title: The role of NRF2 in the effects of methionine restriction on the transcriptome of mouse livers

status: Public on Jun 30 2021

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

country: USA

institute: Pennington Biomedical Research Center

type: Expression profiling by high throughput sequencing

summary: Dietary methionine restriction results in a robust activation of transcription factor, NRF2, and its target gene expression in the liver. In the current study, we observed liver-specific knockout NRF2 did not affect the physiological responses due to MR consumption. Therefore, there are other transcription factors compensate for the loss of NRF2 in the liver to mediate the effect of MR. The RNAseq experiment was comducted to compare the effect of MR diet in NRF2 WT and KO mice on hepatic transcriptome.

overall_design: Comparison of the effect of methionine restriction (MR) on the hepatic transcriptome in NRF2 WT (each 6 samples from CON and MR fed mice) and NRF2 liver-specific KO mice (each 6 samples from CON and MR fed mice). The Control diets contain 0.86% methionine, the MR diets 0.17% methionine.

first: Han

last: Fang

first: Kirsten

last: Stone

first: Jasleen

last: Kaur

first: Richard

middle: P

last: Carmouche

first: Sara

middle: M

last: Webb

first: Sujoy

last: Ghosh


title: Gene expression in cauliflower curds

city: Grenoble

first: Jérémy

last: LUCAS

address: 17 avenue des Martyrs

country: France

institute: CNRS

summary:
Description of gene expression in various types of cauliflower (including Romanesco type)
Cauliflower structures develop on inflorescences from plants such as the apetala1 cauliflower double mutant in Arabidopsis thaliana or in the edible Brassica oleracea var botrytis or Romanesco. Whereas the genetic basis for the development of such structure is well understood in the model plant Arabidopsis thaliana, it is less understood in Brassica oleracea. In order to gain insight into the gene expression present in cauliflower and Romanesco curds, we performed RNA-seq analyses of mature cauliflowers and Romanesco curds and from growing cauliflowers curds. This analysis allowed to establish the nature of genes from the APETALA1 and CAULIFLOWER clade that are either mutated or expressed at very low levels in curd structures. These results shed light on the molecular nature of structures that have been selected in the domestication process.

overall_design: Cauliflower were harvested from field experiments or bought at producer and RNA-seq was performed on curd sample

last: Lucas

first: Marie

last: LeMasson

first: Gabrielle

last: Tichtinsky

first: François

last: Parcy


title: mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting bodies in Ophiocordyceps Sinensis [mRNA-seq dataset]

city: Chengdu

last: Zhang

state: Sichuan

address: No.1166 Liutai Avenue

department: College of Pharmacy

country: China

institute: Chengdu University of Traditional Chinese Medicine

summary: Ophiocordyceps sinensis (Berk.) Sacc., a complex of larval carcass (sclerotium) and stroma formed by the fungus of Hirsutella sinensis infecting Hepialidae insect larvae, whose fruiting body is also the main fungal structure used for taxonomic identification. However, the induction of fruiting body is still inefficient and the high cost resulting in the large-scale artificial cultivation of this fungus has been unsuccessful in China.In this study,important factors and target genes associated with the fruiting body induction during the development of O. sinensis were identified, providing a basic molecular mechanism for facilitating the large-scale artificial cultivation of O. sinensis.

overall_design: mRNA profiles of the mycoparasite complex (MC), the sclerotium (ST) and the whole O. Sinensis with fruiting body (FB) stages.

first: Jinlin

last: Guo


title: Dysregulation of acrosome formation network by 8-oxoguanine (8-oxoG) in infertile sperm

city: Pyeongchang-gun

first: Eun Seo

last: Kim

address: 25354 Pyeongchang-daero, Daehwa-myeon

department: Department of International Agricultural Technology

country: South Korea

institute: Seoul National University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Various environmental factors contribute to dysregulated spermatogenic gene network, abnormal spermatogenesis, and eventually impaired sperm fertility. 8-hydroxyguanine (8-oxoG) is the most common and well-studied oxidative DNA lesion of the four DNA bases and unrepaired 8-oxoG modifications are associated with DNA fragmentation in sperms. However, the molecular effects of 8-oxoG generated in sperm DNA by oxidative stress on spermatogenesis are not entirely understood.  Here, we identified one infertile Korean native striped cattle at 6-year old (C14) due to asthenozoospermia and teratozoospermia. We compared global concentration of 8-oxoG by reverse-phase liquid chromatography/mass spectrometry (RP-LC/MS), the genomic distribution of 8-oxoG by next-generation sequencing (OG-seq), and expression of sperm proteins by 2-dimensional electrophoresis followed by mass spectrometry (2D/MS) in sperms of C14 with those of normal counterpart (C13).   We found that averaged levels of 8-oxoG in C13 and C14 sperms were 0.027% and 0.044% of total dG and 8-oxoG was significantly greater in infertile sperm DNA (p = 0.0028). More than 81% of the 8-oxoG loci were distributed around the transcription start site (TSS) and 8-oxoG harboring 165 genes, including phospholipases, were annotated exclusively into infertile sperm DNA. Gene set enrichment analysis (GSEA) and the protein-protein interaction networking revealed that the Golgi apparatus was significantly enriched with the 8-oxoG genes of infertile sperm (q = 2.20E-07). Proteomic analysis verified that acrosome-related proteins including Acrosin-binding protein (ACRBP) and Sperm equatorial segment protein 1 (SPESP1) were 1.6-fold and 2.6-fold down-regulated in infertile sperm, respectively.  These results suggest that 8-oxoG formation during spermatogenesis would dysregulate the acrosome-related gene network, causing structural and functional defects of sperm, leading to infertility.

overall_design: We identified one infertile Korean native striped cattle at 6-year old (C14) due to asthenozoospermia and teratozoospermia. We compared global concentration of 8-oxoG by reverse-phase liquid chromatography/mass spectrometry (RP-LC/MS), the genomic distribution of 8-oxoG by next-generation sequencing (OG-seq), and expression of sperm proteins by 2-dimensional electrophoresis followed by mass spectrometry (2D/MS) in sperms of C14 with those of normal counterpart (C13)

first: Sung

first: Jongsoo

last: Mok

first: Eun

middle: S

first: Bongki

first: Joonghoon

last: Park


title: Expression data from JVM13 cells with cyclin D1 exogenous overexpression

city: Barcelona

first: Santiago

last: Demajo

state: Barcelona

address: Rosselló 153

country: Spain

institute: IDIBAPS - Hospital Clínic Barcelona

summary:
Mantle cell lymphoma (MCL) is an aggressive B-cell neoplasm characterized by the t(11;14)(q13;q32) translocation leading to cyclin D1 overexpression. Cyclin D1 is a major cell cycle regulator and also has a role in transcription, but the effect of the latter in tumorigenesis remains largely unknown. Here, we investigated the transcriptional role of cyclin D1 in MCL and its impact on the pathogenesis of this neoplasm. Integrating genome-wide expression analysis of cyclin D1-silenced and overexpressing cells with cyclin D1 chromatin binding profiles, we identified a cyclin D1-activated transcriptional program in MCL cells.
We used microarrays to analyze the genome-wide expression modulation in cyclin D1 overexpression models established in the cyclin D1-negative lymphoblastoid cell line JVM13.

overall_design: We generated cyclin D1 inducible overexpression models in JVM13, with wild type cyclin D1 or a highly stable form of the protein with the T286A mutation. Control cells were generated in parallel with the corresponding empty vector. We then treated the cells with doxycycline to induce the expression of cyclin D1 and we extracted RNA to performed expression microarrays.

first: Robert

last: Albero

first: Guillem

last: Clot

first: Pedro

last: Jares


title: Next Generation Sequencing Facilitates Quantitative Analysis of ventilated and unventilated preterm lambs and normal full-term lambs.

city: Salt Lake City

middle: Allen

last: McKnight

state: UT

address: Wakara Way

department: Pediatrics

institute: University of Utah

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

overall_design: Refer to individual Series


title: Srsf3 mediates alternative RNA splicing downstream of PDGFRα signaling.

city: Aurora

first: Katherine

middle: Ann

last: Fantauzzo

state: CO

address: 12801 East 17th Avenue, MS 8120

department: Craniofacial Biology

institute: University of Colorado Anschutz Medical Campus

summary: Signaling through the platelet-derived growth factor receptor alpha (PDGFRa) is critical for mammalian craniofacial development, though the mechanisms by which the activity of downstream intracellular effectors is regulated to mediate gene expression changes have not been defined. We find that the RNA-binding protein Srsf3 is phosphorylated at Akt consensus sites downstream of PI3K-mediated PDGFRa signaling in palatal mesenchyme cells, leading to its nuclear translocation. We further demonstrate that ablation of Srsf3 in the neural crest lineage leads to facial clefting due to defective cranial neural crest cell specification and survival. Finally, we show that Srsf3 regulates the alternative RNA splicing of transcripts encoding protein kinases in the facial process mesenchyme to negatively regulate PDGFRa signaling. Collectively, our findings reveal that PI3K/Akt-mediated PDGFRa signaling primarily modulates gene expression through alternative RNA splicing in the facial mesenchyme and identify Srsf3 as a critical regulator of craniofacial development.

overall_design: mRNA profiles from three biological replicates each of mouse Pdgfra+/+ versus PdgfraPI3K/PI3K E13.5 palatal shelf mesenchyme and Srsf3fl/fl;Wnt1-Cre+/+ versus Srsf3fl/fl;Wnt1-Cre+/Tg E11.5 maxillary process mesenchyme

first: Brenna

middle: J

last: Dennison

first: Eric

middle: D

last: Larson

first: Rui

last: Fu

middle: A


title: Next Generation Sequencing of PD-iPSC derived midbrain dopaminergic(mDA) neurons treated with CDC (C021 dihychloride) or BAG (BAG 956)

city: BALTIMORE

first: Minseong

state: MD

address: 733 NORTH BROADWAY, SUITE 763, Euodwood Apt 308

department: ICE

institute: JHMI

summary:
Purpose: The goals of this study are to identify cellular pathways to recover a-syn aggregation-mediated toxicity induced in response to CDC or BAG treatment on PD-iPSC derived mDA neurons.
Methods: mRNA profiles of 30-day-old PD-mDA neurons with CDC or BAG treatment for 1 day were generated by deep sequencing, in duplicate, using Illumina HiSeq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.
Conclusions: Our study represents the detailed analysis of mDA neuronal transcriptomes in response to CDC or BAG treatments, with biologic replicates, generated by RNA-seq technology. Our results show that CDC or BAG treatment could rescue the toxcity from a-syn aggregation via purine metabolism / ion transport pathways.

overall_design: mRNA profiles of 30-day-old PD-mDA neurons DMSO, bluelight + DMSO or bluelight with CDC or BAG treatment for 1 day (Bluelight - 34 μW/mm2 at 470 nm, 0.17 Hz, 0.5s, 24hrs - is used for inducing alpha-synuclein aggregation)

last: Ra

first: Gabsang

last: Lee


title: Myeloid-specific ATP-citrate lyase deletion alters macrophage phenotype in vitro and in vivo without affecting tumor growth

city: Amsterdam

first: Menno

last: de Winther

address: Meibergdreef 9

department: Medical Biochemistry

country: Netherlands

institute: Academic Medical Center University of Amsterdam

summary: Cancer cells rely on ATP-citrate lyase (Acly)-derived acetyl-CoA for lipid biogenesis and proliferation, marking Acly as promising therapeutic target. However, inhibitors may have side effects on tumor-associated macrophages (TAMs). TAMs are innate immune cells abundant in the tumor microenvironment (TME) and play central roles in tumorigenesis, progression and therapy response. Since macrophage Acly deletion was previously shown to elicit macrophages with a potential anti-tumor phenotype in vivo, we hypothesized that Acly targeting may elicit anti-tumor responses in macrophages, whilst inhibiting cancer cell proliferation. Here, we used a myeloid-specific knockout model to validate that absence of Acly decreases IL-4-induced macrophage activation. Using two distinct tumor models, we demonstrate that Acly deletion slightly alters tumor immune composition and TAM phenotype in a tumor type-dependent manner without affecting tumor growth. Together, our results indicate that targeting Acly in macrophages does not have detrimental effects on myeloid cells.

overall_design: RNA-seq of bone marrow-derived macrophages from female AclyM-WT and AclyM-KO mice.

first: Kyra

middle: E

last: de Goede

first: Sanne

middle: G

last: Verberk

first: Jeroen

last: Baardman

first: Karl

last: Harber

first: Yvette

last: van Kooyk

first: Sjoerd

middle: T

last: Schetters

first: Jan

last: Van den Bossche


title: Comparative analysis of the effect of different diets on histone H3K4me3 distribution in mouse liver chromatin reveals the epigenetic efficacy of cyanidin-3-O-glucoside dietary intake

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary:
Background: Different diets result in significantly different phenotypes through metabolic and genomic reprogramming. Epigenetic marks, identified in humans and mouse models upon caloric restriction, high fat diet or the intake of specific bioactives, suggest that genomic reprogramming drives this reprogramming and mediates the effect of nutrition on health. Histone modifications encode the epigenetic signal that adapts genome functions to environmental conditions, including diets, by tuning the structure and properties of chromatin. So far, the effect of different diets on the genome-wide distribution of critical histone marks has not been determined
Methods: We investigated by chromatin immunoprecipitation sequencing the distribution of the trimethylation of lysine 4 of histone H3 in the liver of mice fed for one year with five different diets including: chow containing corn powder as extra source of plant bioactives or specifically enriched with the cyanidin-3-O-glucoside, high fat enriched obesogenic and caloric restricted pro-longevity diets
Conclusions: The comparison of the resulting histone mark profiles revealed functional food containing cyanidin determines broad effect.

overall_design: Fifteen C57Bl/6 females, belonging to 6 litters, were randomly divided in 5 groups (n=3 mice/group) at the age of three months and each group was fed for ten months with the following five different diets: 1) calorie restriction (CR); 2) high fat-diet ad libitum (HF); 3) purple corn-based ad libitum (RD); 4) yellow corn-based ad libitum (YD); 5) standard diet ad libitum (SD)

first: Giuseppe

last: Persico

first: Francesca

last: Casciaro

first: Alessandra

last: Martinelli

first: Katia

last: Petroni

first: Chiara

last: Tonelli

first: Marco

last: Giorgio


title: mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting bodies in Ophiocordyceps Sinensis [miRNA-seq dataset]

first: Han

last: Zhang

type: Non-coding RNA profiling by high throughput sequencing

overall_design: sRNA profiles of the mycoparasite complex (MC), the sclerotium (ST) and the whole O. Sinensis with fruiting body (FB) stages.

first: Jinlin

last: Guo


title: Hypoxia regulates endogenous double-stranded RNA production via reduced mitochondrial DNA transcription

city: Oxford

first: Adrian

middle: L

last: Harris

address: John Radcliffe Hospital

department: Department of Medical Oncology

country: United Kingdom

institute: University of Oxford

summary: Hypoxia is a common phenomenon in solid tumours strongly linked to the hallmarks of cancer. Increasing evidence shows that hypoxia promotes local immune suppression and downregulates the expression of type I interferon (IFN) pathway which is actively involved in current anti-cancer therapies’ success. It was recently described that double-stranded RNA (dsRNA), transiently generated during mitochondrial transcription, endogenously activate the type I IFN pathway. The aims of this study were to determine the effects of hypoxia on the generation of mitochondrial dsRNA (mtdsRNA) in breast cancer, and the mechanisms involved.  A significant decrease in dsRNA production was observed in different cell lines under hypoxia in a HIF1/2α-independent manner. dsRNA from mitochondrial fraction was responsible for activation of the type I IFN and significantly decreased after hypoxia treatment. Mitochondrial encoded genes were downregulated in hypoxic samples and in dsRNA-pull-down experiments using the J2 antibody suggesting a reduction in mitochondrial transcription during hypoxia.

overall_design: Sequencing of RNA extracted from MCF7 cell lines under normoxia and hypoxia conditions & those immunoprecipitated by J2 antibodies in the same cell lines in hypoxia and normoxia conditions

first: Esther

last: Arnaiz

first: Ana

last: Miar

first: Antonio

last: Dias

first: Naveen

last: Prasad

first: Ulrike

last: Schulze

first: Dominic

last: Waithe

last: Rehwinkel


title: Transcriptome analysis of productive and unproductive pathways of in vitro megakaryocytopoiesis and their control by he AHR antagonist SR1

city: Strasbourg

first: Henri

last: de la Salle

address: 10 rue Spielmann

institute: EFS Grand-Est

summary: Human CD34+ progenitors can be in vitro differentiated into proplatelet-producing megakaryocytes (MKs) within 17 days. During this course, 4 cell populations emerge, phenotypically defined as CD34+CD41+ at day 7 (D7) and CD34+CD41+CD9- at D10 and D14 —qualified as “productive” because they can differentiate into proplatelet-forming cells during the D14-D17 period— and CD34-CD41+ or CD34+CD41+CD9+ at day 10 —qualified as “unproductive”, because unable to form proplatelets later. The productive pathway is boosted by the addition of SR1 at D0 and D7. To clarify the features of the productive and unproductive pathways, as well as the effect of SR1, the transcriptomes of the cell populations present at D0, 7, 10 and 14, generated in the presence of the absence of SR1 were determined by RNA-Seq.

overall_design: 95% pure human CD34+ cells were in vitro differentiated into megakaryocytes using a 14-day long protocol, in the absence or the presence of SR1. Cells populations were isolated according to their phenotype at D7, 10 or 14, their RNAs were extracted and processed for RNA-seq library preparation and analysis. For each condition (i.e. cell subpopulation, day of culture, SR1- or SR1+ condition), three independent biological replicates were processed.

first: Léa

last: Malo

first: Valentin

last: Do Sacramento

first: Catherine

last: Strassel

first: Damien

last: Plassard


title: Global impact of CMP-001 on various immune cell subsets

city: Iowa City

first: George

last: Weiner

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

summary:
Purpose: The goal of this study was to investigate the impact of CMP-001 on gene expression patterns within various immune cell subsets.
Methods: Unfractionated PBMCs from a healthy donor were isolated via ficol gradient and treated with and without anti-Qbeta coated CMP-001 (10ug/ml) for 24 hours. Untreated and treated fractions were sequenced on an Illumina HiSeq4000 system. FASTQ files were generated from basecall files with the bcl2fastq software (Illumina) provided by the University of Iowa Institute of Human Genetics. Data files were subsequently downloaded to Argon and mapped to the prebuilt GRCh38 genome with CellRanger (version 3.0.1). After initial mapping datasets were merged together and clustering was performed based on merged data sets using Cell Ranger software. Cells with unique gene counts fewer than 300 or more than 4,000 per cell were eliminated along with a mitochondria gene cutoff of 25%. Log normalization of aggregated reads was performed with Seurat (version 3.0.2) using a scale factor of 10,000. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1).
Results: A total of 17,280 cells were recovered after filtering. Clusters were identified based on expression of unique gene markers. Differential expression analysis identified genes enriched in each population of cells corresponding to untreated versus treated libraries. Particular emphasis was given to genes enriched in monocytes.
Conclusions: We report that CMP-001 induces a variety of immune responses in each cell cluster, with a unique gene signature displayed by monocytes.

overall_design: Human PBMCs from a healthy donor were treated with CMP-001 and anti-Qbeta for 24 hours. mRNA profiles were generated using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina HiSeq4000.

first: Shakoora

last: Sabree


title: Expression data from Arabidopsis Col, C24 and their F1 hybrid at 15 DAS

city: Tsukuba

first: Naoya

last: sugi

address: 1-1-1 Ten-nodai

country: Japan

institute: Univ. of Tsukuba

summary:
To obtain new insights for heterosis mechanisms in Arabidopsis, transcript profiling of arabidopsis F1 hybrid and their parentral lines was obtained from Affymetrix GeneChips ATH array.
The microarray analysis exhibited that there were 44 up-regulated and 12 down-regulated genes with more than a 1.5-fold changes in the profiles of F1 hybrid against those of each parent. Gene ontology analyses highlighted up-regulated genes as organic nitrogen-related in the F1 hybrid.

overall_design: Whole rosette of Col, C24, and F1 hybrid(C24xCol) with three replications.

last: Sugi


title: mRNA-seq and miRNA-seq profiling analyses reveal molecular mechanisms regulating induction of fruiting bodies in Ophiocordyceps Sinensis

first: Han

last: Zhang


title: The type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis in HeLa cells and dynamic investigation upon transcription inhibition by ActD treatment

city: Beijing

first: Tong

last: Liu

address: Life Science Park Road

institute: State Key Laboratory of Proteomics

summary: Developing a psoralen probe (PP)-based method for RNA tagging and RNA-protein complex (RP-complex) enrichment, isolating of both coding and noncoding RNAs from HeLa cells was achieved by PP enrichment. Exploring the type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis. And dynamic investigation of RNA upon transcription inhibition by ActD treatment.

overall_design: The type and relative distribution of RNAs in HeLa cells  by PP enrichment and TRIzol, RNA readcounts in HeLa cells treating with ActD

first: Zheng

first: Hangyan

last: Dong


title: RNA-sequencing in MCL cell lines after silencing cyclin D1

first: Santiago

last: Demajo

summary: Mantle cell lymphoma (MCL) is an aggressive B-cell neoplasm characterized by the t(11;14)(q13;q32) translocation leading to cyclin D1 overexpression. Cyclin D1 is a major cell cycle regulator and also has a role in transcription, but the effect of the latter in tumorigenesis remains largely unknown. Here, we investigated the transcriptional role of cyclin D1 in MCL and its impact on the pathogenesis of this neoplasm. Integrating genome-wide expression analysis of cyclin D1-silenced and overexpressing cells with cyclin D1 chromatin binding profiles, we identified a cyclin D1-activated transcriptional program in MCL cells.

overall_design: We generated cyclin D1 silenced MCL cell lines (in Granta-519 and JeKo-1) by shRNA. We then performed RNA-sequencing experiments in shCyclinD1 (shCycD1) and control (shCtrl) cells to analyze the cyclin D1-dependent genome-wide expression modulation. Three biological replicates were included in the experiment.

first: Giancarlo

last: Castellano

first: Pedro

last: Jares


title: RNA expression in ventilated preterm lamb lungs [RNA-seq]

first: Robert

last: McKnight

summary:
Purpose: The goal of this study was to measure by RNA-seq the impact of preterm birth and invasive mechanical ventilation verses noninvasive respiratory support on the lung transcriptome
Methods: Lung mRNA profiles were generated for: 1) Unventilated preterm lamb, 2) preterm lambs delivered at gd131 and intubated and mechanically ventilated for 3 days, 3) preterm lambs delivered at gd131 and not intubated and resuscitated by placing a face mask over the nose and mouth and controlling O2 delivery via a computer-controlled electronic blower device, 4) unventilated naturally delivered full-term lambs.
Results: Using an optimized data analysis workflow, we mapped between 61 and 81 million sequence reads per sample to the sheep genome Oar_v3.1/oviAri3
Conclusions: Our study represents the first detailed analysis of ventilated preterm lung transcriptomes, with biologic replicates, generated by RNA-seq

overall_design: Lung mRNA profiles were generated for preterm lambs ventilated for 3 days by either mechanical ventilation or not intubated and resuscitated through a mask computer-controlled electronic blower device.

first: Kurt

middle: H

last: Albertine


title: Identification of histone modifications reveals an association of H2b monoubiquitination with gonadal transdifferentiation

city: Wuhan

first: Lai

last: fengling

address: Wuhan University, Wuchang District, Hubei Province

institute: Wuhan university

summary: Gonadal trans-differentiation from ovary to testis occurs in a same individual, suggesting a role of  epigenetic regulation. However, histone modifications concerning the sex reversal process remain elusive. Here, we report a developmental atlas of histone modifications in the gonadal differentiation, including acetylation, methylation, and ubiquitination, using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We provided a detail distribution map of these modification sites including novel histone modifications along histones H2a, H2b, H3, and H4, and revealed their relationship with types of gonadal differentiation. We then determined a testis-enriched histone modification site, H2b monoubiquitination at K120, and its association with spermatogenesis. ChIP-seq demonstrated that the modification was highly enriched in the male sex-determining gene dmrt1, in particular association with its exon regions, suggesting its role in transcriptional elongation of dmrt1 in testis. Together, these data not only provide a new resource for epigenetic study in gonadal development, but also define an association of histone modifications in gonadal differentiation from ovary to testis.

overall_design: ChIP-seq of histone H2BK120ub in ovary and testis of Monopterus albus

first: Fengling

last: Lai

first: Yibin

last: Cheng

first: Juan

last: Zou

first: Haoyu

last: Wang

first: Xin


title: Transcriptomic responses induced in muscle and adipose tissues of growing pigs by intravenous infusion of sodium butyrate

city: Nanjing

first: Yong

last: Su

address: Weigang 1#

institute: Nanjing Agricultural University

summary: Butyrate has a central function in the regulation of energy metabolism as a metabolite of bacterial fermentation. However, information on the direct impact of butyrate on peripheral organs or tissues is very limited, especially for muscle and adipose tissues. Therefore, this study evaluated the effects of intravenous sodium butyrate (SB) administration on the transcriptome of muscle and adipose tissue of pigs. Twelve crossbred barrows (Duroc × Landrace × Large White, 60 days of age) were fitted with a medical polyethylene cannula via internal jugular vein and were daily infused with 10 ml SB (200 mmol/l) or the same volume of physiological saline. After a 7-day experimental period, all pigs were slaughtered, and the longissimus dorsi muscle and dorsal subcutaneous adipose tissue were collected for holistic transcriptomic analysis. In muscle tissue, the expression of 12 oxidative phosphorylation related genes and seven glycolysis related genes were downregulated. Furthermore, the mRNA expression of fatty acid synthase (FASN) and stearyl coenzyme A desaturase (SCD) were significantly upregulated by SB treatment. This indicates a decrease in oxidative phosphorylation and glucose catabolism, and an increase in fat synthesis. In adipose tissue, the expressions of seven oxidative phosphorylation-related genes were downregulated, while nine glucose metabolism related genes were upregulated. Moreover, the mRNA expressions of FASN and peroxisome proliferator-activated receptor gamma (PPARγ) were upregulated, while fatty acid binding protein 3 (FABP3) and acyl-CoA synthetase long-chain family member 1 (ACSL1) were downregulated in the SB group. This indicates a decrease in oxidative phosphorylation and an increase in glucose metabolism and fat synthesis. The results suggest that short-term intravenous SB infusion can modulate muscle and adipose tissue metabolism at the transcriptional level by decreasing both oxidative phosphorylation and fat synthesis. In addition, intravenous SB decreases the glucose catabolism in muscle tissue and increases the glucose catabolism in adipose tissue. This suggests that systemic butyrate may display discriminative metabolic regulation in different tissues of barrows.

first: K

last: Yu

first: E

last: Ren

first: R

last: Xu

first: X

last: Chen

first: Y


title: Macrophagic S100A4 drives macrophage protumor activation and promotes tumor growth through controlling PPAR-γ induction

city: beijing

first: shuangqing

last: liu

address: datun street

institute: institute of biophysics

summary: The lipid-metabolism up-regulation-mediated M2 polarization provides tumor-associated macrophages (TAMs) with protumor phenotypes during tumor development and progression. However, how TAMs reprogram their lipid-metabolism responding to M2 activators remains unclear. Here, we report that S100A4 is a determinant of macrophage M2 polarization. We find that the growth of carcinoma grafts was impaired in myeloid S100A4-deficient mice. Coincidentally, ablating S100A4 in macrophages reduced their capability of macrophage into utilization utilize of exogenous fatty acids as their major energy source for oxidation. Mechanistic analysis demonstrates that the induction of PPAR-γ responding to Th2 cytokine, IL-4, was halted in s100a4-deleted TAMs, as well as in bone marrow-derived macrophages, and as well as in Raw264.7 cells. Further molecular analyses reveal that CD36, downstream from S100A4-PPARγ, is the major effector for lipid uptake of S100A4+ macrophages. FurthermoreImportantly, higher levels of S100A4 is closely associated with tumor resistance to chemotherapy in murine models as well as poor prognosis of cancer patients in clinic . Our study thus suggests that blocking S100A4 constitutes a treatment strategy to reprogram macrophages toward an antitumor state by inhibiting PPAR-γ-induction mediated gene up-regulation.

overall_design: Protein-coding mRNA sequencing (RNA-seq) analysis of S100A4+ and S100A4- TAMs. There were three samples for each cell population.

first: Shuangqing

last: Liu

first: Huilei

last: Zhang

first: Zhaoqing

first: Zhihai

last: Qin


title: Immune effects of CMP-001 vs. controls on various immune cell subsets

first: Michael

last: Chimenti

address: 431 Newton Road

department: Iowa Institute of Human Genetics

summary:
Purpose: The goal of this study was to investigate the TLR9 specific immune effects of anti-Qbeta-coated CMP-001 using the following groups: untreated, anti-Qbeta coated CMP-001,  anti-Qbeta coated CMP-001 with methylated and thus, inactive ODN (mCMP-001), and G10 (naked TLR9 agonist).
Methods: Unfractionated PBMCs from a healthy donor were isolated via ficol gradient and treated with and without anti-Qbeta coated CMP-001 (10ug/ml), anti-Qbeta coated mCMP-001 (inactive ODN; 10ug/ml), or G10 (naked TLR9 agonist; 2.5ug/ml) for 24 hours. Untreated and treated fractions were sequenced on an Illumina NovaSeq 6000 system. FASTQ files were generated from basecall files with the bcl2fastq software (Illumina) provided by the University of Iowa Institute of Human Genetics. Data files were subsequently downloaded to Argon and mapped to the prebuilt GRCh38 genome with CellRanger (version 3.0.1). After initial mapping datasets were merged together and clustering was performed based on merged data sets using Cell Ranger software. Cells with unique gene counts fewer than 300 or more than 4,000 per cell were eliminated along with a mitochondria gene cutoff of 25%. Log normalization of aggregated reads was performed with Seurat (version 3.0.2) using a scale factor of 10,000. Feature selection was performed with the variance stabilizing transformation before integration was performed with Seurat (v3.0.1).
Results: A total of 17,280 cells were recovered after filtering. Clusters were identified based on expression of unique gene markers. Differential expression analysis identified genes enriched in each populatin of cells corresponding to untreated versus treated libraries. Particular empasis was given to genes enriched in monocytes.
Conclusions: We report that CMP-001 induces a variety of immune responses in each cell cluster, with a unique gene signature displayed by monocytes.

overall_design: Human PBMCs from a healthy donor were treated with and without anti-Qbeta coated CMP-001 (10ug/ml), anti-Qbeta coated mCMP-001 (inactive ODN; 10ug/ml), or G10 (naked TLR9 agonist; 2.5ug/ml) for 24 hours. mRNA profiles were generated using 10X Genomics Chromium single-cell system followed by sequencing on an Illumina NovaSeq 6000.

first: George

last: Weiner

first: Shakoora

last: Sabree


title: RNA-seq analysis on SW480 cells treated with or without YH-620 under hypoxia

city: Los Angeles

first: Kahn

last: Michael

state: CA

address: NRT 4501, 1450 Biggy Street

department: Department of Biochemistry and Molecular Biology

institute: University of Southern California

summary: To globally assess the role of alternatively translated 63 kDa NKRF, we performed and report on RNA-seq analysis on SW480 cells treated with or without novel small molecule HIF antagonist YH-620 under hypoxia. This study provides a framework for understanding the effect of novel small molecule HIF antagonist YH-620 on downstream targets. In addition, we also performed RNA-seq analysis on SW480 cells treated with or without specific small molecule CBP/catenin antagonist ICG-001 under hypoxia.

overall_design: Examination of effect of YH-620 treatment on SW480 cells.

last: Kahn


title: Genome-wide DNA access sites in ventilated preterm lamb lungs [ATAC-seq]

first: Robert

last: McKnight

summary:
Purpose: ATAC-seq was performed on preterm lambs that were ventilated by invasive mechanical ventilation or noninvasive respiratory support utilizing a mask and compared to gestation-age-matched preterm lambs that were not ventilated and naturally delivered term lambs.
Methods: Lung chromatin access profiles were generated for: 1) Unventilated preterm lamb, 2) preterm lambs delivered at gd131 and intubated and mechanically ventilated for 3 days, 3) preterm lambs delivered at gd131 and not intubated and resuscitated by placing a face mask over the nose and mouth and controlling O2 delivery via a computer-controlled electronic blower device, 4) unventilated naturally delivered full-term lambs.
Results: Using an optimized data analysis workflow, we mapped between 76 and 96 million sequence reads per sample to the sheep genome
Conclusions: Our study represents the first detailed analysis of ventilated preterm lung chromatin access, with biologic replicates, generated by ATAC-seq

overall_design: Lung chromatin access profiles were generated for preterm lambs ventilated for 3 days by either mechanical ventilation or not intubated and resuscitated through a mask computer-controlled electronic blower device.

first: Kurt

last: Albertine


title: The type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis in HeLa cells.

first: Tong

summary: Developing a psoralen probe (PP)-based method for RNA tagging and RNA-protein complex (RP-complex) enrichment, isolating of both coding and noncoding RNAs from HeLa cells was achieved by PP enrichment. Exploring the type and relative distribution of the PP isolated RNAs by RNA-sequencing analysis.

overall_design: The type and relative distribution of RNAs in HeLa cells  by PP enrichment and TRIzol.

first: Zheng

first: Hangyan

last: Dong


title: Plasma-derived exosomes boost the healing of irradiated wound by regulating cell proliferation and ferroptosis

city: Chengdu

first: Feihong

last: Gan

address: No.14, Third Section, Ren Min Nan Road

institute: Sichuan University

summary: Ionizing radiation (IR) therapy for malignant tumors can damage adjacent tissues, leading to severe wound complications. Plasma-derived exosome treatment has recently emerged as a safe and impactful cell-free therapy. Herein, we aimed to determine whether plasma-derived exosomes could improve the healing of post-radiation wound. Rat plasma-derived exosomes (RP-Exos) were locally injected on cutaneous wounds created on the backs of irradiated rats and boosted the healing process as well as the deposition and remodeling of the extracellular matrix with collagen formation. Subsequently, the effects of RP-Exos were further evaluated on irradiated fibroblasts in vitro. The results suggested that exosomes promoted fibroblast proliferation, migration, cell cycle progression, and cell survival. Moreover, transcriptome sequencing, analysis, and quantitative polymerase chain reaction validation were performed to identify the underlying molecular mechanisms. RP-Exos enhanced the expression of cell proliferation and radioresistance-related genes, and yet downregulated ferroptosis pathway in irradiated fibroblasts. Inhibition of ferroptosis by RP-Exos was further confirmed through colorimetric assay, fluorescence probe and flow cytometry in ferroptosis-induced fibroblasts. Our results suggest that RP-Exos regulate cell proliferation and ferroptosis in radiated fibroblasts, thereby boosting the healing of radiated wounds. These findings support plasma-derived exosomes as a potential therapeutic method for post-radiation wound complications.

overall_design: For transcriptome sequencing, 6 samples from exosomes group and PBS group (3 duplicates for each groups) were analyzed.

first: Raokaijuan

last: Wang

first: Ping

last: Lyu

first: Yanxi

last: Li

first: Ruijie

last: Fu

first: Yu

last: Du

last: Gong

first: Yang

last: Yao


title: Illumina NGS RNA-seq and RRBS Sequencing on Spaceflight Mouse Retina

city: Loma Linda

first: Charles

address: 11021 Campus Street

department: Department of Basic Sciences

institute: Loma Linda University

type: Methylation profiling by high throughput sequencing

summary: We reported the retinal transcriptome and methylome profiles of spaceflight and habitat control mice. The retinal transcrtiome was generated including 764 million paired-end 75x2 bp RNA-seq data. The methylome was generated including 788  million 75-bp RRBS DNA methylation data. We identified 177 differentially expressed genes (DEGs) induced by spaceflight based on the RNA-seq dataset, and 643 differentially methylated genes (DMGs) based on RRBS dataset. Functional enrichement analysis based on DEGs and DMGs revealed that spaceflight altered extracellular matrix component (EMC), cell to cell junction, inflammation pathway, wound-healing process, etc. Integration analysis based on transcriptome and methylome  suggested that modifications on DNA methylation were correlated with transcriptome changes for several significant biological processes and/or pathways.

overall_design: This study was under the umbrella of the NASA Rodent Research-1 project consortium. In this project, 16-week-old female C57 BL/6J mice were sent to International Space Station (ISS) in NASA's animal enclosure modules (AEM) and were kept inside ISS middeck for 37 days. We used transcrptomic and methylomic approaches to investigated the spaceflight-associated neuro-ocular syndrome (SANS) using retinas from those spaceflight mice.

first: Xiao

last: Mao


title: DNA-RNA three-stranded hybrids: from the telomere to the genome

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

institute: Nice Sophia Antipolis

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: RNA-seq data for ABL1 knockdown in Huh7 cells

city: Maywood

first: Wei

last: Qiu

address: 2160 S 1st Ave

institute: Loyola University Chicago

summary: RNA-seq data for ABL1 knockdown (KD) in Huh7 cells

overall_design: We knocked down ABL1 using shRNA in Huh7 cells and compared scrambled and ABL1 KD cells by RNA-seq. 3 triplicates for each group.

first: Fang


title: Hemispheric lateralization of gene expression profile in stressed mice

city: Daejeon

first: Sujin

last: Chae

address: 291 Daehak-ro

institute: KAIST

summary: Chronic stress increases the risk of emotional disorders by altering brain structure and function. Patients with post-traumatic stress disorder (PTSD) or depressions show activity difference between the two hemispheres in the prefrontal cortex (PFC) but molecular targets associated with this laterality remains unclear. Here, we reveal that chronic social defeats later gene-expression profile differentially between the left and right medial prefrontal cortices (mPFC) in mice.

overall_design: Micorarray data comparing Left and Right mPFC transcripts in resilient and susceptible mice of social defeated mice

first: Keunsoo

last: Kang

first: Daesoo

last: Kim


title: DNA-RNA three-stranded hybrids: from the telomere to the genome (human dataset)

first: Leila

last: Kianmehr

summary: The origin and possible functions of local three-stranded DNA-RNA hybrid regions in the mammalian genome is still a matter of discussion. R-loops have been so far essentially detected by immunodetection of the DNA-RNA hybrid regions (DRIP assay). This powerful and easy to implement method relies on recognition by a unique monoclonal antibody and may not detect all the hybrid regions. Starting from simple logical steps, we developed a preparative method that allows detection and physical isolation of stable DNA-RNA triplexes in a complex genome. A modification of the popular TRIzol extraction procedure first identifies RNAs stably bound to DNA in RNaseH-sensitive complexes, which can be isolated and further characterized by RNA-seq. We first tested the efficiency of the approach by a search for a generalized three-stranded state of the human and mouse telomeres. While such a structure is suggested by the complementarity of the long chromosomal CCCTAA repeats and the noncoding RNA TERRA, it was only in one class of cancer cells that telomeric R-loops were so far evidenced by DRIP assay. The proposed method allowed us to generalize to the mouse and human genomes the notion of terminal R-loop complexes with TERRA molecules synthesized from local promoters. When further applied to murine sperm genome, it evidenced a reproducible genome-wide profile of RNA complexes.

overall_design: Examination of DNA/RNA hybrids and free-RNAs in sperm

first: François

last: Cuzin

first: Ali

last: Sharifi-Zarchi


title: L3-L4 Developmental Transcriptome of the human parasitic nematode Brugia malayi and its Wolbachia endosymbiont

city: Liverpool

first: Mark

last: Taylor

address: Pembroke Place

department: Tropical Disease Biology

institute: Liverpool School of Tropical Medicine

summary: Lymphatic filarial nematodes maintain a mutualistic association with the intracellular bacterium Wolbachia. Wolbachia populations expand following infection of the mammalian host, to support larval growth and development. Utilizing transcriptomic data from Brugia malayi over the first two weeks post-infection, we present an analysis of the biochemical pathways that are involved in Wolbachia population growth and regulation in support of larval development. In Wolbachia, we observe coordinated regulation of carbon metabolism with an alternating pattern of glycolysis and TCA cycle pathways reminiscent of the ‘Warburg effect’. Wolbachia's purine, pyrimidine and haem biosynthesis and Type IV secretion pathways are also upregulated and correlate with the upregulation of the nematode’s DNA replication pathway. In the nematode we observe up-regulation of the autophagy pathway, a key regulator of Wolbachia populations. These findings support a key role for nucleotide and haem provisioning from Wolbachia in support of the larval growth and development of its nematode host.

sample_organism: Wolbachia endosymbiont strain TRS of Brugia malayi

overall_design: Examination of 4 time-points spanning the first two weeks after B. malayi infection of a jird animal model model: 3, 7, 11, and 14 days post-infection. Samples were sequenced as single-end samples in triplcate using an Illumina GA-Iix instrument.

first: Shannon

last: Quek

first: Christina

last: Bronowski

first: Simon

last: Wagstaff


title: ZBTB12-HERVH-LncRNA axis is a molecular barrier for  dedifferentiation of human stem cells

city: santa barbara

first: Guojing

last: Liu

address: 552 University Rd

institute: University of California, santa barbara

summary: Development is generally viewed as one-way traffic of cell state transition from primitive to developmentally advanced states. However, molecular mechanisms that ensure the unidirectional transition remain largely unknown. NanoCAGE sequencing identified an evolutionarily conserved zinc finger repressor, ZBTB12, as a molecular barrier for dedifferentiation of human pluripotent stem cells (hPSCs). Single cell RNA sequencing revealed that ZBTB12 is essential for three germ layer differentiation by blocking hPSC dedifferentiation. Mechanistically, ZBTB12 serves as a master repressor of human endogenous retrovirus H (HERVH). Active HERVH loci drive the expression of overlapping long non-coding RNAs (lncRNAs) whose downregulation by ZBTB12 is necessary for pluripotency exit and lineage derivation. Overall, we have identified a ZBTB12-HERVH-lncRNA axis as molecular machinery that safeguards the unidirectional transition of stem cell fates.

overall_design: To identify TFs that regulate hESC differentiation, we established an hESC-derived neural differentiation model and performed nanoCAGE sequencing from cells collected at Day 0, Day 5, Day 15 and Day 23 with two replicates at each time point. Novel candidate TF-ZBTB12  was identified for further functional study. Then ChIP-seq data of ZBTB12 was done to show its binding sites. Moreover, transcriptome was profiling for the  KD of ZBTB12 and NANOG in hESC cells.

first: Kenneth

last: Kosik

first: Jiwon

last: Jang


title: DNA-RNA three-stranded hybrids: from the telomere to the genome (mouse dataset)

overall_design: Examination of DNA/RNA hybrids and free-RNAs in sperm and testis


title: The quantitative analysis of transcriptomes derived from MLL-AF10 flox cells and MLL-AF10 (Tip60 flox/flox, Cre-ERT2) cells with or without the treatment of 4-OHT

city: Tokyo

first: Kazutsune

last: Yamagata

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

department: Hematological Malignancy

institute: National Cancer Center Research Institute

summary: Chromosome translocations involving the MLL gene are common rearrangements in leukemia. Such translocations fuse the MLL 5’-region in frame to partner genes , and the resultant fusion proteins can cause MLL-related leukemia. MLL-fusions activate transcription of target genes such as the HoxA cluster and Meis1, but the underlying mechanisms remain elusive. We found that the MLL-AF10 fusion recruits Tip60 to the Hoxa9 locus, where it acetylates H2A.Z, thereby promoting Hoxa9 expression. Following conditional deletion of Tip60, hypoacetylation of H2A.Z was accompanied by recruitment of Ezh2, the catalytic subunit of PRC2, suggesting that nucleosomes with hypoacetylated H2A.Z are the preferential targets of Ezh2. Our findings suggest that MLL-AF10 achieves active chromatin states by recruiting Tip60, which acetylates H2A.Z to prevent gene silencing by Ezh2.

overall_design: The comprisons of transcriptomes between 4-OHT-treated and non-treated MLL-AF10 flox cells (MAflox cells) and between 4-OHT-treated and non-treated MLL-AF10 (Tip60 flox/flox, Cre-ERT2; MATIP)  cells (MATIP cells).

first: Issay

last: Kitabayashi


title: A New Liver-Regeneration Molecular Mechanism Involving Hepatic Stellate Cells, Kupffer Cells, and Glucose-Regulated Protein 78 as a New Hepatotrophic Factor

status: Public on Jun 29 2021

city: Maebashi

first: hagiwra

last: kei

state: Gunma

address: 3-39-22 Showa-machi

department: General Surgical Science

institute: Gunma University Graduate School of Medicine

summary: Background and aims: Lethal liver failure is an important clinical issue. To overcome liver failure, we focused on liver regeneration mechanisms by activation of HSCs and KCs. It is known that the HSC-secreted Mac-2 binding protein glycan isomer (M2BPGi) has a function to activate Kupffer cells (KCs) in fibrotic liver. However, the importance and functional mechanism of liver regeneration by HSCs/M2BPGi/KCs axis in remnant liver after hepatectomy are still unknown. The aim of this study is to clarify whether the HSCs-derived M2BPGi can activate KCs in damaged-liver by not only fibrosis but also after hepatectomy and to elucidate the new molecular mechanism of liver regeneration by HSCs and KCs.  Methods: We examined the effect of M2BPGi on human hepatocytes and KCs, and explored secretory factors from M2BPGi-activated KCs by proteomics approach. Further, the effect of Glucose-regulated protein 78 (GRP78) as one of the M2BPGi-related secreted proteins on liver regeneration was examined in in vitro analysis and mouse hepatectomy model.  Results: Although M2BPGi had no hepatocyte promoting effect, M2BPGi promoted the production of GRP78 in KCs. The KCs-drived GRP78 promoted hepatocyte proliferation. GRP78 administration facilitated liver regeneration in 70% hepatectomy mice and increased the survival rate in lethal 90% hepatectomy mice with liver failure.   Conclusion: The M2BPGi activated-KCs extract the GRP78 which facilitates liver regeneration via activation of the proliferation potency of hepatocytes. Moreover, GRP78 administration could improve the survival in the lethal mice model. Our data suggested that the new hepatotrophic factor GRP78 may be a promising therapeutic tool for lethal liver failure in the clinic.

overall_design: The PXB cells cultured in the media with or without GRP78 (1600 ng/ml) in 6 hours.

first: Kei

last: Hagiwara

first: Norifumi

last: Harimoto

first: Ken

last: Shirabe


title: Transcriptomic analysis of induced pluripotent stem cells (iPSC) and differentiated hepatocytes (iPSC-Heps) from a cohort of healthy subjects and patients with nonalcoholic fatty liver disease (NAFLD)

city: San Francisco

first: Jacquelyn

last: Maher

address: 513 Parnassus Avenue

department: Medicine

institute: University of California San Francisco

summary: We report that the transcriptomic profiles of iPSC-Heps from NAFLD patients are distinct from those of healthy controls. This is in contrast to the transcriptomic profiles of the parent iPSC, which are similar between NAFLD patients and healthy controls.

overall_design: iPSC were generated from peripheral blood mononuclear cells from 16 healthy control subjects and 21 patients with biopsy-proven NAFLD.  iPSC from all 37 subjects were differentiated to hepatocytes (iPSC-Heps).  RNA from iPSC and iPSC-Heps were analyzed independently using the Illumina HiSeq 3000 Sequencing System.

first: Caroline

middle: C

last: Duwaerts

first: Chris

last: Her

first: Eric

last: Hoffman

first: Kevin

last: Siao

first: Nathaniel

last: Phillips

first: Holger

last: Willenbring

first: Aras

middle: N

last: Mattis


title: Tumor cells in light-chain amyloidosis and multiple myeloma show different transcriptional rewiring of the normal plasma cell development [single-cell RNA-seq]

city: Pamplona

first: Ibai

last: Goicoechea

state: Navarra

address: Centro de Investigación Médica Aplicada (CIMA) Avenida Pío XII, 55

institute: Universidad de Navarra

summary: Transcriptional atlas of normal PC development in secondary lymphoid organs (SLO), peripheral blood (PB) and BM for comparison with the transcriptional programs (TPs) of tumor PCs in AL,  MM and MGUS based on bulk and single-cell RNAseq

first: Bruno

last: Paiva


title: Tumor cells in light-chain amyloidosis and multiple myeloma show different transcriptional rewiring of the normal plasma cell development


title: Molecular characterization of hepatocellular carcinoma in patients with non-alcoholic steatohepatitis

city: Barcelona

first: Marta

last: Piqué

address: Rosselló, 153

institute: IDIBAPS

summary:
Non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinoma (HCC) is increasing globally, but its molecular features are not well defined. We aimed to identify unique molecular traits characterizing NASH-HCC compared to other HCC aetiologies.
We collected 80 NASH-HCC and 125 NASH samples from 5 institutions. Expression array (n=53 NASH-HCC; n=74 NASH) and whole exome sequencing (n=50 NASH-HCC) data were compared to HCCs of other aetiologies (n=184). Three NASH-HCC mouse models were analysed with RNAseq/expression-array (n=20). ACVR2A was silenced in HCC cells and proliferation assessed by MTT and colony formation assays.
Mutational profiling of NASH-HCC tumours revealed TERT-promoter (56%), CTNNB1 (28%), TP53 (18%) and ACVR2A (10%) as the most-frequently mutated genes. ACVR2A mutation rates were higher in NASH-HCC than in other HCC aetiologies (10% versus 3%, p<0.05). In vitro, ACVR2A silencing prompted a significant increase in cell proliferation in HCC cells. We identified a novel mutational signature (MutSig-NASH-HCC) significantly associated with NASH-HCC (16% vs 2% in viral/alcohol-HCC, p=0.03). Tumour mutational burden (TMB) was higher in non-cirrhotic than in cirrhotic NASH-HCCs (1.45 versus 0.94 mutations/Mb; p<0.0017). Compared to other aetiologies of HCC, NASH-HCCs were enriched in bile and fatty acid signalling, oxidative stress and inflammation, and presented a higher fraction of Wnt/TGF-β proliferation subclass tumours (42% versus 26%, p=0.01) and a lower prevalence of the CTNNB1 subclass. Compared to other aetiologies, NASH-HCC showed a significantly higher prevalence of immunosuppressive cancer field. In three murine models of NASH-HCC key features of human NASH-HCC were preserved.
NASH-HCCs display unique molecular features including higher rates of ACVR2A mutations and the presence of a newly identified mutational signature.

overall_design: 53 NASH-HCCs, 29 adjacent non-tumor NASH liver samples and 74 NASH samples were analysed, as well as 6 healthy livers and 8 cirrhotic livers as a control.

first: Josep

last: Llovet

first: Roser

last: Pinyol

first: Sara

last: Torrecilla


title: FOXO3 knockdown is toxic for BL cell lines.

city: Ulm

first: Alexey

last: Ushmorov

address: Albert-Einstein-Allee 11

department: Institute of Physiological Chemistry

country: Germany

institute: Ulm University

summary: We found that FOXO3 knockdown induces apoptosis in BL cell lines BL-41, Namalwa and Jiyoye.

overall_design: BL cell lines BL-41, Namalwa and Jiyoye were either transduced with FOXO3 shRNA or scrambled control in the pRSI12-U6-shUbiC-TagRFP lentiviral vector (BioCat, Heidelberg, Germany). Transduced cells were isolated on day 4 post transduction. RNA was isolated with the RNeasy mini kit (QIAGEN). RNA-sequencing and data processing was done by BGI (Hong-Kong). RNA libraries were prepared for sequencing using standard BGI protocols. SOAPnuke was used for data filtering and Bowtie2 was used to map clean reads to reference. RSEM was used to calculate gene expression levels and DEseq2 was used to detect DEGs. hg38 was used as reference genome.

first: Franziska

last: Gehringer

first: Thomas

last: Wirth


title: Transcriptome analysis of BMDCs treated with nanovesicle vaccines

first: Chao

last: Zhang

address: tongjiaxiang 24

institute: China Pharmaceutical University

summary: We carried out in vitro transcriptome analysis of BMDCs treated with PEG-IM-MP and PEG-MP nanovesicles to understand the regulatory pathway of the immune response concerning gene expression.

overall_design: Examination of  the immune response concerning gene expression in BMDCs treated with 2 different nanovesicles and PBS.

first: Zhenzhen


title: Tumor cells in light-chain amyloidosis and multiple myeloma show different transcriptional rewiring of the normal plasma cell development [bulk RNA-seq]

overall_design: Transcriptional atlas of normal PC development in secondary lymphoid organs (SLO), peripheral blood (PB) and BM for comparison with the transcriptional programs (TPs) of tumor PCs in AL,  MM and MGUS based on bulk and single-cell RNAseq

first: Daniel

last: Alameda


title: Whole Transcriptome RNA-seq in primary fibroblasts of outbred Peromyscus maniculatus

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

institute: University of South Carolina

summary: Whole transcriptome RNA sequencing in primary fibroblasts of outbred Peromyscus maniculatus was generated to explore the degree of coordination in gene expression.

overall_design: Ear tissues of 10 Peromyscus maniculatus were collected and cultured to obtain fibroblasts for RNA sequencing and coordination analysis in gene expression.

first: Zhang

last: Youwen

first: Ji

last: Hao

first: Kiaris

last: Hippokratis


title: Identification of the dnCRTC-regulated genes in lung cancer cells

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida


title: Identification of the dnCRTC-regulated genes in lung cancer cells [RNA-seq]

summary: Gene expression profiling was performed on dnCRTC-expressing vs GFP-expressing lung cancer A549 cells, and genes that were differentially regulated by dnCRTC vs GFP were identified.

overall_design: There were two groups of A549 cells: one transduced with pMSCV retroviruses expressing GFP control and the other transduced with pMSCV retroviruses expressing dnCRTC [CRTC1(1-55aa)-nls-GFP]. Two biological replicates for each group were included.  Cells were independently cultured and RNAs were then harvested for RNA-seq analysis.


title: A functional genetic screen identifies Aurora kinase b as a critical regulator of Sox9-positive embryonic lung progenitor cells.

city: Melbourne

first: Casey

last: Ah-Cann

state: Victoria

address: 1G Royal Parade, Parkville

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

summary: We developped an in vitro 3D sphere culture system of lung embryonic cells called pneumosphere, that is amenable to genetic and chemical manipulation. This series describes the transcriptome of pneumospheres after 3, 7, and 10 days of culture.

overall_design: E11.5 mouse embryonic lung were dissected and dissociated into a single cell suspension. Lung epithelial cells were enriched through differential attachment of mesenchymal cells. Cells were plated in 3D culture and passaged at day 3, 7, and 10. RNAseq was performed at each passage to evaluate molecular changes that occur during culture.

first: Charity

last: Law

first: Marie-Liesse

last: Asselin-Labat


title: Mesenchymal Stem Cell derived exosome induced changes in Breast Cancer Cells

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

institute: Rutgers NJ Medical School

summary: We report effects of MSC-derived exosomes on a late-progenitor subset of breast cancer cells.

overall_design: single cell RNA sequencing on breast cancer cells treated with/without MSC exosomes.

first: Oleta

last: Sandiford

first: Lauren

last: Sherman


title: RNAseq of oncogene-induced senescent murine macrophages

city: Montreal

first: Gerardo

last: Ferbeyre

address: 2900 Edouard Montpetit Boulevard

department: Department of Biochemistry and Molecular Medicine

country: Canada

institute: Université de Montréal

summary: Aging organisms accumulate senescent cells, which are the result of exposure to important stress such as telomere attrition, irradiation, oncogene activation, oxidative stress or cytotoxic drugs. These senescent cells are characterized by a stable cell cycle arrest and an important secretion of pro-inflammatory factors. This senescence-associated secretory phenotype (SASP) has been shown to promote chronic inflammation leading to age-associated diseases. While a lot of in vitro models of senescence focus on senescent fibroblasts, it has been shown that a major portion of the burden of senescent cells in old mice are macrophages. Senescent macrophages have been shown to contribute to atherosclerosis, neurodegenerative diseases and macular degeneration. Yet little is known about senescent macrophages. Considering their potential role in age-associated diseases, we think these senescent macrophages and their secretions need to be investigated. Here we aimed to establish and characterize an in vitro model for oncogene-induced senescence in macrophages, to characterize secretions of these senescent macrophages and to assess impacts of these secretions on recipient cells.

overall_design: RNA profiles of 3 days post-induction of control (vehicle treated) and oncogene-induced senescent (4-hydroxytamoxifen treated) murine RAW264.7 macrophages in triplicate. RAW 264.7 macrophages were retrovirally infected to express a ∆Raf-1:ER construction which allows conditional activation of Raf-1 oncoprotein upon 4-hydroxytamoxifen treatment.

first: Stéphane

last: Lopes-Paciencia

first: Véronique

last: Bourdeau

first: Camille

last: Laliberté


title: Major MLL fusion partners regulate promoter-proximal pausing and release of RNA polymerase II

city: Shanghai

first: Gang

last: Wei

state: Select a State or Province

address: No 2005, Songhu Rd, Yangpu District

institute: Fudan University

summary: 1Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. 2Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, NY 10065, USA. 3Systems Biology Center, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA. 4CCTS Bioinformatic Program, The Rockefeller University, New York, NY 10065, USA. 5State Key Laboratory of Genetic Engineering & Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China

overall_design: Study the roles of major fusion partners of MLL1 in mixed lineage leukemia, including AFF1, AFF4, AF9, and ENL, and H3K79 methyltransferase, DOT1L, in transcriptional regulation by ChIP-seq, RNA-seq, and Pro-seq.

first: Robert

last: Roeder

first: Ming

last: Yu

first: Wenjing

last: Yang

first: Yupu

last: Liang


title: Transcriptome analysis of TPR1/TPL mutant lines during Pst AvrRps4- triggered immunity

city: Cologne

first: Thomas

last: Griebel

address: Carl-von-Linne-Weg 10

department: Department of Plant Microbe Interactions

institute: Max-Planck Institute for Plant Breeding Research

summary: Plant Topless (TPL) and Topless-related (TPR) corepressors are important regulators of plant hormone and immunity signaling. We present here the transcriptome of tpr1 and tpr1 tpl tpr4 triple mutant lines (t3) during TNL-triggered immunity in Arabidopsis thaliana after infection with Pst avrRps4 (OD 0.005). Col-0 and eds1-2 were analysed as controls.

overall_design: mRNA transcripts of Col-0, tpr1, tpr1 tpl tpr4 (t3), and eds1-2 at 0 (immediately after infiltration), 8 and 24 hpi (hours post infection) with Pst avrRps4 (OD 0.005) were deep sequenced in triplicates using illumina. In three independent experiments, we harvested syringe-infected plant leaf material of 5-week-old Arabidopsis thaliana plants.

first: Jane

last: Parker

first: Dmitry

last: Lapin

first: Barbara

last: Kracher


title: Genome-wide identification of Scx transcriptional target genes in tendon development II

status: Public on Jun 28 2021

city: cincinnati

first: HAN

last: LIU

state: oh

address: 3333 burnet avenue

department: DEVELOPMENTAL BIOLOGY

institute: CINCINNATI CHILDREN'S HOSPITAL

summary: Despite their important roles in the musculoskeletal system, tendon and ligaments are much less studied comparing to bone, cartilage and muscle. The lack of knowledge in tendon biology severely hinders the understanding of the etiologies of tendon related diseases and development of efficient clinical treatments. In mouse, Scx gene, encoding a Twist family bHLH transcription factor, is expressed in progenitors of all tendons and ligaments, as well as in mature tenocytes. Previous studies show that inactivation of Scx gene results in absence or severe hypoplastia of force transmitting tendons, with muscle anchoring tendons and ligaments are less affected. Here we report a set of ChIPseq data from E13.5 forelimbs of novel Scx-2xFlag tagged mice in which a Scx-Flag fusion protein is expressed recapitulating endogenous Scx expression, and a set of RNAseq data of Scx-GFP positive cells from E13.5 Scx wildtype, E15.5 Scx wildtype and homozygous mutant forelimbs. Using RNAseq and ChIPseq assays, we identify several genes exhibiting Scx-dependent tendon expression druing differentiation, with Scx binding peaks located within their promoter/enhancer regions. Thus these genes may play critical roles in mediating Scx regulated tendon cell differentiation. Our results provide new insights in the mechanisms of tendon development.

overall_design: We generated mice expressing a 2xFLAG epitope-tagged endogenous Scx protein using the CRISPR/Cas9-mediated genome editing technology. 10 pairs of E13.5 forelimb samples were pooled together as a single biological replicate, and 3 replicates were used for ChIP with anti-FLAG antibodies (Sigma #1804). Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit (Rubicon Genomics, Ann Arbor MI). Sequencing was performed on an Illumina NextSeq 500 (Illumina, San Diego CA). Raw FASTQ files were aligned to mm10 reference genome. FACS sorted GFP positive cells from E15.5 Scx wildtype and homozygous mutant embryos were used for total RNA preparation. 3 pairs of controls and mutants were included. Sequencing libraries were generated by using Illumina Nextera DNA Sample Prep Kit and sequenced using Illumina NovaSeq 6000. Sequenced reads were mapped to the reference mouse genome (mm10).

first: Han

last: Liu

first: Hee

last: Lim

first: Jingyue

last: Xu

first: Rulang

last: Jiang


title: RNA-seq analysis of mouse pluripotent stem cells derived cells

city: Hangzhou

first: Wei

last: Shan

state: Zhejiang

address: Bone Marrow Transplantation Center, The First Afﬁliated Hospital, School of Medicine, Zhejiang University, No.79 Qingchun Road, Hangzhou, Zhejiang, PR China.

institute: Zhejiang University

summary: To detect the role of OP9 stromal cells in our optimized 3D self-assembling peptide induction system followed by the OP9 coculture system. First, we used RNA-seq to analyze mouse pluripotent stem cells derived total cells at day5 between the 3D+OP9 and 3D+0.1% group in our hematopoietic differentiation system.  In addition, to further evaluate hematopoietic transcriptome differences between Lin-Sca-1+c-kit+CD201+ cells and  Lin-Sca-1+c-kit+CD201- cells, we used RNA-seq to analyze  mouse pluripotent stem cells derived Lin-Sca-1+c-kit+CD201+ and Lin-Sca-1+c-kit+CD201- cells  at day5 in our 3D+OP9 hematopoietic differentiation system.Meanwhile,we used the mouse embryonic stem cell(mESC) as negative control and bone marrow derived Lin-Sca-1+c-kit+CD201+ and fetal liver derived Lin-Sca-1+c-kit+CD201+ as positive control.

overall_design: two groups together:  3 sample of 3D+OP9 and 3 sample of 3D+0.1%gel;  five groups together :  3 sample of D5-LSKCD201+     3 sample of D5-LSKCD201- 3 sample of mESC    3 sample of  BM-LSKCD201+    3 sample of FL-LSKCD201+

first: Xiangjun

last: Zeng


title: Identification of the dnCRTC-regulated genes in lung cancer cells [microarray]

first: Lizi

last: Wu

overall_design: There were two groups of A549 cells: one transduced with pMSCV retroviruses expressing GFP control and the other transduced with pMSCV retroviruses expressing dnCRTC [CRTC1(1-55aa)-nls-GFP]. Two biological replicates for each group were included.  Cells were independently cultured and RNAs were then harvested for microarray analysis.


title: Bulk RNAseq of Sort-purified IV- Primary (1M) or Quaternary (4M) Tcirc (IV- CD69-/CD103-) or Trm (IV- CD69+/CD103+) Memory P14 cells isolated from Spleen or Mediastinal Lymph Nodes

city: Iowa City

first: John

last: Harty

state: Iowa

address: 25 S. Grand Ave, 1020 ML, University of Iowa

institute: University of Iowa

summary:
Purpose: The goals of this study are to compare the phenotypic, transcriptomic, trafficking and functional atttibutes of Influenza-experienced circulating or resident memory phenotype cells from the spleen or lung-draining mediastinal lymph nodes.
Results: Following read alignment, gene expression profiles were computed using featureCounts. Filtering and visualization of differentially expressed genes with a log2fold change >1.5<-1.5 and a p value of less than 0.05 were identified using Partek GS software and for some figures values from Partek were normalized and displayed using GraphPad Prism. Gene set enrichment and functional assignment were performed in DAVID bioinformatics resources and software from the Broad Institute.

overall_design: B6 mice containing CD90.1 congenic Primary (1M) or Quarternary (4M) Memory P14 cells at 23-30 days post Intranasal Influenza (PR8-GP33) infection were IV labeled with CD45.2-BV450 3 minutes prior to sacrifice. Pooled splenocytes (6-10 samples/sort) or Mediastinal Lymph Nodes (15-25 samples/sort) were isolated, processed through a 70uM cell strainer, stained with APC-labeled -CD19, -NK1.1 and -CD4 and CD103-PE, CD69-PE-CY7, CD90.1-PerCP-eFluor710, Live/Dead-e780. Samples were negatively enriched with aAPC-beads and Macs columns, resuspended in MACS buffer with DNAse for subsequent sorting. Populations of IV- CD69-/CD103- (Tcirculating) and IV- CD69+/CD103+ (Tms) were sort purified and resuspended in TRIzol. Freshly sorted 1M or 4M P14s were (as indicated above) were re-suspended in TRIzol and RNA was purified using a RNAeasy kit (Qiagen) according to the manufacturer’s protocol. RNA was assessed for purity and quality using an Agilent 2100 Bioanalyzer and RNA seq was performed using the single cell/low input library kit (NEB), full-length cDNAs were sequenced on the Illumina HiSeq 2500 High output platform using 2x150 Paired-end Libraries. The sequence reads quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and were aligned to the mouse genome version mm10 using STAR aligner.

first: Scott

last: Anthony

first: Natalija

middle: V

last: Brackel-Budimir

first: Vladimir

last: Badovinac


title: Genome-wide distribution of H1foo and somatic H1s in mouse embryonic cells.

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka

department: Department of Toxicology, Faculty of Veterinary Medicine

institute: Okayama University of Science

summary: We report genome-wide distribution of linker histone variant H1foo and somatic H1s in mouse embryonic stem cells. We found that H1foo was mainly located at around transcriptional start site of genic area, positively correlated with the gene expression.

overall_design: ChIP-seq of linker histone variant H1foo and somatic H1s in mouse embryonic stem cells.


title: Maternal Piwi regulates primordial germ cells to ensure the fertility of female progeny in Drosophila

city: New Haven

first: Haifan

last: Lin

state: Connecticut

address: 10 Amistad Street

institute: Yale University

summary: PIWI proteins and their associated small noncoding piRNAs, which guide PIWI to target RNAs by base-pairing, are among the maternal components deposited into the germline of the early embryo in Drosophila. Piwi has been extensively studied in the adult ovary and testis, where it is required for transposon suppression, germline stem cell self-renewal, and fertility. Consequently, loss of Piwi in the adult ovary using piwi-null alleles or knockdown from early oogenesis results in complete sterility, limiting investigation into possible embryonic functions of maternal Piwi. In this study, we show that the maternal Piwi protein persists in the embryonic germline through gonad coalescence, suggesting that maternal Piwi can regulate germline development beyond early embryogenesis. Using a maternal knockdown strategy, we find that maternal Piwi is required for the fertility and normal gonad morphology of female, but not male, progeny. Following maternal Piwi knockdown, transposons were mildly derepressed in the early embryo but were fully repressed in the adult ovaries of progeny. Furthermore, the maternal piRNA pool is diminished, reducing the capacity of the PIWI/piRNA complex to target some zygotic genes during embryogenesis. Examination of embryonic germ cell proliferation and gene expression in the adult ovary showed that the germline of female progeny is partially masculinized upon maternal Piwi knockdown . This reveals a novel role for maternal Piwi in the germline development of female progeny and suggests that the PIWI/piRNA pathway is involved in germline sex determination in Drosophila.

overall_design: Total RNA-seq and Small RNA-seq of embryos depleted of maternal Piwi

first: Lauren

last: Gonzalez

first: Xiongzhuo

last: Tang


title: Loss-of-function genetic screening identifies ALDOA as an essential driver for hepatocellular carcinoma cell growth under hypoxia

city: Guangzhou

first: Yi

last: Niu

address: No.2, Zhishan Garden, No.132, East Outer Ring Road

institute: Sun Yat-sen University

summary: Hypoxia is a common feature of tumor microenvironment (TME), which promotes tumor progression, metastasis and therapeutic drug resistance via a myriad of cell activities in tumor and stroma cells. While targeting hypoxic TME is emerging as a promising strategy for treating solid tumors, preclinical studies with this approach are lacking in hepatocellular carcinoma (HCC). From a genome-wide CRISPR/Cas9 gene knockout screening, we identified aldolase A (ALDOA), a key enzyme in glycolysis and gluconeogenesis, as a master driver for HCC cell growth under hypoxia. To delineate the functional implications of ALDOA in HCC, transcriptome sequencing is performed to interrogate the differential gene expression in ALDOA-knockdown HepG2 cells under hypoxia.

overall_design: The HCC cells are cultured in 20% O2 and 1% O2 for 3 days to mimic normoxia and hypoxia, genome-wide CRISPR/Cas9 knockout library screening and sequencing to identify essential genes responding to hypoxia in HCC tumor cells. RNA sequencing is performed to interrogate the differential gene expression in ALDOA-knockdown HepG2 cells under hypoxia.

first: Guohui

last: Wan


title: Suppression of lysosomal acid alpha-glucosidase impacts the modulation of transcription factor EB translocation and mitophagy in pancreatic cancer

city: Minato-ku

first: Ryoga

last: Hamura

state: Tokyo

address: Nisi-shinbashi, 3-25-8

department: Research Center of Medical Sciences

institute: Jikei University School of Medicine

summary: Lysosomal degradation plays a crucial role in the metabolism of biological macromolecules supplied by autophagy. Recent evidence demonstrated the regulation of the autophagy-lysosome system, which contributes to intracellular homeostasis, chemoresistance, and tumor progression, as a promising therapeutic approach for pancreatic cancer (PC). However, the details of lysosomal catabolic function in PC cells is not fully elucidated. In this study, we show evidence that suppression of acid alpha-glucosidase (GAA), one of the lysosomal enzymes, improves chemosensitivity and exerts apoptotic effects on PC cells through the disturbance of mitophagy via migration of the transcription factor EB. The levels of lysosomal enzyme were elevated by gemcitabine in PC cells. In particular, the levels of GAA were responsive to gemcitabine in a dose- and time-dependent manner. Small interfering RNA against the GAA gene (siGAA) suppressed cell proliferation and promoted apoptosis in gemcitabine-treated PC cells. In untreated PC cells, we observed accumulation of depolarized mitochondria. Gene therapy using adenoviral vector carrying short hairpin RNA against the GAA gene increased the number of apoptotic cells and decreased the tumor growth in xenograft model mice. These results indicate that GAA is one of the key targets to improve the efficacy of gemcitabine and develop novel therapies for PC.

overall_design: Gemcitabine induced gene expression in PANC-1 cell was analyzed by  compareing between the expression profile of the cells  treated with gemcitabine (1 µM) for 24h and non-treated (control) cells.  Three independent experiments were performed .

first: Yoshihiro

last: Shirai

first: Yohta

last: Shimada

first: Nobuhiro

last: Saito

first: Tomohiko

last: Taniai

first: Takashi

last: Horiuchi

first: Naoki

last: Takada

first: Yumi

last: Kanegae

first: Toru

last: Ikegami

first: Toya

last: Ohashi

first: Katsuhiko

last: Yanaga


title: RNA Sequencing of human THP-1 derived macrophages transcriptomes

city: Chengdu

first: Miao

last: Xu

address: 37#,Guoxue alley, Wuhou district

department: Clinical Nutrition

institute: West China hospital of Sichuan university

summary: THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA) at 25μg/ml for 48h.Then remove PMA and rest for 24h to obtain M0 macropahges. Further applied LPS and IFNγ or IL-4 and IL-13 for 24h to obtain M1, M2 macrophages, respectively. During polarization, cells were growth within control medium(LN) or medium with extra lipid mixture(LH).M0,M1,M2 cells were collected and applied to RNA-sequencing. We found that differential activation of macrophage had distinct metabolic signature.Extra lipids supplement did not significantly alter transcriptomes of macrophages.

overall_design: mRNA profiles of 3 different activation states of THP-1 derived macrophages within growth medium with/without extra lipid mixture were examined by Illumina Hiseq.

first: Hui

last: Yang


title: Arginine starvation elicits chromatin leakage and cGAS-STING activation via epigenetic silencing of metabolic and DNA-repair genes [ChIP-seq]

city: Hsinchu

first: Sheng-Chieh

last: Hsu

address: No. 101, Section 2, Kuang-Fu Road

department: Institute of Biotechnology

country: Taiwan

institute: National Tsing Hua University

summary: One of the most common metabolic defects of cancer cells is the deficiency in arginine synthesis due to suppressed expression of argininosuccinate synthetase 1 (ASS1) which renders cancer cells auxotrophic to external arginine supply. Arginine deprivation has been effectively used as a treatment for leukemias, with several clinical trials on solid tumors underway.  We previously showed that in prostate cancer arginine depletion induced mitochondrial dysfunction and excessive ROS production resulting in chromatin autophagy, nuclear DNA leakage, and cellular death, but the detailed mechanism of arginine starvation-induced cell death remains unclear. In this study, we demonstrated that arginine deprivation coordinately suppressed metabolic genes, including those responsible for mitochondrial oxidative phosphorylation (OXPHOS), nucleotide metabolism, and DNA repair. The consequent ROS production and impaired DNA damage response resulted in nuclear DNA leakage and cGAS-STING activation which is accompanied by upregulation of type I interferon response. We also showed that coordinated silencing of OXPHOS and DNA repair genes is caused in part by the depletion of α-ketoglutarate (αKG) and inactivation of histone demethylases. Supplementing cell-permeable dimethyl α-ketoglutarate (DMKG) both reduced repressive histone methylations and partially restored OXPHOS gene expressions, mitochondrial functions, and mitigated nuclear DNA leakage. Using our dietary arginine-restriction model, we demonstrate that arginine starvation slows prostate cancer growth with evidence of enhanced interferon responses and recruitment of immune cells. Our data suggests arginine starvation induces cell killing of ASS1-low cancer cells by metabolic depletion and epigenetic silencing of metabolic genes, leading to DNA damage and leakage. Resulting cGAS-STING activation may further enhance these killing effects.

overall_design: CWR22Rv1 cells were treated with ADI-PEG20 for 48 h, and H3K9me3 and H3K27me3 occupancy on the promoter regions was determined by ChIP-seq


title: Arginine starvation elicits chromatin leakage and cGAS-STING activation via epigenetic silencing of metabolic and DNA-repair genes.

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

overall_design: Refer to individual Series


title: Differential expression levels of Sox9 in early neocortical radial glial cells regulate the decision between stem cell maintenance and differentiation

city: Natal

first: Diego

middle: Marques

last: Coelho

state: RN

address: Av. Nascimento de Castro, 2155

department: Bioinformatics

country: Brazil

institute: UFRN

summary: Radial glial progenitor cells (RGCs) in the dorsal forebrain directly or indirectly produce excitatory projection neurons and macroglia of the neocortex. Recent evidence shows that the pool of RGCs is more heterogeneous than originally thought and that progenitor subpopulations can generate particular neuronal cell types. Using single cell RNA sequencing, we have studied gene expression patterns of two subtypes of RGCs that differ in their neurogenic behavior. One progenitor type rapidly produces postmitotic neurons, whereas the second progenitor remains relatively quiescence before generating neurons. We have identified candidate genes that are differentially expressed between these RGCs progenitor subtypes, including the transcription factor Sox9. Using in utero electroporation, we demonstrate that elevated Sox9 expression in progenitors prevents RGC division and leads to the generation of upper-layer cortical neurons from these progenitors at later ages. Our data thus reveal molecular differences between cortical progenitors with different neurogenic behavior and indicates that Sox9 is critical for the maintenance of RGCs to regulate the generation of upper layer neurons.

overall_design: Cortical primordium  mRNA profiles of E13.5 wild type (WT) CAG-mRFP / Hes5p-GFP mice

first: Jaime

last: Fabra-Beser

first: Jessica

last: Araujo

last: Marques-Coelho

first: Loyal

last: Goff

first: Marcos

middle: R

last: Costa

first: Ulrich

last: Müller

first: Cristina

last: Gil-Sanz


title: Arginine starvation elicits chromatin leakage and cGAS-STING activation via epigenetic silencing of metabolic and DNA-repair genes [microarray]

summary:
One of the most common metabolic defects of cancer cells is the deficiency in arginine synthesis due to suppressed expression of argininosuccinate synthetase 1 (ASS1) which renders cancer cells auxotrophic to external arginine supply. Arginine deprivation has been effectively used as a treatment for leukemias, with several clinical trials on solid tumors underway.  We previously showed that in prostate cancer arginine depletion induced mitochondrial dysfunction and excessive ROS production resulting in chromatin autophagy, nuclear DNA leakage, and cellular death, but the detailed mechanism of arginine starvation-induced cell death remains unclear. In this study, we demonstrated that arginine deprivation coordinately suppressed metabolic genes, including those responsible for mitochondrial oxidative phosphorylation (OXPHOS), nucleotide metabolism, and DNA repair. The consequent ROS production and impaired DNA damage response resulted in nuclear DNA leakage and cGAS-STING activation which is accompanied by upregulation of type I interferon response. We also showed that coordinated silencing of OXPHOS and DNA repair genes is caused in part by the depletion of α-ketoglutarate (αKG) and inactivation of histone demethylases. Supplementing cell-permeable dimethyl α-ketoglutarate (DMKG) both reduced repressive histone methylations and partially restored OXPHOS gene expressions, mitochondrial functions, and mitigated nuclear DNA leakage. Using our dietary arginine-restriction model, we demonstrate that arginine starvation slows prostate cancer growth with evidence of enhanced interferon responses and recruitment of immune cells. Our data suggests arginine starvation induces cell killing of ASS1-low cancer cells by metabolic depletion and epigenetic silencing of metabolic genes, leading to DNA damage and leakage. Resulting cGAS-STING activation may further enhance these killing effects.
We used microarray to analyze the expression difference between control and arginine-depleted cells to find out what genes involved in the regulation of mitochondrial function and arginine deprivation-induced cell death.

overall_design: CWR22Rv1 and PC3 cells were cultured in arginine-free medium for indicated duration. For the control group, the cells were maintained in the same arginine-free medium supplemented with arginine as the ATCC suggested. Gene expression difference was analyzed with Clariom™ S Assay, human (Affymatrix).


title: Transcriptional responses in TFAM-deficient renal epithelial cells

city: Nashville

first: Volker

middle: Hans

last: Haase

state: TN

institute: Vanderbilt University Medical Center

summary: Mitochondrial transcription factor A (TFAM) was deleted in renal epithelial cells using the Six2-Cre transgene. To characterize gene expression in TFAM-deficient renal epithelial cells, renal cortices from mutant and Cre-negative control mice were compared.

overall_design: Renal cortices from 4 control mice were compared with 4 mutant kidney cortices.

first: Hanako

last: Kobayashi

first: Ken

last: Ishii


title: Gene expression profiling of side population (SP) cells and non-SP cells in Hodgkin Lymphoma (HL) cell lines_1

city: Tokyo

first: Makoto

last: Nakashima

address: Building 2, West-side of 3rd floor, 1-4-6 Shirokanedai, Minatoku

institute: University of Tokyo

summary: SP cells in HL cell lines are characterized by up-regulation of genes related to TNF-alpha Signaling via NF-κB, Inflammatory Response and Hypoxia compared to the non-SP cells.

overall_design: SP cells and non-SP cells in HL cell lines were sorted using flow cytometry, then analyzed using microarray based comprehensive gene expression in these cells to elucidate why the intracellular concentration of ROS is low in the SP compared to the non-SP.

last: Nakahisma

first: Mariko

last: Watanabe

first: Kazumi

last: Nakano

first: Kaoru

last: Uchimaru

first: Ryouichi

last: Horie


title: Gene expression profiling of side population (SP) cells and non-SP cells in Hodgkin Lymphoma (HL) cell lines


title: Gene expression profiling of side population (SP) cells and non-SP cells in Hodgkin Lymphoma (HL) cell lines_2


title: A role for tRNA modifications in the expansion of proteome diversity

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

summary: The mechanisms that drive the evolution of proteome diversity are poorly understood. Here we investigate the functional significance of eight eukaryotic tRNAs that contain inosine in the wobble position of the anticodon (I34-tRNAs). We find that these modified tRNAs are essential to translate a subset of the eukaryotic proteome composed of eukaryote-specific, low-complexity polypeptides involved in interactions with the extracellular environment, including proteins containing mucin-like domains. Depletion of I34-tRNAs in human cells leads to impaired translation of these proteins, and morphological and cell adhesion phenotypes. We further show that translation defects are strictly dependent on codon distribution and composition of transcripts. Genes coding for the precursors of I34-tRNAs are almost absent in prokaryotes and abundant in eukaryotes. We conclude that I34-tRNAs bestowed eukaryotes with the ability to expand their proteomes with a new set of highly-biased genetic sequences that provided these organisms with novel extracellular functionalities.

overall_design: RNA-Seq obtained from Total RNA and from high-polysomal fractions of HEK293T cells Control and HEK293T (CRISPR/Cas9-mediated) ADAT2 KD cells

first: Adrián

last: Torres

last: Reina García

first: Lluis

last: Ribas de Pouplana

first: Eva

middle: M

last: Novoa


title: HERV-K ENV expression is a therapeutic target in atypical teratoid rhabdoid tumors

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

summary: Human Endogenous Retroviruses (HERVs) are exogenous viral elements that integrated into the germline millions of years ago.  They comprise 8% of the human genome and play a critical role in cellular differentiation during development.  HERV-K(HML-2) is the most recently integrated and actively transcribed HERV. It is found to be highly expressed in pluripotent stem cells and strongly downregulated during cellular differentiation. Moreover, expression of HERV-K in terminally differentiated neurons results in cytotoxicity. Expression of HERVs has been implicated in carcinogenesis and is suggested to confer stem cell like features important for cell growth. Atypical Teratoid / Rhabdoid Tumor (AT/RT) is a rare pediatric brain cancer that results from incomplete neuronal differentiation during embryonic development.  In this paper, we investigated the cytopathic effect of Ouabain, a cardiac glycoside that induces cytotoxicity in stem cells, on AT/RT cells. We characterized four AT/RT cell lines by immunostaining and observed variable levels of stem cell, Oct4 and Pax6, and neuronal differentiation markers, TUBB3 and MAP2, as well as HERV-K envelope (env), polymerase (pol), and gag transcripts.  We stained formalin-fixed brain tissues from 20 AT/RT patients and 5 unaffected controls for HERV-K ENV protein expression. 40% of AT/RT patient tissues showed ENV expression.  In contrast, no ENV immunostaining was observed in all 5 control brain tissues. We used Ouabain, known to be cytotoxic to stem cells, observed up to 50% toxicity at 24 hr and 80% toxicity at 48 hr after treatment.  While AT/RT primarily exist as large cell aggregates in suspension, Ouabain treatment downregulated HERV-K ENV protein and caused disruption of cell-to-cell interactions. Similarly, when AT/RT cells were transfected with a CRISPR/Cas9 construct designed to repress HERV-K promotor activity, cell aggregates separated and cell viability decreased significantly. Using a luciferase reporter construct under the control of a HERV-K promotor, we observed a significant decrease in HERV-K promotor activity at 8 to 72 hr post treatment with 0.5 uM Ouabain.  Given that downregulation of HERV-K alone was sufficient to cause cytotoxicity in the cells, HERV-K expression may be essential for AT/RT growth and survival.  Ouabain and other compounds that modulate HERV expression may provide an alternative or adjunctive therapeutic option for treatment of embryonal tumors.

overall_design: RNA-Seq profiles for 4 human Atypical Teratoid Rhabdoid Tumor (ATRT) cell lines available from ATCC (www.atcc.org): CHLA 02, CHLA 04, CHLA 05, CHLA 06.  Two of the cell lines, CHLA 04 and CHLA 06, were seqeunced twice; providing for a pair of technical profiles each.

first: Tara

last: Doucet-O'Hare

first: Brianna

middle: B

last: DiSanza

first: Jeffery

last: Kowalak

first: Lisa

last: Henderson

first: Nasir

last: Malik

first: Joeseph

last: Stiener

first: Avindra

last: Nath


title: Comprehensive transcriptome analysis provides novel insight into pistil abortion mechanism in Japanese apricot

city: Nanjing

first: Shahid

last: Iqbal

state: Jiangsu

address: Nanjing, China

institute: Nanjing Agriculture University

summary: Flower development is a key stage in the life cycle of fruit trees and its proper development is considered its reproductive success. Pistil abortion is a widely distributed phenomenon in fruit plants and its mechanism in Japanese apricot is quite unclear. The present study was carried out to get a deep insight about the regulatory mechanism of pistil abortion in Japanese apricot using transcriptomic approach. A large number of DEGs (24,683) were identified in normal (N) and abortive pistil stages i.e. style browning (STYB), stigma browning (STIB) and ovary browning (OVB). Pair-wise comparison analysis was performed as N vs STYB, N vs STIB, N vs OVB and STIB vs OVB, and produced 9592, 8691, 8660 and 8103 transcripts, respectively. The Gene Ontology (GO) showed that different metabolic processes, plant hormones, flower development and photosystem related genes were involved in pistil abortion. The pathway analysis revealed that plant hormones signal transduction and circadian rhythm pathways were found significantly enriched. Furthermore, transcription factors such as MYB, MADS-box and NAC family remained highly expressed. Maximum number of the genes were grouped to cluster 11, and were highly expressed at OVB stage, suggesting that this stage might be critical for pistil abortion. This study provides an alternatives to be consider for further studies and understanding of pistil abortion processes in Japanese apricot, and provide a reference related to this issue for other deciduous fruit crops.

overall_design: The flower buds of Japanese apricot (P. mume) cv. ‘Daqiandi’ and ‘Longyan’ were collected Longyan pistils were used as normal pistil (control) and Daqiandi pistils were used as abortive pistils. Three key stages of pistil abortion (cv. Daqiandi pistils) i.e. style browning (STYB), stigma browning (STIB) and ovary browning (OVB) were selected

first: Zhihong

last: Gao


title: Identification of miRNAs as biomarkers of drug response of Pien Tze Huang in Hepatic Fibrosis Treatments

city: Shanghai

first: Jinhang

last: Zhu

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

summary: Pien Tze Huang (PZH) is herbal traditional Chinese medicine which was widely utilized in Asia for hepatic diseases. We constructed two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group replacing PZH with double distilled water. All 12 mice were fed for 8 weeks and then killed to have their liver tissue taken out. Small RNA-seq were used to identify miRNAs of PZH medicine effect for hepatic fibrosis. We found the expression of these miRNAs (mmu-miR-205-5p, mmu-miR-3064-5p, mmu-miR-205-5p, mmu-miR-370-3p, mmu-miR-665-3p) were changed in PZH medicine treatment for hepatic fibrosis study. Furthermore, Hmga2 and Fgf9, miRNAs corresponding target genes (Sp4, Slc2a6, Tln2, Hmga2, Ank3, Pax9, Fgf9), have been reported association with hepatic fibrosis.

overall_design: We constructed two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group replacing PZH with double distilled water. Small RNA-seq were used to identify miRNAs of PZH medicine effect for hepatic fibrosis.

first: Shengying

last: Qin

first: Di

last: Zhang


title: RNA-seq and H3K27ac ChIP-seq of Y1 cells treated with FGF-2

status: Public on Jun 27 2021

city: Philadelphia

first: Peder

last: Lund

state: PA

address: 3400 Civic Center Blvd, Smilow 9-176

institute: University of Pennsylvania

summary: In addition to driving cell cycle progression, oncogenes may also trigger pathways leading to senescence, thereby inhibiting the growth of tumorigenic cells.  Paradoxically, Y1 cells, which carry an amplification of Ras, become senescent after treatment with the mitogen FGF-2.  To understand how FGF-2 promotes senescence, we profiled the epigenome, transcriptome, proteome, and phospho-proteome of Y1 cells stimulated with FGF-2.  FGF-2 caused delayed acetylation of histone H4 and higher levels of H3K27me3.  Sequencing analysis revealed decreased expression of cell cycle-related genes with concomitant loss of H3K27ac.  In contrast, FGF-2 promoted the expression of p21 and various cytokines and MAPK-related genes.  Nuclear envelope proteins, particularly lamin B1, displayed increased phosphorylation in response to FGF-2.  Proteome analysis suggested alterations in cellular metabolism, as evident by modulated expression of enzymes involved in purine biosynthesis, tRNA aminoacylation, and the TCA cycle.  Altogether, the response of Y1 cells to FGF-2 is consistent with oncogene-induced senescence.  We propose that Y1 cells enter senescence due to deficient cyclin expression and high levels of p21, which may stem from DNA damage or TGFb signaling.

overall_design: Y1 cells were serum-starved for 48 hrs and then treated with FBS alone (10%) or FBS with FGF-2 (10 ng/ml) for 5 hrs.  RNA-seq was performed on polyA-enriched RNA in triplicate for each condition.  ChIP-seq for H3K27ac was performed on sonicated chromatin extracted from the nuclei of previously frozen cell pellets that were cross-linked with formaldehyde upon thawing.  Data was acquired in duplicate for each condition along with input controls.

first: Mariana

last: Lopes

first: Benjamin

last: Garcia

first: Julia

middle: P

last: da Cunha