Gene Census (CCGC). Thus, 82% of genes found to have mutations likely have no role in the etiology or biology of ACC; while the role of the other 18%, if any, remains to be proven. Finally, the transcript length for the 38 most frequently mutated genes in ACC is statistically longer than the average of all coding genes, raising the question of whether transcript length in part determined mutation probability.   Conclusions: We conclude that the mutational and expression profiles of advanced and metastatic tumors is very similar to those from newly diagnosed patients –with very little in the way of genomic aberration to explain it. Our data and that in the previous analyses finds the rate of mutations in ACCs lower than that in other cancers and suggests an epigenetic basis for the disease should be the focus of future studies.
The Exiqon miRCURY LNA microRNA array v.11.0 platform was used for the microRNA profiling.

overall_design: Tumor samples embedded in OCT were sectioned, stained with hematoxylin and eosin and reviewed by a pathologist. RNA was extracted from 50-100 mg of tumor using the Qiagen miRNeasy Kit and then used for microRNA pofiling. Author states 'I have no raw data'.  Thus, this submissionis incomplete.

first: Susan

middle: E

last: Bates

first: Antonio

last: Fojo


title: Gene expression analysis of metastatic adrenocortical tumors

summary:
Background: Adrenocortical carcinoma (ACC) is a rare, often-aggressive neoplasm of the adrenal cortex, with a 14.5-month median overall survival. We asked whether tumors from patients with advanced or metastatic ACC would offer clues as to putative genes that might have critical roles in disease progression or in more aggressive disease biology.   Methods: We conducted comprehensive genomic and expression analyses of 43 ACCs.  Results: Copy number gains and losses matched that previously reported. We identified a median mutation rate of 3.38 per megabase (Mb), somewhat higher than in a previous study possibly related to the more advanced disease. The mutational signature was characterized by a predominance of C>T, C>A and T>C transitions. As in previously reports, only cancer genes TP53 (26%) and beta-catenin (CTNNB1, 14%) were mutated in more than 10% of samples. The TCGA-identified putative cancer genes MEN1 and PRKAR1A were found in low frequency – 4.7% and 2.3%, respectively. Most of the mutations were in genes not implicated in the etiology or maintenance of cancer. Specifically, amongst the 38 genes that were mutated in more than 9% of samples, only four were represented in Tier 1 of the 576 COSMIC Cancer Gene Census (CCGC). Thus, 82% of genes found to have mutations likely have no role in the etiology or biology of ACC; while the role of the other 18%, if any, remains to be proven. Finally, the transcript length for the 38 most frequently mutated genes in ACC is statistically longer than the average of all coding genes, raising the question of whether transcript length in part determined mutation probability.   Conclusions: We conclude that the mutational and expression profiles of advanced and metastatic tumors is very similar to those from newly diagnosed patients –with very little in the way of genomic aberration to explain it. Our data and that in the previous analyses finds the rate of mutations in ACCs lower than that in other cancers and suggests an epigenetic basis for the disease should be the focus of future studies.
The Affymetrix PrimeView platform was used for the gene expression profiling.

overall_design: Tumor samples embedded in OCT were sectioned, stained with hematoxylin and eosin and reviewed by a pathologist. RNA was extracted from 50-100 mg of tumor using the Qiagen miRNeasy Kit and then used for cDNA array analyses.


title: Whole Genome DNA Methylation and Gene Expression Profiling of Oropharyngeal Cancer Patients in North-Eastern India

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

country: India

institute: North Eastern Hill University

type: Methylation profiling by genome tiling array

summary: Methylation of CpG Islands within promoter regions of genes has been associated with gene silencing, suggesting loss of tumor suppressor function and tumorigenesis. The northeastern states of India are leaders in the country for cancers of several sites. Almost no reports are available of any DNA methylation biomarker for oropharyngeal cancers of the northeastern states. The present study aimed to identify targets of CpG hypermethylation and hypomethylation in oropharyngeal cancer prevalent in northeast India. Using Illumina Infinium Human Methylation 450K microarray platform a genome wide screening has been done for differentially methylated genes, including genes not previously implicated in carcinogenesis. Differential gene expression correlated to their methylation status was elaborated using transcriptome profiling. The new genes identified may be used to develop promising panels of DNA Methylation biomarkers for oropharyngeal screening and detection at a very early stage.

overall_design:
Whole genome DNA methylation profiling of oropharyngeal cancer in patients from north-east India. The Illumina Infinium 450k Human DNA methylation Beadchip was used to screen the entire DNA methylation profiles across 485577 CpG sites per sample at single-nucleotide resolution.
Bisulphite converted DNA from the 16 paired and 10 unpaired samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip

first: Lastborn

last: Marthong


title: BAHCC1 couples H3K27me3 to gene silencing and tumorigenesis via a conserved BAH module

city: Chapel Hill

first: Gang

middle: Greg

state: NC

address: 450 West Drive

department: BCBP

institute: UNC Lineberger Comprehensive Cancer Center

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: Transcriptomic analysis of APC knock down HCEC 1CT cells compared to the wild type HCEC 1CT cells.

city: Yuseong-gu

first: Jeong-Ryeol

last: Gong

state: Daejeon

address: 291, Daehak-ro

country: South Korea

institute: KAIST

summary: We performed RNA sequencing analysis of two human colon epithelial cell lines (HCEC 1CT_WT and HCEC 1CT_APC KD).

overall_design: Expression profiles of HCEC 1CT_WT and APC KD cells were generated by RNA sequencing, in triplicate, using Illumina NextSeq 500.

first: Chae

middle: Y

last: Hwang

first: Kwang-Hyun


title: PAX6 mutation alters circadian rhythm and β cell function in mice without affecting glucose tolerance

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary: The transcription factor PAX6 is involved in the development of the eye and pancreatic islets, besides being associated with sleep-wake cycles. Here, we investigated a point mutation in the RED subdomain of PAX6, previously described in a human patient, to present a comprehensive study of a homozygous Pax6 mutation in the context of adult mammalian metabolism and circadian rhythm. Pax6Leca2 mice lack appropriate retinal structures for light perception and do not display normal daily rhythmic changes in energy metabolism. Despite β cell dysfunction and decreased insulin secretion, mutant mice have normal glucose tolerance. This is associated with reduced hepatic glucose production possibly due to altered circadian variation in expression of clock and metabolic genes, thereby evading hyperglycemia. Hence, our findings show that while the RED subdomain is important for β cell functional maturity, the Leca2 mutation impacts peripheral metabolism via loss of circadian rhythm, thus revealing pleiotropic effects of PAX6.

overall_design: We performed mRNA expression microarray analysis on homozygous Pax6-Leica2 mutant mice and control animals

first: Nirav

last: Chhabra

first: Moya

last: Wu

first: Oana

last: Amarie

first: Daniel

last: Gradinger

first: Marina

last: Rubey

first: Martin

last: Irmler

first: Birgit

last: Rathkolb

first: Eckhard

last: Wolf

first: Jovica

last: Ninkovic

first: Magdalena

last: Götz

first: Joachim

last: Graw

first: Jan

last: Rozman

first: Gerhard

middle: K

last: Przemeck

last: Hrabě de Angelis


title: Transcriptomic and functional deficits in human TREM2-/- microglia impair response to Alzheimer's pathology in vivo

status: Public on Sep 24 2020

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road, Room 3200

department: Neurobiology and Behavior

institute: University of California, Irvine


title: Transcriptomic and functional deficits in human TREM2-/- microglia impair response to Alzheimer's pathology in vivo [bulk RNA-seq]

summary: Bulk RNA sequencing data comparing TREM2 WT and KO microglia responses to treatment with dead neurons.

overall_design: Microglia were derived from two iPSC lines (n=3 each). The GFP lines were subsequently treated with dead neurons for 24 hours.

first: Amanda

last: McQuade

first: Jonathan

last: Hasselmann


title: Dengue specific immunoglobulin repertoires comparison between the repeated and epitope-decreased immunizations

status: Public on Sep 23 2020

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

summary: This study aims to under the characteristics and diversitification of Dengue speicific immunoglobulin repertoires after different immunization strategies in mouse. We propose two different immunization strategies in dengue vaccine development, one is repeated strategy, which DENV1 virus  and administrated three times. The other one is epitope-decreased sequential strategy, which sequetially administrated DENV1 virus, DENV1 E protein and DENV1 E protein domain III subunit.

overall_design: C57BL/6J (B6) mice were injected with either repeated or sequential strategy.  The Dengue specific B cells were fished out from immunized mice splenocytes by Dengue Env protein probes. After cDNA and Ig specific amplification, the RNA-seq libraries were preparated and subjected to MiSeq V3 2 × 301 bp sequencing.

first: Jianzhu

last: Chen

first: Jue

last: Hou


title: Macrophages Maintain Epithelium Integrity by Limiting Fungal Product Absorption

city: Hinxton

first: Francesca

last: Nadalin

address: Wellcome Genome Campus

institute: EMBL-EBI

summary: We report presence of Macrophage population in distal colon, which is transcriptomically different and  are specialized in the sampling of fluids absorbed by the epithelium. This population limits epithelial absorption of fungal metabolites thus protecting epithelial barrier from their cytotoxicity.

overall_design: Examination of transcriptomic profiles of Macrophages isolated from proximal and distal colon of mice.

first: Aleksandra

last: Chikina

first: Ana-Maria

last: Lennon-Duménil

first: Danijela

last: Vignjevic


title: APC knock down HCEC 1CT cells compared to the wild type HCEC 1CT cells

first: Jeong-Ryeol

last: Gong


title: RNA-seq of HEK 293T cells treated with Val-boroPro

city: New York

first: Daniel

middle: A.

last: Bachovchin

state: NY

address: 408 E 69th St

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

summary: We report the application of RNA-seq for profiling gene transcription upon treatment of dipeptidyl peptidases 8 and 9 inhibitor, Val-boroPro (VbP). We find no significant changes in gene transcription upon treatment of mammalian cells with Val-boroPro.

overall_design: Examination of gene transcription levels upon treatment of Val-boroPro in HEK 293T mammalian cells over the course of 48 hours, compared to DMSO control. 4 replicates were analyzed per sample.

first: Elizabeth

middle: L

last: Orth

first: Ashley

last: Chui

first: Kuo

last: Gai

middle: A


title: Brachypodium distachyon identification of MeJA responsive genes in wild type and MTL-overexpression plants

city: Frederiksberg C

first: Stephan

last: Wenkel

address: Thorvaldsensvej 40

summary: Plants were treated with MeJA and mRNA was extracted and sequenced

overall_design: Examination of 2 genotypes (Wildtype/ MTL-OX) and 2 treatments (mock/MeJA); 2 biol. Reps; MTL-OX plants were earlier named ABI


title: Overcoming primary and acquired resistance to anti-PD-L1 therapy by induction and activation of tumor-residing cDC1s

city: Buffalo

first: Mark

middle: D

last: Long

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: T-cell exclusion from the tumor microenvironment (TME) is a significant obstacle in cancer immunotherapy. Evidence indicates crucial roles of Batf3-dependent dendritic cells for inducing antitumor T-cell immunity. However, strategies to maximize the engagement of Batf3-dependent dendritic cells  into such ‘cold tumors’ remain elusive.  Using multiple syngeneic orthotopic mouse models of non-T cell-inflamed tumors, we hypothesized that in situ induction and activation of tumor-residing Batf3-dependent dendritic cells  overcomes poor T-cell infiltration.  In situ immunomodulation with Flt3L, radiotherapy, and TLR3/CD40 stimulation induces an influx of stem-like Tcf1+Slamf6+CD8+ T cells, triggers robust regression not only of primary, but also untreated distant tumors, and renders non-T cell-inflamed tumors responsive to anti-PD-L1 therapy. Furthermore, serial ISIM reshapes repertoires of intratumoral T cells, overcomes acquired resistance to anti-PD-L1 therapy, resulting in eradication of tumors, and establishes tumor-specific immunological memory. These findings provide new insights into Batf3-dependent dendritic cells  biology as a critical determinant to the formation of a T cell-inflamed TME.

overall_design: To investigate treatment effects on tumor infiltrating immune cell populations, we sorted live tumor-infiltrating CD45+ cells from subcutaneous (s.c.) AT-3 tumors, which were treated with either ISIM (I), aPD-L1 (P), both (IP) or left untreated (NT) and performed scRNA-seq. Droplet-based 3’ end massively parallel single-cell RNA sequencing was performed by encapsulating sorted live CD45+ cells into droplets and libraries prepared using Chromium Single Cell 30 Reagent Kits V3 according to manufacturer’s protocol (10x Genomics).

first: Takaaki

last: Oba

first: Fumito

last: Ito


title: Identification of human endogenous retroviruses working as enhancers in cancer cells

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

institute: The Institute of Medical Science, The University of Tokyo

summary: Human endogenous retroviruses (HERVs) are a sort of transposable elements. HERVs harbor abundant regulatory elements in their sequences and have a potential to work as enhancers modulating the expressions of the adjacent genes. Some HERV-enhancers are particularly activated in cancer cells and suspected to be associated with cancer progression. To verify the enhancer activity of HERVs on the gene expressions in lung adenocarcinoma cells, we established the HERV-excised A549 cell lines using a CRISPR-Cas9 system and performed RNA sequencing (RNA-Seq) analysis of these cells.

overall_design: First, an A549 cell line stably expressing Cas9 (referred to as A549/Cas9 cell) was established. Second, a pair of guide RNAs that are specific to the 5´- and 3´-flanking regions of the target HERV were co-transfected into A549/Cas9 cells. Through limiting dilution, single cell clones were picked up and screened by genotyping PCR. The resultant clones in which the targeted HERV was excised homozygously were obtained. As a control, the A549/Cas9 cells that were transfected with non-target control guide RNA were prepared and cloned as described above. Total RNA was extracted from these cells by QIAamp RNA Blood Mini Kit (QIAGEN #52304) and treated with RNase-Free DNase Set (QIAGEN #79254). Quality check of the purified RNA, library construction, and sequencing were performed by Novogene (https://en.novogene.com). Pair-ended and 150bp read length sequencing was performed by Illumina Novaseq6000.

first: Izumi

last: Kimura

first: Andrew

last: Soper

first: Naoko

last: Misawa

first: Jumpei


title: Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

city: Lincoln

first: GEN

last: XU

state: Nebraska

address: 383 Plant Science Hall  Department of Agronomy and Horticulture

institute: University of Nebraska-Lincoln

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a ubiquitous chromatin feature — in maize, more than 25% of cytosines in the genome are methylated. Recently, major progress has been made in describing the molecular mechanisms driving methylation, yet variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here we leveraged whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to investigate the adaptive and phenotypic consequences of methylation variations in maize. By using a novel estimation approach, we inferred the methylome site frequency spectrum (mSFS) to estimate forward and backward methylation mutation rates and selection coefficients. We only found weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) were identified in population-wide that are correlated with recent selection. Further investigation revealed that DMRs are enriched in 5’ untranslated regions, and that maize hypomethylated DMRs likely helped rewire distal gene regulation. For two trait-associated DMRs, vgt1-DMR and tb1DMR, our HiChIP data indicated that the interactive loops between DMRs and respective downstream genes were present in B73, a modern maize line, but absent in teosinte. Functional analyses suggested that these DMRs likely served as cis-acting elements that modulated gene regulation after domestication. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.

overall_design:
We collected whole-genome sequencing and bisulfite sequencing data of 51 samples, including the wild ancestor of maize — teosinte (Zea mays ssp. parviglumis, N=20), Mexican landraces (N=17),and modern maize inbred lines (N=14) to understand the impact of epigenetics on maize domestication.
The "modern maize inbred lines (N=14)" were downloaded from NCBI.  The descriptive details for all 51 samples are in supplementary file metadata_51samples.xls.

first: Gen

last: Xu

first: Jing

last: Lyu

first: Qing

last: Li

first: Han

last: Liu

first: Dafang

last: Wang

first: Mei

last: Zhang

first: Nathan

first: Jeffrey

last: Ross-Ibarra

first: Jinliang

last: Yang


title: Gene expression profiling of CD34+/CD38- stem cells and CD34+/CD38+ progenitor cells from healthy control samples versus acute myeloid leukemia (AML) and chronic myeloid leukemia (CML)

status: Public on Sep 21 2020

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

summary: In an attempt to identify novel markers and immunologic targets in leukemic stem cells (LSC) in acute myeloid leukemia (AML) and chronic myeloid leukemia (CML), we screened samples of patients with AML, CML, and controls for expression of cell surface antigens on CD34+/CD38− and CD34+/CD38+ cells by multi-color flow cytometry. In addition, we examined mRNA expression profiles in highly purified CD34+/CD38− and CD34+/CD38+ cells by gene array- and qPCR analyses. Aberrantly expressed markers were identified in all patient cohorts examined.

overall_design: To define differences in mRNA expression patterns in stem- and progenitor cells from three healthy donors, three patients with AML and three patients with CML, gene array analyses were performed

first: Harald

last: Herrmann

first: Irina

last: Sadovnik

first: Peter

last: Valent


title: Sperm DNA methylation changes after nut supplementation in healthy men consuming a Western-style diet

city: Salt Lake City

first: Albert

last: Salas-Huetos

state: UT

address: 675S Arapeen Dr

department: Andrology

institute: University of Utah

summary:
Background
Many environmental and lifestyle factors have been implicated in the decline of sperm quality, with diet being one of the most plausible factors identified in recent years. Moreover, several studies have reported a close association between the alteration of specific sperm DNA methylation signatures and semen quality.

Objectives
To evaluate the effect of tree nuts consumption on sperm DNA methylation patterns in healthy individuals reporting eating a Western‐style diet.

Material and Methods
This is a post‐hoc analysis conducted in a subset of participants (healthy, non‐smoking, and young) from the FERTINUTS 14‐wk randomized‐controlled, parallel‐trial, recruited between December 2015 and February 2017. The participants included in the current study (n=72) were randomly selected in a proportion 2:1 from the original FERTINUTS trial between the 98 participants that completed the entire dietary intervention (nut group, n=48; control group, n=24). Sperm DNA methylation patterns were examined at baseline and after 14 weeks in 48 individuals consuming 60 g/d of mixed nuts (nuts group) and in 24 individuals following the usual Western‐style diet avoiding consumption of nuts (control group).

Results
Over the course of the trial, no significant changes in global methylation were observed between groups. However, in the nuts group, we identified 36 genomic regions that were significantly differentially methylated between the baseline and the end of the trial and 97.2% of the regions displayed hypermethylation. We identified no such change in the control group over the same period of time. We also utilized the recently developed germ line age calculator to determine if nut consumption resulted in alterations to the epigenetic age of cells and no significant differences were found.

Discussion and Conclusion
Adding nuts to a regular Western‐style diet subtly impacts sperm DNA methylation in specific regions, demonstrating that there are some sperm epigenome regions that could respond to diet.

overall_design: Bisulphite converted DNA from the 96 samples (24 baseline and 24 after nuts consumption (nuts group) and 24 baseline and 24 after non nuts consumption (control group)) were hybridised to the Infinium® MethylationEPIC BeadChip microarrays.

first: Emma

middle: R

last: James

first: Jordi

last: Salas-Salvadó

first: Monica

last: Bulló

first: Kenneth

middle: I

last: Aston

first: Douglas

middle: T

last: Carrell

first: Timothy

last: Jenkins


title: Small RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; msh1 mutant; dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_sRNA-seq]

status: Public on Sep 20 2020

city: University Park

first: Hardik

last: Kundariya

address: 361 N. Frear

institute: The Pennsylvania State University

summary: Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the small RNA sequencing. Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the small RNA sequencing.

overall_design: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1 grafts were sequenced. 3 plants from msh1 mutant and dcl2,3,4,msh1 quadruple mitant rootstocks  were sequenced.

first: Xiaodong

first: Sally

last: Mackenzie


title: RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_root_RNA-seq]

summary: Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1) and on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on 0.5M MS growth medium and root tissue was collected after 12 days and used for the RNA sequencing.

overall_design: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1 grafts were sequenced.


title: Bisulfite (methylome) sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0; msh1 mutant; dcl2,3,4,msh1 quadruple mutant in Arabidopsis [msh1_graft_BS-seq]

summary: Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the bisulfite sequencing (methylome). Tissue from the msh1 mutant and dcl2,3,4,msh1 quadruple mutants used as rootstocks was similarly collected at the bolting stage and used for the bisulfite sequencing.

overall_design: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1; Col-0 on Col-0 grafts were sequenced. 3 plants from msh1 mutant and dcl2,3,4,msh1 quadruple mitant rootstocks  were sequenced.


title: Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants [Tomato_graft_RNAseq]

summary: RNA sequencing  of progenies of Rutgers CV. Wild type  grafted on Rutgers transgenic MSH1-RNAi ; Rutgers CV. Wild type  grafted on Rutgers Wild type

overall_design: The young leaf tissue of 3 progenies plants from Rutgers CV. Wild type  grafted on Rutgers transgenic MSH1-RNAi  and Rutgers CV. Wild type  grafted on Rutgers CV. Wild type  were sequenced.


title: Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants

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

sample_organism:
Arabidopsis thaliana
Solanum lycopersicum

overall_design: Refer to individual Series


title: Transcriptomic and functional deficits in human TREM2-/- microglia impair response to Alzheimer's pathology in vivo [scRNA-seq]

status: Public on Sep 19 2020

first: Mathew

last: Blurton-Jones

summary: scRNA-sequencing of human xenotransplanted microglia isogenic for TREM2 after exposure to amyloid pathology

overall_design: Single-cell comparison of WT and KO TREM2 microglia isolated from 6 month old WT and 5X-MITRG mice

first: Amanda

last: McQuade

first: Jonathan

last: Hasselmann


title: Heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants [tomato_graft_methylome]

summary: Bisulfite (methylome) sequencing of progenies of Rutgers CV. Wild type  grafted on Rutgers MSH1-RNAi line; Rutgers CV. Wild type  grafted on Rutgers Wild type

overall_design: The young leaf tissue of 3 progenies plants from Rutgers CV. Wild type  grafted on Rutgers MSH1-RNAi line and Rutgers CV. Wild type  grafted on Rutgers CV. Wild type  were sequenced.

last: Yang


title: FHOD formin and SRF promote striated muscle development through separate pathways in C. elegans

city: Syracuse

first: David

last: Pruyne

address: 766 Irving Avenue

department: Cell and Developmental Biology

institute: SUNY Upstate Medical University

summary: We show that striated muscle-expressed genes affected by reduction in UNC-120/SRF activity are not similarly affected by absence of the FHOD-1 formin. This suggests FHOD-1 does not affect striated muscle development via promotion of UNC-120/SRF-dependent transcription.

overall_design: mRNA-seq was performed on the Illumina NextSeq 500 platform to measure gene expression in N2 wild-type, XA8001 fhod-1(tm2363), and RW364 unc-120(st364) L3 stage C. elegans larvae grown at 15˚C.

first: Curtis

last: Yingling


title: Total RNA sequencing of progenies of Col-0 grafted on msh1; Col-0 grafted on dcl2,3,4,msh1; Col-0 grafted on Col-0 in Arabidopsis [msh1_graft_leaf_RNA-seq]

summary: Col-0 floral stem was grafted on the msh1 mutant (Col-0/msh1); on the dcl2,3,4,msh1 quadruple mutant (Col-0/dcl2,3,4,msh1); on Col-0 (Col-0/Col-0). Seeds were collected from the grafted Col-0 scion after grafts were established. Seed coming from the graft then were grown on the peat mix, leaf tissue was collected at the bolting and used for the total RNA sequencing.

overall_design: 3 progenies plants from each Col-0 on msh1; Col-0 on dcl2,3,4,msh1; Col-0 on Col-0 grafts were sequenced.


title: Next Generation Sequencing of Chimeric antigen receptor T (CAR-T) cells polarized under Th9 condition

status: Public on Sep 18 2020

city: Houston

first: Lintao

last: Liu

state: Texas

address: 6550 FANNIN ST, RI-SMITH8-053

department: Cancer

institute: Houston Methodist Research Insititute

summary: Isolated human T cells was stimulated by anti CD3/CD28 Dynabeads and polarized under Th1 (IL2) or Th9 (IL4 plus TGF beta) condition.After 24 hours, cells were transduced with lentivirus. Medium were renewed every 2 days and cells were maintained at a concentration of 1 million per milliliter. On day 16 of culture total RNA was isolated from CAR-T cells using RNeasy Mini kits (Qiagen) following the manufacturer's instruction. Quality of total RNA was evaluated using RNA 6000 Nano LabChip. Qualified RNA was subject to next generation sequencing.

overall_design: Next ggeneration sequencing was performed on chimeric antigen receptor T cells polarized under Th1 or Th9 condition.


title: LncRNA AC010789.1 promotes colorectal cancer progression by targeting microRNA-432-3p/ZEB1 axis and the Wnt/β-catenin signaling pathway

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

institute: The Second Hospital of Shandong University

summary: Accumulating literatures have indicated that long non-coding RNAs (lncRNAs) are crucial molecules in tumor progression in various human cancers, including colorectal cancer (CRC). However, the clinical significance and regulatory mechanism of a vast majority of lncRNAs in CRC remain to be determined. The current study aimed to explore the function and molecular mechanism of lncRNA AC010789.1 in CRC progression.

overall_design: The expression profiles and clinical value of lncRNAs in CRC were analyzed by The Cancer Genome Atlas (TCGA) database. The level of AC010789.1 was evaluated by quantitative real-time PCR (qRT-PCR) and in situ hybridization (ISH). Subsequently, AC010789.1 was silenced to investigate the abilities in proliferation, migration, invasion and epithelial-to-mesenchymal transition (EMT) of CRC cells. Nude mice models were used to asses tumor growth and metastasis in vivo. Furthermore, we conducted bioinformatics analysis, dual-luciferase reporter assays and RNA sequencing to determine the underlying regulatory mechanism of AC010789.1-mediated CRC progression.

first: Weili

last: Duan

first: Xue

last: Kong

first: Juan

last: Li

first: Peilong

first: Yinghui

last: Zhao

first: Tong

first: Helen

middle: B

last: Binang

first: Yunshan

last: Wang

first: Lutao

last: Du

first: Chuanxin


title: Impact of transcription factor ETV1 on HCT116 colon cancer cells.

status: Public on Sep 22 2020

city: Oklahoma City

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

summary: We identified that ETV1 downregulation affects growth of HCT116 cells, and concomitantly affects their transcriptome. This suggests that ETV1 might be involved in colon cancer formation and/or progression.

overall_design: HCT116 cells were infected with retrovirus expressing control shRNA or two different ETV1 shRNAs (#1 and #5). RNA was extracted and subjected to RNA-sequencing.

first: Ralf

last: Janknecht

first: Willard

last: Freeman


title: Transcriptome mapping of alveolar macrophages developing under Scgb1a1 deficiency.

city: Phoenix

first: Deepak

last: Nayak

state: Arizona

address: 475 N. 5th Street

institute: University of Arizona College of Medicine

summary: Alveolar macrophage (AM) is a mononuclear phagocyte key to the defense against respiratory infections. To understand AM’s role in airway disease development, we examined the influence of Secretoglobin family 1a member 1 (SCGB1A1), a pulmonary surfactant protein, on AM development and function. In a murine model, high-throughput RNA-sequencing and gene expression analyses were performed on purified AMs isolated from mice lacking in Scgb1a1 gene and were compared with that from mice expressing wild type Scgb1a1 at weaning (4wk), puberty (8wk), early adult (12wk) and middle age (40wk). AMs from early adult mice under Scgb1a1 sufficiency demonstrated a total of 37 upregulated biological pathways compared to that at weaning, from which 30 were directly involved with antigen presentation, anti-viral immunity and inflammation. Importantly, these pathways under Scgb1a1 deficiency were significantly downregulated compared to that in the age-matched Scgb1a1-sufficient counterparts. Furthermore, AMs from Scgb1a1-deficient mice showed an early activation of inflammatory pathways compared with that from Scgb1a1-sufficient mice. Our in vitro experiments with AM culture established that exogenous supplementation of SCGB1a1 protein significantly reduced AM responses to microbial stimuli where SCGB1a1 was effective in blunting the release of cytokines and chemokines (including IL-1b, IL-6, IL-8, MIP-1a, TNF-a and MCP-1). Taken together, these findings suggest an important role for Scgb1a1 in shaping AM-mediated inflammation and immune responses, and in mitigating cytokine surges in the lungs.

overall_design: Examination of AM transcriptome from 2 mouse strains (Scgb1a1+/+, WT and Scgb1a1-/-, KO) at 4 time points (4, 8, 12 and 40 weeks of age) in triplicates

first: Min

last: Xu

first: Wei


title: Next generation sequencing analysis of primary rat lung fibroblast, primary rat lung alveolar type 2 cell and a novel 10-4A rat lung cell line transcriptomes

city: Ulm

first: Manfred

last: Frick

address: Albert-Einstein Allee 11

country: Cote d'Ivoire

institute: University of Ulm

summary: Purpose: We report the application of single-molecule-based sequencing technology for high-throughput profiling of a novel 10-4A rat lung fibroblast cell line and compared the transcriptome to freshly isolated primary rat lung fibroblasts and freshly isolated primary rat lung alveolar type 2 cells.

overall_design: Methods: mRNA profiles 10-4A, primary fibroblasts and primary alvelar type 2 cells were generated by deep sequencing, in triplicates or quadruplicates, using Illumina HiSeq2000. Sequenced read quality was checked with FastQC v0.11.2. Duplication rates of the RNA-Seq samples were computed with bamUtil v1.0.11 to mark duplicate reads and the dupRadar v1.4 Bioconductor R package for assessment. The gene expression profiles were quantified using Cufflinks software version 2.2.

first: Julia

last: Nemeth

first: Annika

last: Schundner

first: Karsten

last: Quast


title: Small RNA sequencing from siERH or control siRNA treated cells

status: Public on Sep 17 2020

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Small RNA sequencing experiments were performed to check whether ERH affects miRNA biogenesis.

overall_design: Mature miRNAs were sequenced from HEK293E or K562 cells which had been transfected with siERH or control siRNAs.

first: S

middle: C

first: V

middle: N

last: Kim


title: Wnt / Beta-Catenin signalling controls epiblast self-organization in naive and paused states of pluripotency

city: Bern

first: Jie

last: Wu

state: Bern

address: Freiestrasse 3

institute: Department of Chemistry, Biochemistry and Pharmaceutical Sciences

summary: ES cells grown in growth factor depleted matrigel could recapitulate the morphogenesis of the epiblast from E4.5 to E5.5. This process is characterized with the establishment of epithelial polarity. We used Next-generation sequencing (NGS) technique to analyze the transcriptional change of ES cells grown in 3D culture conditions in the presence of DMSO, 2i, CH or FGF2/Activin. The comparison of transcriptom between different conditions helps us to understand the molecular mechanism underlying morphogenesis of the epiblast. We found naïve pluripotency factors are kept in a high level in 2i and CH treatment in comparison with DMSO and FGF2/Activin treatment. We identified 5 naïve pluripotency factors which may have potential regulatory function in epithelial polarity. To further analyze these 5 pluripotency factors, we found Esrrb is the core transcriptional factor countering epithelial polarity. We also used Next-generation sequencing (NGS) technique to analyze the transcriptional change of Esrrb delta/delta (+4OHT) and control Esrrb fl/fl (-4OHT) ES cells in the presence of CH. Esrrb delta/delta (+4OHT) cell grown in 3D become polarized at 24 hours, whereas the control Esrrb fl/fl (-4OHT) ES cells are still non-polarized. By analyzing the RNA-Seq data, we found the enrichment of MAPK, Apoptosis, Focal adhesion and Tight junction KEGG pathways in Esrrb delta/delta compared to control Esrrb fl/fl cells. This result suggests the essential function of Esrrb in regulating epithelial polarity.

overall_design: We performed RNA-sequencing on ES cells grown in growth factor depleted matrigel with 4 different culture conditions and each culture condition has 3 replicates. We also performed RNA-sequencing on  Esrrb delta/delta (+4OHT) and control Esrrb fl/fl (-4OHT) ES cells grown in growth factor depleted matrigel in the presence of CH and each treatment has 3 replicates.


title: RNA editing in cancer impacts mRNA abundance in immune response pathways

city: Los Angeles

first: Xinshu

last: Xiao

address: 610 Charles E. Young Drive S

institute: University of California, Los Angeles

summary: RNA editing generates modifications to RNA sequences, thereby increasing protein diversity and shaping various layers of gene regulation. Recent studies have revealed global shifts in editing levels across many cancer types, as well as a few specific mechanisms implicating individual sites in tumorigenesis or metastasis. However, most tumor-associated sites, predominantly in noncoding regions, have unknown functional relevance. Here, we carry out integrative analysis of RNA editing profiles between epithelial (E) and mesenchymal (M) tumors, since epithelial-mesenchymal transition (EMT) is a key paradigm for metastasis. We identify distinct editing patterns between E and M tumors in seven cancer types using TCGA data, an observation further supported by single-cell RNA-seq data and ADAR perturbation experiments in cell culture. Through computational analyses and experimental validations, we show that differential editing sites between E and M phenotypes function by regulating mRNA abundance of their respective genes. Our analysis of >120 RNA-binding proteins revealed ILF3 as a potential regulator of this process, supported by experimental validations. Consistent with the known roles of ILF3 in immune response, E-M differential editing sites are enriched in genes involved in immune and viral processes. The strongest target of editing-dependent ILF3 regulation is the transcript encoding PKR, a crucial player in immune and viral response. Our study reports widespread differences in RNA editing between epithelial and mesenchymal tumors and a novel mechanism of editing-dependent regulation of mRNA abundance. It reveals the broad impact of RNA editing in cancer and its relevance to cancer-related immune pathways.

overall_design:
eCLIP-seq in A549 cells.
RNA-seq in A549 cells upon knockdown of ADARs.

first: Tracey

last: Chan

first: Ting

last: Fu

first: Jae

middle: H

last: Bahn

first: Hyun-Ik

last: Jun

first: Jae-Hyung

last: Lee

first: Giovanni

last: Quinones-Valdez

first: Chonghui

last: Cheng


title: Comparison of epithelial cells from various epithelia and hair follicle stem cells [microarray]

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

institute: University of Lausanne

summary: The potency of an adult stem cell is restricted to certain lineages during embryonic life, in response to a specific microenvironment (the niche) and it is maintained for life. Lineage restriction is considered immutable. We have investigated if adult stem cells isolated from different epithelia could change fate by exposing them to a hairy skin niche. We have demonstrated that clonogenic stem cells restricted to a single epithelial lineage and cultured from various Tp63-expressing tissues e.g, the bladder the oral mucous, the oesophagus or the thymus can acquire new functionality. When exposed to a hair skin microenvironment, these stem cells acquire the capacity to generate hair follicles and sebaceous glands, thus behaving like bona fide hairy skin multipotent stem cells. Genome wide-screen analysis has demonstrated that the stem cells express transcription factors typical of hair follicle differentiation, even though they continue to express some of the genes linked to their origin. This increase in potency demonstrates that lineage restriction is not immutable.

overall_design: Expression profile difference between hair follicle and cells from various epithelia before and after transplantation into skin

first: Stephanie

last: Claudinot

first: Hideo

last: Oshima

first: Christele

last: Gonneau

first: Paola

last: Bonfanti

first: Geert

last: Martens

first: Daniel

last: Littman

first: Michael

last: Nicolas

first: Ariane

last: Rochat

first: Yann

last: Barrandon

first: Sylvain

last: Pradervand

first: Otto

last: Hagenbüchle


title: Comparison of epithelial cells from various epithelia and hair follicle stem cells

summary: The potency of an adult stem cell is restricted to certain lineages during embryonic life, in response to a specific microenvironment (the niche) and it is maintained for life. Lineage restriction is considered immutable. We have investigated if adult stem cells isolated from different epithelia could change fate by exposing them to a hairy skin niche. We have demonstrated that clonogenic stem cells restricted to a single epithelial lineage and cultured from various Tp63-expressing tissues e.g, the bladder,  the vagina, or the thymus can acquire new functionality. When exposed to a hair skin microenvironment, these stem cells acquire the capacity to generate hair follicles and sebaceous glands, thus behaving like bona fide hairy skin multipotent stem cells. Genome wide-screen analysis has demonstrated that the stem cells express transcription factors typical of hair follicle differentiation, even though they continue to express some of the genes linked to their origin. This increase in potency demonstrates that lineage restriction is not immutable.

last: Calderon Copete


title: Expression of germinal center T follicular helper (GC-Tfh) cells and pre-Tfh cells from tonsils (Tons) and follicular lymphoma lymph nodes (FL).

status: Public on Sep 16 2020

city: Rennes

first: Patricia

last: Amé-Thomas

address: 2 Avenue du Pr Léon Bernard

department: Faculté de Médecine

institute: INSERM UMR1236

summary: GEP on Affymetrix Genechip HTA 2.0 microarrays was performed on ex vivo cell-sorted GC-Tfh and pre-Tfh from TONS and FL

overall_design: GEP was performed on 3 GC-Tfh cell samples and 3 pre-Tfh cell samples from non malignant TONS, and  3 GC-Tfh cell samples and 3 pre-Tfh cell samples from FL.

last: Amé


title: RNAseq of MLL-AF9+ lin- ckitlo sca1- (LKlo) cells was performed after sorting these cells from the BM of Nes-creERT2;iDTA (N=8) or control (N=6) mice.

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

institute: CNIC

summary: Gene expression changes in leukemic LKlow cells after depleting nestin+ cells in vivo

overall_design: Sorted cells were combined for a total of 3 biological replicates (each consisting of pooled LKlo cells from from 2-3 mice). Total RNA was isolated using the Arcturus Picopure RNA Isolation Kit (Thermo Fisher Scientific). RNA was amplified and prepared for RNA-Seq using the Ovation RNA-Seq System v2 (NuGEN) following the manufacturer’s recommendations.

first: Dorian

last: Forte

first: María

last: García-Fernández

first: Abel

last: Sánchez-Aguilera

first: Vaia

last: Stavropoulou

first: Claire

last: Fielding

last: Martín-Pérez

first: Juan

last: Antonio López

first: Ana

middle: S

last: Costa

first: Laura

last: Tronci

first: Efterpi

last: Nikitopoulou

last: Barber

first: Paolo

last: Gallipolli

first: Ludovica

last: Marando

first: Carlos

last: Fernández de Castillejo

first: Alexandar

last: Tzankov

first: Sabine

last: Dietmann

first: Michele

last: Cavo

first: Lucia

last: Catani

first: Antonio

last: Curti

first: Jesús

last: Vázquez

first: Christian

last: Frezza

first: Brian

last: Huntly

first: Juerg

last: Schwaller

first: Simón

last: Méndez-Ferrer


title: IRF3 prevents colorectal tumorigenesis via inhibiting the nuclear translocation of β-catenin

city: BEIJING

first: Qingren

last: Meng

address: BEIJINGCHAOYANG

institute: BIG

summary: Occurrence of Colorectal cancer（CRC）is relevant with gut microbiota. However, role of IRF3, a key signaling mediator in innate immune sensing, has been barely investigated in CRC. Here, we unexpectedly found that the IRF3 deficient mice are hyper-susceptible to the development of intestinal tumor in AOM/DSS and Apcmin/+ models. Genetic ablation of IRF3 profoundly promotes the proliferation of intestinal epithelial cells via aberrantly activating Wnt signaling. Mechanically, IRF3 in resting state robustly associates with the active β-catenin in the cytoplasm, thus preventing its nuclear translocation and cell proliferation, which can be relieved upon microbe-induced activation of IRF3. In accordance, the survival of CRC is clinically correlated with the expression level of IRF3. Therefore, our study identifies IRF3 as a negative regulator of the Wnt/β-catenin pathway and a potential prognosis marker for Wnt-related tumorigenesis, and describes an intriguing link between gut microbiota and CRC via the IRF3-β-catenin axis.

overall_design: Colon and colon tumor tissue mRNA profiles of AOM/DSS day 90 wild type (WT) and IRF3-/- (KO) mice

first: Miao

last: Tian

first: Xiaojian

last: Wang


title: A Global CRISPR/Cas9 Screen Identifies Mitochondrial Translation as an Essential Process for Latent KSHV Infection in Human Endothelial Cells

city: Seattle

first: Michael

last: Lagunoff

state: WA

address: 750 Republican St.

department: Microbiology

institute: University of Washington

summary: We report on a CRISPR/Cas9 screen in human endothelial cells comparing uninfected to KSHV infected cells.

overall_design: Comparison of sgRNA abundance between uninfected and KSHV infected cells in both the living cells and dead cells over an 8 day selection period.

first: Daniel

last: Holmes


title: Bovine monocyte derived macrophages from peripheral blood

city: Juiz de Fora

first: Raquel

middle: Morais de Paiva

last: Daibert

address: Av. Eugenio do Nascimento, 610

country: Brazil

institute: Embrapa Dairy Cattle

summary: Resistance traits of parasitic infestation and diseases in bovine breeds display various unknown differences in the immune response indicating to be related to the host`s genomic background. We studied the differential gene expression of monocyte-derived macrophages (MDMs) stimulated or unstimulated with LPS in vitro, from two bovine breeds by RNA sequence methodology. MDMs were grown in supplemented RPMI medium for 11 days. Then, 100 ng/ml LPS was added to medium for 48h in treated samples. Total RNA was extracted from macrophages and sequenced by RNA-Seq technology. Resulting sequences were mapped to the bovine reference genome and gene expression was compared between breeds. We found several differences in immune response activation, as leucocyte recruitment, immune response, antigen processing and presentation, positive regulation of NFκB and cell cycle biological processes in unstimulated cells and lipid metabolism, inflammatory response, regulation of cell proliferation and cycle and arginine catabolism in LPS treated cells. Finally, LPS seems to trigger inflammation by distinct pathways in these two bovine breeds.

overall_design: Comparison between bovine primary monocyte derived macrophage cultured cells from two differrent breeds treated and not-treated with LPS for 48h

first: Wanessa

last: Carvalho

first: Marco

last: Machado


title: Expression data of human stromal cells isolated from tonsils

first: Patricia

last: Amé-Thomas

summary: GEP on Affymetrix U133+2.0 microarrays was performed on in vitro expanded stromal cells

overall_design: GEP was performed on 3 different stromal cell samples derived from tonsils, stimulated (FRCLs) or not (TSCs) with lymphotoxin-alpha1béta2 and tumor necrosis factor-alpha


title: Liver Epithelial Focal Adhesion Kinase Modulates Fibrogenesis and Hedgehog Signaling

status: Public on Sep 15 2020

city: san francisco

first: Tammy

last: Chang

state: ca

address: 513 parnassus

department: surgery

country: USA

institute: UCSF

summary: Focal adhesion kinase (FAK) is an important mediator of extracellular matrix-integrin mechano-signal transduction that regulates cell motility, survival, and proliferation.  As such, FAK is being investigated as a potential therapeutic target for malignant and fibrotic diseases, and numerous clinical trials of FAK inhibitors are underway.  The function of FAK in non-malignant non-motile epithelial cells is not well understood.  We previously showed that hepatocytes demonstrated activated FAK near stiff collagen tracts in fibrotic liver.  In this study, we examined the role of liver epithelial FAK by inducing fibrotic liver disease in mice with liver epithelial FAK deficiency.  We found that mice that lack FAK in liver epithelial cells develop more severe liver injury and worse fibrosis as compared to controls.  Increased fibrosis in liver epithelial FAK-deficient mice is linked to the activation of several pro-fibrotic pathways, including the hedgehog-smoothened pathway.  FAK-deficient hepatocytes produce increased Indian hedgehog in a matrix stiffness-dependent manner.  Furthermore, there is increased expression of the hedgehog receptor, smoothened, in macrophages and biliary cells of hepatocyte-specific FAK-deficient fibrotic liver.  These results indicate that liver epithelial FAK has important regulatory roles in the response to liver injury and progression of fibrosis.

overall_design: RNA-seq, RNA-scope, histology, and collagen analysis were used to investigate the role of FAK in liver epithelial-specific FAK-deficient mice.

first: Yun

last: Weng

first: Tyler

last: Lieberthal

first: Vivian

middle: X

last: Zhou

first: Maya

last: Lopez-Ichikawa

first: Manuel

last: Armas-Phan

first: Tristan

last: Bond

first: Miya

last: Yoshida

first: Won-Tak

last: Choi


title: RNA sequencing analysis of mouse follicular B cells, memory B cells, plasmablasts and plasma cells

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

institute: Francis Crick Institute

summary: The purpose of this study was to compare relative mRNA transcript levels between mouse follicular B cells, memory B cells, plasmablasts and plasma cells.

overall_design:
Six different B cell subsets were purified by fluorescence-activated cell sorting in triplicate and processed for RNA sequencing. Follicular B cells (FO) were isolated from spleens of  C57BL/6J female mice that had not been deliberately immunised.
IgG1+ or IgM+ memory B cell (MBC) subsets were isolated from C57BL/6J female mice that had been immunised with 4-Hydroxy-3-nitrophenylacetyl (NP) conjugated to chicken gamma globulin (CGG) in alum 35d prior to isolation of cells.
Splenic plasmablasts (PB) and plasma cells (PC) and bone marrow PC were isolated from C57BL/6J-Blimp1GFP mice that had been immunised 35d earlier with NP-CGG in alum.
Splenic germinal centre (GC) cells were isolated from C57BL/6J mice that had been immunised 10d earlier with NP-CGG in alum.

first: Jennifer

last: Müller-Winkler

first: Richard

last: Mitter


title: Human immature neutrophils as a functional biomarker of systemic vascular pathologies

city: Oxford

first: Erinke

last: van Grinsven

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

institute: University of Oxford

summary: We used an ex vivo system of murine ER-Hoxb8 neutrophils that phenotypically and morphologically recapitulate neutrophil maturation stages during five days of in vitro culture in the presence of G-CSF. To investigate the development of the ROS system in neutrophils during their development, we compared transcriptomes of D0, D1, D3 and D5 Hoxb8 neutrophils.

overall_design: Paired-end sequencing of mRNA of Hoxb8 neutrophils of different in vitro differentiation stages, of two biological replicates, using Illumina HiSeq4000.

first: Lihui

last: Wang

first: Zhichao

last: Ai

first: Tariq

last: Khoyratty

first: Irina

last: Udalova


title: Expression data from the cerebral cortex of sugarcane top ethanolic extract (STEE)-administered SAMP8 mice, water-administered SAMP8 mice, and water-administered SAMR1 mice.

status: Public on Sep 14 2020

city: Tsukuba

first: Kengo

last: Iwata

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary:
STEE regulated a wide range of biological processes in the cerebral cortex of SAMP8 mice.
RNA samples were extracted from cerebral cortices with Isogen (Nippon Gene, Toyama, Japan) and were amplified and biotinylated with Affymetrix 3’ IVT PLUS Reagent Kit (Affymetrix, Santa Clara, CA), according to the manufacturer’s instructions. The integrity of RNA was quantified using NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and one hundred ng of total RNA from each sample was used to generate amplified and biotinylated complementary RNA (cRNA) from poly (A) RNA in a total RNA. Biotinylated cRNA was hybridized onto Affymetrix Mouse Genome 430 PM array strips (Affymetrix) for 16 hrs at 45℃ in the hybridization station. The hybridized arrays were washed, stained, and scanned with GeneAtlas Fluidics and Imaging Station.

overall_design: Microarray analysis was performed in duplicates for each samples. Water-administrated SAMP8 mice are controls to STEE-administrated SAMP8 mice. Water-treated SAMR1 mice are normal aging mice.


title: Changes in Northern Elephant Seal Skeletal Muscle Following Thirty Days of Fasting and Reduced Activity

city: College Station

first: Traver

last: Wright

state: TX

address: 675 John Kimbrough Blvd., TAMU 4253

department: Health and Kinesiology

institute: Texas A&M University

summary: Northern elephant seals (NES, Mirounga angustirostris) undergo an annual molt during which they spend ~40 days fasting on land with reduced activity and lose approximately one-quarter of their body mass. Reduced activity and muscle load in stereotypic terrestrial mammalian models results in decreased muscle mass and capacity for force production and aerobic metabolism. However, the majority of lost mass in fasting female NES is from fat while muscle mass is largely preserved. Although muscle mass is preserved, potential changes to the metabolic and contractile capacity are unknown. To assess potential changes in NES skeletal muscle during molt, we collected muscle biopsies from 6 adult female NES at the beginning of the molt and after ~30 days at the end of the molt. Skeletal muscle was assessed for respiratory capacity using high resolution respirometry, and RNA was extracted to assess changes in gene expression. Despite a month of reduced activity, fasting, and weight loss, skeletal muscle respiratory capacity was preserved with no change in OXPHOS respiratory capacity. Molt was associated with 162 upregulated genes including genes  favoring lipid metabolism and regulating cell cycles. We identified 172 downregulated genes including those coding for ribosomal proteins and genes associated with skeletal muscle force transduction and glucose metabolism. Following ~30 days of molt, NES skeletal muscle metabolic capacity appears largely preserved although mechanotransduction may be compromised. In the absence of exercise stimulus, fasting-induced shifts in skeletal muscle lipid metabolism may stimulate lipid signaling pathways associated with preserving the mass and metabolic capacity of slow oxidative muscle.

overall_design: Skeletal muscle biopsies were taken from adult female northern elephant seals within 5 days of arrival on the beach for the annual molt. Muscle biopsies were taken again (not exclusively paired to the same animals) after an average of 34 days of molt before returning to sea. Samples were preserved in chilled RNAlater for 24 hours before freezing.

first: Randall

middle: W

last: Davis

first: Rachel

last: Holser

first: Luis

last: Huckstadt

first: Christopher

middle: P

last: Danesi

first: Craig

last: Porter

first: Steven

middle: G

last: Widen

first: Terrie

middle: M

last: Williams

first: Daniel

last: Costa

first: Melinda

last: Sheffield-Moore


title: RNA-Seq analysis of genes affected by Cyclophilin A/DIAGEOTROPICA (DGT) in tomato root development

city: Corvallis

first: Molly

last: Megraw

state: Oregon

address: 2082 Cordley Hall

institute: Oregon State University

summary: Cyclophilin A/DIAGEOTROPICA (DGT) has been linked to auxin-regulated development in tomato and appears to affect multiple developmental pathways. Loss of DGT function results in a pleiotropic phenotype that is strongest in the roots, including shortened roots with no lateral branching. Here, we present an RNA-Seq dataset comparing the gene expression profiles of wildtype (Ailsa Craig variety) and dgt tissues from three spatially separated developmental stages of the root tip (differentiation zone, elongation zone, and meristem), with three replicates for each tissue and genotype.

overall_design: RNA-Seq of tissues from three root developmental zones in WT and dgt tomato plants, with three replicates for each tissue and genotype.

first: Maria

last: Ivanchenko

first: Olivia

last: Ozguc