title: Bulk RNA sequencing of Bone Marrow Endothelial Progenitor Cells from Patients with Myelodysplastic Syndromes

first: Tong

last: Xing

address: No. 11 Xizhimen South Street

institute: Peking University People’s Hospital

summary: Myelodysplastic syndromes(MDS) are a group of heterogeneous disease. Emerging evidence has shown the bone marrow(BM) endothelial progenitor cells(EPCs) are also heterogeneity. To uncover the underlying mechanism of heterogeneous BM EPCs in different types of MDS patients. RNA sequencing(RNA-seq) analyses were performed to analyse BM EPCs at day 7 in culture from lower-risk MDS(N=3), higher-risk MDS(N=3), acute myloid leukemia(AML) patients(N=3) and healthy donors(HDs)(N=3). We analysed the hematopoiesis- and immune-related genes and pathways.

overall_design: mRNA profiles of BM EPCs at day 7 in culture from lower-risk MDS(N=3), higher-risk MDS(N=3), AML patients and HDs

first: Yuan

last: Kong

first: Zhong-Shi

last: Lyu


title: Alkaline nucleoplasm facilitates contractile gene expression in the mammalian heart [RNA-seq]

status: Public on Apr 06 2022

city: Oxford

first: Pawel

last: Swietach

address: Sherrington Building, Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

type: Expression profiling by high throughput sequencing

summary: Cardiac contractile strength is recognised as highly pH-sensitive, but less is known about the influence of pH on cardiac gene expression, which may be relevant during changes in myocardial metabolism or vascularization in development or disease. We sought evidence for pH-responsive cardiac genes and a context in which this has physiological relevance. pHLIP, a peptide-based reporter of acidity, revealed a non-uniform pH landscape in early-postnatal myocardium, dissipating in later life. pH-responsive differentially-expressed genes (pH-DEGs) were identified by transcriptomics of neonatal cardiomyocytes cultured over a range of pH.  Enrichment analysis indicated “striated muscle contraction” as a pH-responsive biological process. Label-free proteomics verified fifty-four pH-responsive gene-products, including contractile elements and the adaptor protein CRIP2.  Using transcriptional assays, acidity was found to inhibit p300/CBP acetylase activity and, as its functional readout, negatively affect myocardin, a co-activator of cardiac gene expression. In cultured myocytes, acid-inhibition of p300/CBP reduced H3K27 acetylation, as demonstrated by chromatin immunoprecipitation.  H3K27ac levels were more strongly reduced at promoters of acid-downregulated DEGs, suggesting an epigenetic mechanism of pH-sensitive gene expression.  By tandem cytoplasmic/nuclear pH imaging, the cardiac nucleus was found to exercise a degree of control over its pH through Na+/H+ exchangers at the nuclear envelope. Thus, we describe how extracellular pH signals gain access to the nucleus and regulate the expression of a subset of cardiac genes, notably those coding for contractile proteins and Crip2. Acting as a proxy of a well-perfused myocardium, alkaline conditions are permissive for expressing genes related to the contractile apparatus.

overall_design: polyA RNA-seq in NRVMs at various pHs

first: Kyung

middle: C

last: Park

first: Alzbeta

last: Hulikova


title: Alkaline nucleoplasm facilitates contractile gene expression in the mammalian heart [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: ChIP-seq in NRVMs at various pHs or treated with A485

first: Nicholas

middle: T

last: Crump

first: Thomas

middle: A

last: Milne


title: Rpd3 regulates single-copy origins independently of the rDNA array by opposing origin stimulation by Fkh1

city: Los Angeles

first: Yiwei

last: He

state: CA

address: 1050 Childs Way RRI 203

department: Molecular Biology

country: USA

institute: University of Southern California

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

overall_design: Refer to individual Series


title: Single cell gene expression profiling of cardiac non-myocytes from CD31 depleted suspensions

city: San Antonio

first: Brian

last: Iskra

state: Texas

address: 8403 Floyd Curl Dr

institute: GCCRI

summary: Cardiac non-myocytes are poorly defined as a cell type. In order to better define them, we performed single cell RNA sequencing to assess heterogeneity.

overall_design: Non-myocytes were isolated by mincing murine cardiac tissue and then performing magnetic bead removal of enodthelial cells to enrich minor non-myocyte populations.

first: Iskra

last: Brian


title: OCT4-free reprogramming of human fibroblasts into pluripotent stem cells

city: Frankfurt am Main

first: Xinlai

last: Cheng

state: Hessen

address: Max-von-Laue-Strasse 15. R. 3.652

department: Chemical Biology

country: Germany

institute: Goethe Frankfurt University. BMLS

summary: Replacing the transcription factor OCT4, one of the master pluripotency regulators, by small molecules has been a long standing challenge to establish small molecule based reprogramming for the generation of human chemically induced pluripotent stem cells (hciPSCs). Using a cell-based high throughput screen, we have previously identified a new series of OCT4-inducing compounds (O4Is). In this paper, we prepared metabolically stable analogues, including O4I4, which strongly activate pluripotency-associated signaling. In combination with a transcription factor cocktail of SOX2, KLF4, MYC, and LIN28 (collectively referred to as CSKML) we achieved to reprogram human fibroblasts into a stable and authentic pluripotent state independent of exogenous OCT4. Transcriptomic analysis of fibroblasts reprogrammed by this approach revealed that O4I4 activated bone morphogenetic protein (BMP)/SMAD/ID signaling at the early stage of reprogramming and subsequent expression of the chromatin modifier, high mobility group A1 (HMGA1), resulting in re-activation of endogenous OCT4 to initiate the reprogramming process. Consistently, chemical or genetic inhibition of BMP/SMAD/ID or HMGA1 was found to block cellular reprogramming. In C.elegans and Drosophila, O4I4 expanded life spans in a BMP-signaling pathway-dependent manner. Given limitations of OCT4-based reprogramming, our findings provide an alternative to OSKM-mediated iPSC generation, and importantly unravel previously-unrecognized molecular mechanisms of pluripotency in the context of regenerative medicine and rejuvenation therapy.

overall_design: RNA was obtained from treated and non-treated human fibroblast and fibroblast-derived induced Pluripotent Stem Cells and treated with an episomal constrcuts of Oct4, Sox2, Klf4 and c-Myc in addition to O4I3

first: Rodrigo

last: Gama-Brambila

first: Han

last: Kang

first: Yasamin

last: Dabiri

first: Katerina

last: Taškova

first: Luuk

middle: N

last: van Oosten

first: Ralf

last: Mrowka

first: Jochen

last: Utikal

first: Miguel

last: Andrade-Navarro

first: Jichang

last: Wang

first: Stefan

last: Wölfl

first: Jun

last: Zhou


title: Glucosamine facilitates cardiac ischemic recovery via recruiting Ly6Clow monocytes in a STAT1 O-GlcNAcylation dependent fashion

city: Suzhou

first: Wenjing

state: 江苏

address: SuZhou JiangSu

country: China

institute: Soochow University

summary: The O-linked β-N-acetylglucosamine (O-GlcNAc) modification on intracellular proteins controls diverse biological processes. Though sustained hyper-O-GlcNAcylation aggravates pathogenesis of many chronic diseases, accumulating evidence also indicates that acute augmentation in O-GlcNAcylation seems to benefit disease healing in some cases. Glucosamine (GlcN) is a freely available and commonly used dietary supplement for human cartilage health, which also activates the hexosamine biosynthesis pathway and induces protein O-GlcNAcylation. Here we show that both GlcN early and late therapies effectively facilitate cardiac recovery in mice by elevating accumulation of Ly6Clow Mo/Mps in infarcted hearts. Eliminating Mo/Mps with clodronate liposomes fully abolishes aforementioned cardiac healing role of GlcN. Importantly, GlcN supplementation accelerates not only in vitro mobility of reparative Mo/Mps but also in vivo infiltration of Ly6Clow Mos. Mechanistically, GlcN positively regulates transcription of myeloid CX3C chemokine receptor 1 (Cx3cr1) by improving STAT1 O-GlcNAcylation, which stabilizes STAT1 and subsequently promotes chemotaxis and infiltration of Ly6Clow Mos. In summary, we identify a novel anti-inflammatory role of GlcN and suggest that its protective effects are mediated through chemotaxis of Ly6Clow Mos in a STAT1/CX3CR1-dependent fashion, which is controlled by O-GlcNAcylation of STAT1. Our study provides a novel clue for Mo/Mps modulator therapies aimed at reducing post-MI hyperinflammation in ischemic myocardium.

overall_design: Ischemic zones from GlcN/E or saline hearts on Day 3 post-MI

first: Weiqian

last: Chen

first: Zhenya

last: Shen

first: Xuan

last: Jiang

first: Qingsong

last: Tang


title: Integrated Analysis of lncRNA and mRNA Expression Profiles Indicates Age-related Changes in Meniscus

city: Beijing

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

type: Non-coding RNA profiling by high throughput sequencing

summary: Little has been known about the role of long non-coding RNA (lncRNA) involves in meniscus degradation with aging.In order to investigate the molecular mechanisms of age-related meniscal degeneration and further explore potential biologic therapeutic targets, we performed microarray analysis of meniscus to determine lncRNAs and mRNAs expression profiles in young and aging adults. Then, we carried out bioinformatics analysis of differentially expressed molecules to identify key molecules and functional pathways in the aged meniscus tissues.

overall_design: The torn segment of the injured meniscus was resected from eight patients who underwent arthroscopic meniscus repair surgery with no significant cartilage degeneration, osteoarthritis, rheumatoid arthritis and other metabolic diseases. For the current study, these tissues were divided into two categories based on patients’ age: young group (n = 4, 20–25 years old) and aging group (n = 4, 50-55 years old).

first: Li-Ya

last: Ai

first: Ze-Ming

last: Du

first: You-Rong

first: Peng-Yan

last: Xia

first: Ji-Ying

last: Zhang

first: Dong


title: RNA-Seq analyses of Hv1 null hearts

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

summary: Our study aims to illustrate potential role of Hv1 in heart.

overall_design: We have 2 groups: Hv1 null mouse hearts and wild-type mouse hearts. Each group has 4 samples. We plan to compare RNA-seq results between groups.

first: Mark

last: Maienschein-Cline

first: Xin

last: Wu

first: Liang

last: Hong


title: Identification of an evolutionarily conserved domain in Neurod1 essential for triggering enteroendocrine cell differentiation

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

summary: ARP/ASCL transcription factors are key determinants of cell fate specification in a wide variety of tissues, coordinating the acquisition of generic cell fates and of specific subtype identities.  How these factors, recognizing highly similar DNA motifs, display specific activities, is not yet fully understood.     To address this issue, we overexpressed different ARP/ASCL factors in zebrafish ascl1a-/- mutant embryos to determine which one is able to rescue the intestinal secretory lineage.  We found that Ascl1a/b, Atoh1a/b and Neurod1 factors are all able to trigger the first step of the secretory regulatory cascade but distinct secretory cells are induced by these factors.  Indeed, Neurod1 rescues the enteroendocrine lineage while Ascl1a/b and Atoh1a/b rescue the goblet cells.  Gain-of-function experiments with Ascl1a/Neurod1 chimeric proteins revealed that the functional divergence is encoded by a 19-aa ultra-conserved element (UCE), present in all Neurod members but absent in the other ARP/ASCL proteins. This novel domain acts as a goblet cell fate repressor and inhibits Gfi1aa expression, known to be important for goblet cell differentiation. Deleting the UCE domain of the endogenous Neurod1 protein leads to an increase in the number of goblet cells concomitant with a reduction of several EE subtypes, validating the importance of the UCE domain in enteroendocrine cell differentiation. Importantly, the neurod1 null mutant displays very similar defects supporting the crucial function of the UCE domain for NeuroD1 activity in the intestine.  As Gfi1 acts as a binary cell fate switch in several tissues where Neurod1 is also expressed, we can envision a similar role of the UCE in other tissues, allowing Neurod1 to repress Gfi1 to influence the balance between cell fates.

overall_design: RNA-sequencing of 23 samples. Enteroendocrine cell (pax6b:GFP +) transcriptomic profiles of 4dpf (days post fertilization) wild type and neurod1 deleted from its conserved domain (neurod1DelUCE-/-)  zebrafish embryos were generated in in 3 replicates and 4 replicates, respectively.  Endodermal cells (sox17:dsRed +) transcriptomic profiles of 52hpf (hours post fertilization) WT or transgenic (hsp70:ascl1a, hsp70:neurod1, hsp70: neurod1DelUCE, hsp70: neurod1DelECD) zebrafish embryos were generated in triplicates or in 4 replicates (hsp70:neurod1) after 2 heat-shocks inducing transgene expression.

first: Anne-Sophie

last: Reuter

first: David

last: Stern

first: Alice

last: Bernard

first: Chiara

last: Goosens

first: Lydie

last: Flasse

first: Isabelle

last: Manfroid

first: Marianne

middle: L

last: Voz

first: Bernard

last: Peers


title: Transcriptome sequencing and ceRNA (lncRNA-miRNA-mRNA) network construction in cardiac fibrosis and heart failure

city: shijiazhuang

first: xitian

last: hu

address: No.9 Fangbei Road, Shijiazhaung City 050000, Hebei Province, China

department: Department of Cardiovasology

institute: Shijiazhuang People’s Hospital

summary:
Background: Cardiac fibrosis (CF) and heart failure (HF) are familiar heart diseases that are harmful to health, and severe CF can lead to HF. In this study, we tried to find their common potential molecular markers, which may help the diagnosis and treatment of CF and HF.
Methods: Firstly, RNA library construction and high-throughput sequencing were performed. In addition, the DESeq2 package in R was used to screen genes with differentially expressed between different samples. Then, take the intersection of the differential mRNA, miRNA and lncRNA obtained for the two diseases. Thirdly, the ConsensusPathDB (CPDB) was used to perform biological functions enrichment for intersection differentially expressed mRNAs (DEmRNAs). Fourthly, construct gene interaction network and screen out key genes. Fifthly, RT-PCR verification was performed. Lastly, GSE104150 and GSE21125 data sets were utilized to validate the expression and diagnostic analysis.
Results: There are 1477 DEmRNAs, 502 differentially expressed lncRNA (DElncRNAs) and 36 differentially expressed miRNA (DEmiRNAs) between CF and healthy control group. There are 607 DEmRNAs, 379 DElncRNAs and 42 DEmiRNAs between HF and healthy control group. CH and FH shared 146 DEmRNAs, 80 DElncRNAs, and 6 DEmiRNAs. Hsa-miR-144-3p, CCNE2, C9orf72, MAP3K20-AS1, LEF1-AS1, AC243772.2, FLJ46284 and AC239798.2 were keys genes in lncRNA-miRNA-mRNA network. In addition, hsa-miR-144-3p and CCNE2 may be considered as potential diagnostic gene biomarkers in CF and HF.

overall_design: blood samples from 3 Cardiac fibrosis patients, 3 heart failure patients and 3 healthy controls patients were used for miRNA sequencing.

first: Xitian

last: Hu


city: Changsha

first: Xuejing

last: Sun

state: Hunan

address: Ton-zi po road

department: Department of Cardiology

institute: Third Xinagya Hospital

summary: Liver has a crucial role in the regulation of immune defense in systemic infections. During endotoxemia, the liver transits from an immune-tolerant towards an immune-active state and forms the first line of defense against invading microorganisms. the role of liver parenchymal cells in endotoxemia remains unintelligible. To characterize the liver parenchymal cells in endotoxemia liver, we performed single-cell RNA sequencing of liver parenchymal cells from healthy C57BL/6J mice and murine model of endotoxemia at early or late stage. The single-cell RNA-seq analyses revealed the heterogeneity of liver parenchymal cells in endotoxemia liver.

overall_design: Single-cell RNA sequencing of liver parenchymal cells from healthy C57BL/6J mice (n=6, eight weeks-age) using MGISEQ-2000.  Single-cell RNA sequencing of liver parenchymal cells from murine model of endotoxemia at 3-hour time point (n=6, eight weeks-age) using MGISEQ-2000.  Single-cell RNA sequencing of liver parenchymal cells from murine model of endotoxemia at 12-hour time point (n=6, eight weeks-age) using MGISEQ-2000.

first: Yan

last: Tang

first: Yuanyuan

last: Chen

first: Suzhen

last: Liu

first: Lun

first: Youxiang

last: Jiang

first: Yao

last: Lu

first: Hong

last: Yuan

first: Zhaoyang

first: Jingjing

last: Cai


title: Human B-cell precursor acute lymphoblastic leukemia cells overexpressing ST6Gal1

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: Normal early human B-cells development from lymphoid progenitors in the bone marrow is dependent upon instructions from elements in that microenvironment which include stromal cells as well as extracellular matrix and factors secreted by these cells. Glycosylation is thought to play a key role in such interactions. The sialyltransferase ST6Gal1, with high expression in specific hematopoietic cell types, is the only enzyme thought to catalyze the terminal addition of sialic acids in an a2-6-linkage to galactose on N-glycans in such cells. Expression of ST6Gal1 increases as mouse B cells undergo normal B-lineage differentiation. B-cell precursor acute lymphoblastic leukemias (BCP-ALL) with differentiation arrest at various stages of early B-cell development have widely different expression levels of ST6GALl1 at diagnosis, with high ST6Gal1 in some relapses. We analyzed the consequences of increased ST6Gal1 expression in a diagnosis sample using lentiviral transduction of ST6Gal1 into US7 cells which have a relatively low level of ST6Gal1 expression. Controls were transduced with an empty vector. Gene expression analysis using RNA-seq showed a surprisingly large number of genes with significant differential expression, of which around 60% showed increased transcript levels, in the ST6Gal1 overexpressing BCP-ALL cells.

overall_design: US7 BCP-ALL is stromal-dependent and was grown in co-culture with mitotically inactivated OP9 bone marrow stromal cells. Cells were transduced with empty pLV411G vector or with pLV411G-ST6GAL1. Inserts were introduced into the pLV411G vector by GateWay cloning (Invitrogen). The ST6GAL1 encodes human ST6Gal1 406 amino acid isoform A. Pure cell populations were obtained by flow sorting for EGFP. RNAs were isolated from the cells grown under steady-state conditions on OP9 stromal cells. BCP-ALL cells in the medium supernatant were harvested for RNA isolation. EV and OE conditions were each harvested as biological triplicates.

first: Nora

last: Heisterkamp

first: Mingfeng

last: Zhang

first: Lu

last: Yang


title: Pathological consequences of chronic olfactory inflammation on neurite morphology of olfactory bulb projection neurons

city: Hershey

first: Yuka

last: Imamura Kawasawa

state: PA

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: The effects of chronic olfactory inflammation on the olfactory bulb (OB) were examined. Inflammation was induced in the olfactory epithelium by repeated unilateral intranasal administration of lipopolysaccharide (LPS). After 4 weeks, gene expression profiles were compared between ipislateral and contralateral OBs using RNA sequencing analysis.

overall_design: Total 6 samples were analyzed; ipsilateral and contralateral OBs from 3 mice received unilateral intranasal LPS administration for 4 weeks.

first: Brandon

middle: J

last: LaFever

middle: I

last: Kawasawa

first: Ayako

last: Ito

first: Fumiaki

last: Imamura


title: Response to supraphysiological testosterone is predicted by a distinct AR cistrome [ChIP-seq]

city: Boston

first: Xintao

last: Qiu

state: MA

address: 440 brookline ave

institute: Dana Faber Cancer Institute

summary: We generated transcription factor, histone modification ChIP-Seq in CRPC PDX with SPT treatment

overall_design: ChIP-seq for AR, FOXA1, HOXB13, H3K27Ac

first: Matthew

last: Freedman

first: Mark

middle: M

last: Pomerantz

first: Eva

last: Corey

first: Henry

last: Long


title: Hepatic transcriptome analysis of control and severe acute pancreatitis mice

city: shanghai

first: li

last: zhang

state: shanghai

address: pujian road 160

department: Renji Hospital stem cell centre

institute: li zhang

summary:
Purpose: The purpose of this study was to compare the hepatic transcriptome in the control group and severe acute pancreatitis, in order to identify metabolic gene changes during pancreatitis.
Methods: 6-week Balb/c mice were subjected to control (Saline*12) and SAP (caerulein *12), and mice liver tissues were harvested at 24 hours for RNA preparation (n=6 each group).
Results: Among 18257 mapped genes, 3639 differentially expressed genes were identified by RNA-seq, including 1714 genes induced in SAP compare to Control and 1892 genes down regulated in SAP compare to Control. The genes up regulated were mainly related to immune response and ER stress, while genes that down regulated were associated with fatty acids oxidation and oxidative phosphorylation.
Conclusions: Our study revealed that in SAP, genes associated with immune response are upregulated in liver, fatty acid oxidation related genes are downregulated in liver. Our data revealed the crosstalk between pancreas and liver, illustrated the  change of liver metabolism in  SAP.

overall_design: Liver mRNA profiles of 6 weeks old wild type, SAP mice were generated by sequencing in six repeat,in two mouse models.

first: Jing

last: Xue

first: Li


title: Response to supraphysiological testosterone is predicted by a distinct AR cistrome


title: Response to supraphysiological testosterone is predicted by a distinct AR cistrome [RNA-seq]

summary: We generated RNA-Seq in CRPC PDX with SPT treatment


title: miRNA profiling of rice developing leaves in response to elevated CO2

city: Sendai

first: Yonghyun

last: Kim

state: Miyagi

address: Aramaki, Aoba-ku

department: Graduate School of Agricultural Science

country: Japan

institute: Tohoku University

summary: Elevated CO2 (eCO2) has an influence on developing leaf growth of rice (Oryza sativa cv. Nipponbare), specifically lower growth stage than P4 (plastochron number), resulting in decrease in leaf size compared with that in ambient CO2 (aCO2). Since several micro RNAs are associated with the regulation of plant leaf development, in order to clarify which micro RNAs are involved in the decrease of leaf blade size at eCO2, we carried out high-throughput small RNA sequencing analysis and compared the amount of identified miRNAs in developing rice leaf blade grown between aCO2 and eCO2 condition.

overall_design: Total RNAs were isolated from rice developing leaf at 7 h and 13.5 h after elevated CO2 treatment on daytime. Two independent experiments were performed at each time (7 and 13.5 h) using different samples.

first: Mitsue

last: Miyao


title: Transcriptome sequencing of 36 rice samples was used to identify the cold tolerance mechanism of rice

city: Nanning

first: Zhichi Zeng

last: Zhichi Zeng

address: Nanning

institute: Guangxi University

summary:
Purpose: In this study, RNA-seq was used to analyzed the molecular mechanism of cold tolerance in rice
Methods: Rice 9311 (cold intolerant) and DC907 (cold tolerant) were used as experimental materials for transcriptome sequencing on Illumina HIseq platform. Fastq is used to evaluate the quality of the original data, and NGS QC Toolkit is used to filter the original data to obtain clean reads. Clean reads were compared to the rice 9311 reference genome using HISAT2 software. Put the genome mapping results of all sequenced reads data together, assemble them with cufflinks, and then compare them with known gene models with cuffcompare. The gene expression level of each sample was analyzed by HTSeq software. All treatments were analyzed for differential expression using DEseq.
Results: A total of 36 samples were used for RNA sequencing analysis, with three biological replicates per treatment. Each sample generates at least 2G data. The genes regulated by cold stress treatment (1,3 days) and recovery treatment (1,3 days) were determined by comparative analysis.

overall_design: There were 12 treatments, 3 biological replicates per treatment, a total of 36 samples. Near-isogenic lines DC907 and 931 were used as test materials.

first: Zhichi

last: Zeng

first: Sichen

first: Wenyan

last: Li

first: Baoshan

last: Chen

first: Wenlan


title: A hierarchical regulatory network ensures stable albumin transcription under various pathophysiological conditions

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

summary: Physiologically, albumin is produced by hepatocytes. It remains largely unknown how patients are capable of maintaining essential albumin levels even in the condition of liver failure. Here, we delineate a hierarchical regulatory network that controls albumin transcription under different pathophysiological conditions. The ALB core promoter possesses a TATA box and nucleosome-free area, which allows constitutive binding of RNA Pol II and thus initiation of transcription. In normal conditions, HNF4α and C/EBPα facilitate albumin transcription through binding to its promoter. In severely damaged livers, hepatocellular HNF4α and C/EBPα expression is often inhibited. The absence of HNF4 and C/EBPα increases hedgehog ligand biosynthesis. Hedgehog upregulates FOXA2 expression through transcription factor GLI2 binding to the FOXA2 promoter. Subsequently, FOXA2 maintains albumin expression in the hepatocytes lacking HNF4α and C/EBPα. In patients with massive hepatocyte loss, the expression of albumin is activated in liver progenitor cells. Albumin transcription in these cells is regulated by HNF4α or FOXA2. Taken together, HNF4α, C/EBPα and FOXA2 form a hierarchical regulatory network that ensures stable albumin expression even in pathophysiological conditions.

overall_design: Mouse primary hepatocytes (MPH) were freshly isolated from three mice: Mouse1, Mouse2, Mouse3. RNA sequencing was performed in MPH with or without HNF4α and C/EBPα siRNA treatment for 48 hours.

first: Honglei

last: Weng


title: RNA Sequencing Facilitates Quantitative Analysis of VEGF treated HUVECs Transcriptomesand with or without Verteporfin (VP) pre-treatment

city: Shanghai

first: Gu

last: Ping

address: Manufacturing Road, 833

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

summary:
Purpose: The goals of this study are to compare VEGF-treated HUVECs with or without Verteporfin (VP) pretreatment transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: After serum-starving for 12 hours, HUVECs were divided into two group: VEGF and VEGF+VP. Cells from VEGF+VP group were pretreated with VP (4 μM) for 2 hours and then all cells were treated with VEGF (200 ng/mL) for another 24 hours. Subsequently, total RNA from HUVECs were prepared using Trizol reagent and mRNA library was constructed. RNA-sequencing: RNA-sequencing was carried out by BGI (Beijing Genomic Institute, ShenZhen, China). SOAPnuke software (v1.5.2) was used to filter the data for RNA-sequencing and then these data were mapped to the reference genome using HISAT2 software (v2.0.4). The clean reads were aligned to the gene set by Bowtie2 (v2.2.5). The expression level of genes was then measured by RSEM software (v1.2.12). The heatmap of top 40 different expression genes was drawn according to the gene expression with FPKM (fragment per kilobase of transcript per million). Reactome (https://www.reactome.org/) enrichment analysis of different expression genes was undertaken and the significant levels of terms and pathways were corrected by Q value.
Results: The statistical results of significant DEGS confirmed that approximately 7204 genes of the transcripts showed differential expression between the VEGF group and VEGF+VP group, with a fold change ≥1.5 and p value <0.05. Altered expression of 20 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to angiogenesis. Data analysis with GO analysis and GSEA analysis revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusions: Our study represents the first detailed transcriptomic analysis of VEGF treated HUVECs with or without VP treatment, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: HUVECs mRNA profiles of VEGF treated cells and VEGF+VP treated cells

first: Yahan

last: Ju

first: Ping

last: Gu


title: Expression data of KDM4C knockout by CRISPR in Prostate cancer cell line C4-2B

city: Taipei

first: Ching-Yu

last: Lin

address: R202, Institute of Biological Chemistry National Taiwan University, No. 1, Sec. 4, Roosevelt Rd.

department: Ph.D. Program for Cancer Molecular Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

summary: Histone Demethylase KDM4C promotes prostate cancer metastasis via induction of c-Myc and LDHA

overall_design: Triplicates test of control samples and CRISPR knockout KDM4C samples in the study

middle: Y

first: Bi-Juan

last: Wang

first: Wei-Yi

last: Liu

first: Chih-Pin

middle: P

last: Chuu


title: The impact of Spike protein on macrophage inflammation

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

summary:
Purpose: To elucidate how SARS-CoV-2 spike protein affects macrophage inflammatory responses
Methods: Peritoneal macrophages were isolated from Myeloid-specific IKKβ knockout mice (IKKβΔMye) and control littermates (IKKβ F/F). Then the macrophages were treated with lentivirus expressing Spike protein for 24 hours
Results: Deficiency of IKKβ nearly abolished spike protein-associated geneset scores and DEGs-associated key inflammatory pathways.
Conclusions: These results indicate that SARS-CoV-2 Spike protein induces strong inflammatory responses in macrophages, potentially through activation of canonical IKKβ/NF-κB signaling

overall_design: Macrophagic mRNA profiles of control and IKKβ-deficient macrophages after 24-hour treatment of Lentivirus expressing Spike protein

first: Rebecca

last: Hernandez

first: Zhaojie

last: Meng

first: Tong


title: Histone demethylase SlJMJ4 promotes leaf senescence via removal of H3K27 methylation of senescence-related genes in tomato

city: guangzhou city

first: Ding

last: xiaochun

state: guangdong

address: 723 xingke road, tianhe district

institute: SOUTH CHINA BOTANICAL GARDEN

summary: SlJMJ4 is a positive regulator of leaf senescence in tomato and mediates ABA-induced leaf senescence by activating the transcription of many genes related to ABA synthesis and signaling, and transcription regulation via removal of their H3K27me3 levels.

overall_design: SlJMJ4 target gene identification sample is JMJ7-OE-GFP tomato leaves of 8-week-old plants.

first: Xiaochun

last: Ding

first: Dandan

last: Zhang

first: Guoxiang

last: Jiang

first: Dachuan

first: Zhiwei

first: Hanzhi

last: Liang

first: Hong

last: Zhu

first: Yueming

first: Xuewu

last: Duan


title: RNA sequencing of the spleen of naked mole-rat and  mouse

city: Berlin

first: Valerie

last: Begay

address: Robert-Rössle-Str. 10

institute: Max Delbrück Center

summary: Heathly naked mole-rats kept under normal housing conditions harbor either a small or enlarged spleen. The aim of the study is to compare RNAseq of naked mole-rat (NM-R) small and enlarged spleens between them and to compare them with RNAseq of mouse spleen.

sample_organism:
Mus musculus
Heterocephalus glaber

platform_organism:
Mus musculus
Heterocephalus glaber

overall_design: Dissection of the spleen from NM-R and mice kept under normal housekeeping conditions. We observed that  healthy NM-R have either small or enlarged spleen. We therefore compared 3 groups: NM-R with small spleen, NM-R with enlarged spleen and mouse spleen, n = 3 per group.   After extraction of  total RNA,  RNA sequencing and transcriptome analysis were performed. RNA was sequenced  on the Illumina NovaSeq6000 Platform.

first: Bégay

last: Valérie

first: Cirovic

last: Branko

first: Gary

last: Lewin


title: Comparative analysis of the different Streptomyces bingchenggensis strains by RNA-seq

city: Beijing

first: liyang

last: chu

address: haidian

institute: Chinese Academy of Agricultural Sciences

summary: Streptomyces bingchenggensis is a soil bacterium that produces milbemycins. Milbemycins and their derivatives are valuable biopesticides in the agricultural field.  Owing to their advantages such as high efficiency and safety for human and animal,it was urgent to construct high-yield strain to ensure  low production cost. To obtain genes closely correlated with milbemycin production, we have compared the whole genome microarray expression profiling of two strains (the parent one strain and high-yielding strain). In Streptomyces bingchenggensis, there are abundant exporters, which are responsible for transporting various substrates. In the result, some drug exporters were chosen to enhance production of milbemycin .

overall_design: 6 time points were designed at 18,48,72,96,144,and 192 hours in two strains (wild type and sbbA deletion mutant). The samples were collected at each time point named W1,W2,W3,W4,W5,W6, S1,S2,S3,S4,S5,and S6.

first: Y

first: H

last: He

first: L

last: Chu

first: S

last: Li

first: W

last: Xiang

first: P

last: Jin

first: Z

last: Dong


title: Knock down of Ifitm3 inhibits the adult retinal progenitor cell proliferation

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

summary: Knock down of Ifitm3 inhibits the mouse adult retinal progenitor cell proliferation.

overall_design: The retinal progenitor cell  was transfected with siRNA(Control and Ifitm3) by lipo3000. The total RNA of the two groups of cells were detected with the RNA-seq.

first: Caixia


title: RNA-sequencing transcriptional profile of kidney capsule derived organ fibroblasts from adult mice [KidneyCapsule]

city: Clayton

first: Hieu

middle: Tri

last: Nim

state: VIC

address: Monash University Clayton Campus, Wellington Rd

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

summary: Organ fibroblasts are essential components of homeostatic and diseased tissues, as they participate in sensing the microenvironment and communicating with other resident cells. They are also involved in pathological remodeling and fibrosis, caused by excessive deposition of connective tissue after injury, which impairs organ function. It is estimated that 45% of deaths in developed countries are linked to chronic fibrosis, yet current drugs on the market are both inefficient and non-specific to this condition. We have previously shown that cardiac fibroblasts display a unique cardiogenic identity, important for cardiac pathological remodeling. To determine whether fibroblasts from other organ systems display a molecular signature unique to their organ of origin, we characterized fibroblasts isolated from the adult mouse skin, lung, kidney, gonad and liver, and documented a molecular positional and organ signature that is likely a remnant from embryonic development. This information opens novel opportunities for the treatment of fibrotic diseases in a more precise, organ-specific manner.

overall_design: RNA sequencing of primary cardiac fibroblast, kidney fibroblast, and tail fibroblast from culture and after being transplanted in kidney capsules. The experiment was performed in triplicate.

first: E

last: Forte

first: M

last: Ramialison

middle: B

last: Furtado


title: RNA-sequencing transcriptional profile of human hearts [HumanHeartFailure]

overall_design: RNA-sequencing transcriptional profile of human hearts, including heart failure and healthy control. Samples were obtained from n=5 healthy individuals and n=5 individuals with heart failure.


title: RNA-sequencing transcriptional profile of kidney capsule derived organ fibroblasts from adult mice, CRISPR-knockdown organ fibroblasts from adult mice, and human hearts

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: mRNA-decapping associated DcpS enzyme controls critical steps of neuronal development

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

summary: Homozygous mutations in the gene encoding the scavenger mRNA-decapping enzyme, DcpS, have been shown to underlie developmental delay and intellectual disability. Intellectual disability is associated with both abnormal neocortical development and mRNA metabolism. However, the role of DcpS and its scavenger decapping activity in proper neuronal development is unknown. Here, we show that differentiation of human induced pluripotent stem cell derived neurons, from patients with a DcpS mutation, are impaired and have compromised neurite outgrowth. Moreover, misexpression of DcpS in developing mouse neocortex revealed that DcpS is required for the multipolar morphology acquisition, neurite outgrowth and identity of developing neocortical glutamatergic neurons in the mouse brain. Collectively, these findings demonstrate the scavenger mRNA decapping activity contributes to multiple pivotal roles in neurodevelopment, and further corroborate that mRNA metabolism and neocortical pathologies are associated with intellectual disability.

overall_design: Unbiased RNA sequencing was performed on primary neuronal cell cultures from E13 wild-type (WT) mice neocortices transfected with Ctrl shRNA (n=2) or DcpS shRNA (n=2) to identify novel downstream targets of DcpS.

first: Xiaobing

last: Luo

first: Megerditch

last: Kiledjian


title: RNA-sequencing transcriptional profile of CRISPR-knockdown organ fibroblasts from adult mice [CRISPR]

overall_design: RNA sequencing of primary cardiac fibroblast with Gata4 knockdown, Tbx20 knockdown and control. The experiment was performed in triplicate.


title: Hepatic transcriptome analysis of control, acute pancreatitis and severe acute pancreatitis mice

first: li

last: zhang

summary:
Purpose: The purpose of this study was to compare the hepatic transcriptome in the control group, acute pancreatitis, and severe acute pancreatitis, in order to identify metabolic gene changes during pancreatitis.
Methods: 6-week Balb/c mice were subjected to AP (caerulein), SAP (caerulein and LPS) and control (saline), and mice liver tissues were harvested at 24 hours for RNA preparation (n=8 each group).
Results: Among 11952 mapped genes, 8977 differentially expressed genes were identified by RNA-seq, including 351 genes induced in AP compare to Control and 5249 genes down regulated in SAP compare to AP. The genes up regulated were mainly related to fatty acid oxidation and ketone body synthesis especially Cpt2 and Acadvl, while genes that down regulated were associated with energy metabolism and inflammation. The overlap of two gene sets were 96 genes that involved in fatty acid metabolism.
Conclusions: Our study revealed that in AP, genes associated with ketone body synthesis are upregulated in liver, in SAP, fatty acid oxidation related genes are downregulated in liver. Our data revealed the crosstalk between pancreas and liver, illustrated the difference of metabolism in AP and SAP.

overall_design: Liver mRNA profiles of 6 weeks old wild type, AP and SAP mice were generated by sequencing in eight repeat,in three mouse models.

first: Jing

last: Xue

first: Li

last: Zhang


title: Bone Marrow Derived Macrophages(BMDMs) transcriptome analysis of control, LPS and LPS plus BHB group

summary:
Purpose: The purpose of this study was to compare the BMDMs transcriptome in the control LPS and LPS plus BHB group in order to identify the critical pathway that contributed to the inhibiton of BHB on M1 polarization.
Methods: 1× 106 BMDMs were pre-treated with PBS or BHB for 1 hours before LPS administration. Four hours later, BMDMs were harvested for RNA preparation.
Results: Among 16650 mapped genes, 7325 differentially expressed genes were identified, including 244 LPS inducible BHB down regulated named class A and 537 LPS repressed BHB up regulated genes named class B. The genes in class A were mainly TLR4 and TNF signaling pathway, while genes in class B were associated with negative regulation of transcription and NF-KB signaling. The GSEA showed that BHB have the similar profiles chnage on BMDMs with TSA.
Conclusions: Our study revealed that BHB down regulated TLR4 and NF-KB pathway related genes to inhibited M1 polarization, and BHB have a similar effect on BMDMs with TSA through comparing the genetic changes of two substance caused in cells.

overall_design: BMDMs mRNA profiles of control, LPS and LPS plus BHB groups were generated by sequencing.


title: Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7 II

status: Public on Apr 05 2022

city: Weifang

first: Panpan

address: No.7166 Baotong West Street

institute: Shandong Second Medical University

summary: The goal of this study is to compare  transcriptome-wide Nm-seq on the poly A+ RNA of wild-type Raw264.7 macrophages to transcriptome-wide Nm-seq on the poly A+ RNA of Fbl+/- Raw264.7 macrophages . The Nm-seq profiles  were generated by deep sequencing using Illumina HiSeq4000 sequencer.

overall_design: Transcriptome-wide Nm-seq on the poly A+ RNA of wild-type Raw264.7 macrophages and Fbl+/- Raw264.7 macrophages

first: Yang

last: Liu

first: Renjie

last: Song

first: Lu

last: Zhao

first: Jiang

last: Yang

first: Fengjiao

last: Lu

first: Xuetao

last: Cao


title: Atrial AMP-activated protein kinase is critical to prevent dysregulation of electrical excitability and atrial fibrillation

city: New Haven

first: Lawrence

last: Young

state: CT

address: 300 George Street

department: Internal Medicine

institute: Yale University

summary: Transcriptional profiling to assess atrial gene expression in atrial LKB1 KO vs. AMPK KO vs. WT mice.

overall_design: A total of 12 mice were studied: 4 replicates for each of the 3 genotypes.

middle: H

first: Kevin

last: Su


title: RNA sequencing identifies novel regulated IRE1-dependent decay targets that affect multiple myeloma survival and proliferation

city: Salamanca

first: Norma C.

last: Gutiérrez

state: Salamanca

address: Campus Miguel de Unamuno

department: Hematologia

country: Spain

institute: Centro de Investigación del Cáncer de Salamanca

summary: IRE1 is an unfolded protein response (UPR) sensor with kinase and endonuclease activity. It plays a central role in the endoplasmic reticulum (ER) stress response through unconventional splicing of XBP1 mRNA and regulated IRE1-dependent decay (RIDD), which cleaves RNA at an XBP1-like consensus sequence (CUGCAG) accompanied by a stem-loop structure. MM cells are known to exhibit an elevated level of baseline ER stress, but RIDD activity has not been well studied in this disease. To investigate novel RIDD targets of possible relevance to the survival/proliferation of MM cells we combined in vitro cleavage assay with RNA sequencing. Bioinformatic analysis revealed hundreds of putative IRE1 substrates, 32 of which were chosen for validation. Looking into the secondary structure of IRE1 substrates, we found that the consensus sequences of IRF4, PRDM1, IKZF1, KLF13, NOTCH1, ATR, DICER, RICTOR, CDK12, FAM168B, and CENPF mRNAs were accompanied by a stem-loop structure essential for IRE1-mediated cleavage. We show that mRNA and protein levels corresponding to these targets were attenuated in an IRE1-dependent manner by treatment with ER-stress-inducing agents. Our results demonstrate for the first time that IRE1 is a key regulator of several proteins of importance in MM survival and proliferation.

overall_design: Total RNA obtained from 6 biological replicates of the H929 cell line was exposed to an in vitro cleavage assay in the presence (3 samples) or absence (3 samples) of recombinant IRE1 protein.  We carried out RNA-sequencing from purified poly (A)-containing mRNAs.

first: Dalia

last: Quwaider

first: Luis

last: Corchete

first: Marta

last: Martín-Izquierdo

first: Jesús

last: Hernández-Sánchez

first: Elizabeta

last: de los Ángeles Rojas

first: Ramón

last: García-Sanz

first: Ana

last: Herrero

first: Norma


title: Fetal maturation revealed by amniotic fluid cell-free transcriptome in rhesus macaques

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

summary: In this study, we demonstrate that LAMP5 is essential for proliferation of MLL-rearranged leukemias. Through gene expression changes occurring upon LAMP5 knockdown, we show that LAMP5 maintains an important balance between Type I interferon and NFkB signaling, and that knockdown biases MLL leukemia cells towards activation of the interferon pathway

overall_design:
Accurate estimate of fetal maturity could provide individualized guidance for delivery of complicated pregnancies. However, current methods are invasive, have low accuracy, and are limited to fetal lung maturation. To identify diagnostic gestational biomarkers, we performed transcriptomic profiling of lung and brain, as well as cell-free RNA from amniotic fluid of preterm and term rhesus macaque fetuses. These data predict new and prior associated gestational age differences in distinct lung and neuronal cell populations when compared to existing single-cell and bulk RNA-Seq data. Comparative analyses found over 200 genes coincidently induced in lung and amniotic fluid, and dozens in brain and amniotic fluid. This data enabled creation of computational models that accurately predicted lung compliance from amniotic fluid and lung transcriptome of preterm fetuses treated with antenatal corticosteroids. Cell-free RNA in amniotic fluid may provide a substrate of global fetal maturation markers for personalized management of at-risk pregnancies.

Please note that the raw RNA-Seq data from the current study (n=110) with lung and brain samples sequenced in the previous GSE118438 study (n=18, preterm control and antenatal steroids) were combined in the data processing. The list of the re-analyzed samples (and associated run accessions) is provided in the 're-analyzed_sample_run_list.txt'.

first: Augusto

middle: F

last: Schmidt

first: Beena

middle: D

last: Kamath-Rayne


title: Nm-seq finds modified 2’-O-methylation sites in mRNA of Raw264.7

first: Panpan

last: Li

summary: The goal of this study is to compare  transcriptome-wide Nm-seq on the poly A+ RNA of wild-type Raw264.7 macrophages to transcriptome-wide Nm-seq on the poly A+ RNA of Raw264.7 macrophages after VSV infection . The Nm-seq profiles of wild-type Raw264.7 poly A+ RNA and VSV infected Raw264.7 poly A+ RNA were generated by deep sequencing using Illumina HiSeq4000 sequencer.

overall_design: Transcriptome-wide Nm-seq on the poly A+ RNA of Raw264.7 macrophages with or without VSV infection

first: Yang

last: Liu

first: Renjie

last: Song

first: Lu

last: Zhao

first: Jiang


title: Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT)

city: San Francisco

first: Dawud

last: abduweli uyghurturk

address: 513 Parnassus Ave.

institute: UCSF

summary: Background. Hematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI. Methods. A total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher’s exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of 4 high caries risk (HCR) and 4 low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the 2 groups. Results. There was a statistically significant association between caries risk and BSI (p<0.035) (Fisher’s exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21.39 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries. Discussion. These findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI.

last: Abduweli Uyghurturk

first: Ying

last: Lu

first: Janelle

last: Urata

first: Christopher

last: Dvorak

first: Pamela

last: Den Besten


title: Transcriptome analysis of circulating and skin transplant resident NK cells

city: Boston

first: Marta

last: Requesens Rueda

address: 149, 13th Street

institute: Harvard Medical School

summary: NK cells recruitment into the skin in response to an NK cell activating ligand (m157) and absence of MHC class I expression (B2m knockout) alters the transcriptional profile of the cells compared with circulating NK cells. In this experiment, we compared the gene expression profile of conventional NK cells in circulation with those entering the skin post-transplant as well as with tissue-resident NK cells.

overall_design: Analysis of differentially regulated genes in sorted NK cells from blood, spleen, donor skin and recipient normal recipient skin in two different models. In the first model, m157tgB2m-/- skin was transplanted onto the back of C57BL/6 NKp46iCre/iCre.RosamTmG/mTmG and at day 20 post-transplant CD49b+ NKp46-GFP+ cells were sorted by flow cytometry from blood, spleen, and donor skin as well as CD49a+ NKp46-GFP+ cells from donor skin and recipient skin. In the second model, m157tgB2m+/- skin was transplanted onto the F1 C57BL/+ NKp46+/iCre.Rosa+/mTmG and at day 10 post-transplant CD49b+ NKp46-GFP+ cells were sorted by flow cytometry from blood, spleen, and donor skin as well as CD49a+ NKp46-GFP+ cells from donor skin and recipient skin.

first: Mark

last: Bunting

last: Requesens

first: Adam

last: Langenbucher

first: Michael

middle: S

last: Lawrence

first: Shadmehr

last: Demehri


title: Single-cell RNA sequencing reveals intrahepatic immune characteristics related to disease status in HBV-infected patients

first: Jiesheng

state: 北京

address: Peking University

institute: Peking University

summary: Objective: A comprehensive view of the intrahepatic immune responses to HBV infection at the single-cell resolution is pivotal to HBV cure.   Design We performed single-cell RNA sequencing (scRNA-seq) of 243,000 cells from 46 paired liver and blood samples of 23 individuals, including 6 immune tolerant (IT), 5 immune active (IA), 3 acute resolved (AR), 3 chronic resolved (CR), and 6 HBV-free healthy controls (HC).   Results Both IA and AR were characterized by high levels of intrahepatic exhausted CD8+ T (Tex) cells, which were absent or rarely found in HC, CR, and IT. In IA, Tex cells were mainly derived from liver-resident GZMK+ effector memory T cells and self-expansion. By contrast, peripheral CX3CR1+ effector T cells and GZMK+ effector memory T cells were the main source of Tex cells in AR. In IA but not AR, significant interactions were observed between Tex cells and regulatory CD4+ T cells together with FCGR3A+ macrophages, of which HLA-B and HLA-I together with their receptors CANX and LILR, respectively, may constitute the main axes mediating such cellular interactions. Clinically, intrahepatic Tex cells were positively correlated with serum ALT levels and histological grading scores. By contrast, CX3CR1+ CD8+ T cells were clonally expanded in both liver and blood of AR and showed high consistency, providing a valid surrogate marker candidate for predicting HBV clearance.   Conclusion: Our study dissects the coordinated immune response in relation to disease status and provides a rich resource for understanding immunopathogenesis and developing effective therapeutic strategies for chronic hepatitis B.

overall_design:
We performed single-cell RNA sequencing (scRNA-seq) of 243,000 cells from 46 paired liver and blood samples of 23 individuals, including 6 immune tolerant (IT), 5 immune active (IA), 3 acute resolved (AR), 3 chronic resolved (CR), and 6 HBV-free healthy controls (HC).
NOTE FROM SUBMITTER: Due to the patient privacy restrictions and the China's Human Genetic Resources Policy, the raw data files have not been provided.

first: Chao

last: Zhang


title: RNA-seq of livers from mice treated with/without iD1

city: San Antonio

first: Masahiro

last: Morita

state: Texas

address: 4939 Charles Katz Drive

department: Department of Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

summary: RNA seq was perform to compare expression levels of mRNA in livers of mice treated with a vehicle and iD1.

overall_design: Liver mRNA profiles of 8-week-old mice treated with a vehicle and iD1.

first: Sakie

last: Katsumura


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Fbl+/- Raw264.7 Transcriptomes

first: Panpan

last: Li

summary: The goal of this study is to compare NGS-derived wild-type Raw264.7 transcriptome profiling (RNA-seq) to NGS-derived Fibrillarin knockdown (Fbl+/-) Raw264.7 RNA-seq. The mRNA profiles of wild-type Raw264.7 and Fbl+/− Raw264.7 were generated by deep sequencing, in duplicate, using illumina NovaSeq 6000.

overall_design: The mRNA profiles of wild-type Raw264.7 (WT) and Fibrillarin knockdown Raw264.7 (Fbl+/−)

first: Yang

last: Liu

first: Renjie

last: Song

last: Yang

first: Fengjiao

first: Xuetao

last: Cao


title: Transcriptome analysis of adult wildtype and pdx1+/- zebrafish kidneys through next generation RNA sequencing

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

institute: University Heidelberg

summary: The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates.

overall_design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys

first: Mike

last: Boger

first: Jens

last: Kroll


title: RNA sequencing revealed the different transcriptional profiles of long-term cultured and short-term cultured CAR-T cells

city: Hangzhou

first: XIN

last: GUO

state: Zhejiang

address: yuhangtang road

institute: Zhejiang University

summary: Chimeric antigen receptor (CAR) T cells are known to be potent in recognizing and eliminating tumor cells. They induce marked responses in patients with refractory leukemia and lymphoma, but exhaustion is an inevitable obstacle important barrier for to persistant curative effect. CD19-targeted CAR incorporating the 4-1BB costimulation domain showed a lower tendency toward exhaustion during ex vivo expansion, and downstream differentiation was still observed with a prolonged culture time. We explored the transcriptional changes during the culture process using 4-1BB CD19-targeted CAR-T cells . In contrast to T cells (cultured 5 days in vitro) and short-term cultured (5 days) CAR-T cells,  the pathway for regulation of the cytosolic calcium ion concentration was significantly upregulated in the long-term cultured (11 days) group.

overall_design: We performed RNA-Seq differential expression analysis of T cells (cultured 5 days in vitro), short-term cultured (5 days) CAR-T cells and  long-term cultured (11 days) CAR-T cells.

first: Mi

last: Shao

first: Xinyi

last: Teng

first: Xin

last: Guo


title: RNA sequencing of A673 and monoclonal KO cells treated with DMSO or SP-2509

city: Columbus

first: Jack

last: Tokarsky

address: 700 Children's Drive

department: Center for Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

summary: RNA sequencing data for a Ewing sarcoma cell line, A673 treated with DMSO or the LSD1 inhibitor, SP-2509. Monoclonal cell lines were generated by CRISPR/Cas9 mediated KO of mitochondrial genes MRPL45, UQCRFS1, and CYC1. These cells were treated with DMSO or SP-2509 to determine mitochondrial gene KO derived drug resistance.

overall_design: Cells were treated with 0.1% DMSO or 500 nM SP-2509 for 48 hr. Cells were harvested and their total mRNA purified and submitted for sequencing at Nationwide Children's Hosptial Institute of Genomic Medicine.

first: E

first: Stephen

last: Lessnick

first: Emily

middle: R

last: Theisen


title: Liver tumor gene expression profile of liver-specific PTEN KO, PTEN/SCAP double KO mice

city: Tokyo

first: Hayato

last: Nakagawa

address: 7-3-1 Hongo Bunkyo-ku

institute: The University of Tokyo

summary: Nonalcoholic steatohepatitis (NASH), a severe form of nonalcoholic fatty liver disease, is characterized by hepatic steatosis and hepatocellular injury and progresss cirrhosis and hepatocellular carcinoma. Sterol regulatory elment-binding proteins (SREBPs) are  master regulators of lipogenesis. Liver-specific PTEN knockout (KO) mice show constitutive upregulation of SREBP through PI3K-Akt pathway activation, leading to spontaneous fatty liver and subsequent HCC development. SREBP cleavage-activating protein (SCAP) plays a critical role in SREBP activation. We sought to determine the impact of SREBP inhibition on NASH and HCC development. To this end, we additionaly inhibited SREBP pathway in liver-specific PTEN mice by ablating SCAP and generated liver-specific PTEN/SCAP double KO (DKO) mice. However unexpectedly, inhibition of SCAP/SREBP pathway markedly exacerbated liver injury (5weeks), fibrosis (5months), and carcinogenesis (7 months) in PTEN KO mice. To elucidate the mechanisms of liver tumorigenesis in liver-specific PTEN/SCAP DKO mice, we conducted transcriptome analyses of the livers.

overall_design: PTEN F/F and PTEN/SCAP F/F mice were crossed to Alb-Cre mice to generate liver-specific PTEN KO, SCAP KO and PTEN/SCAP DKO mice, respectively. Liver-specific PTEN KO and PTEN/SCAP DKO mice were fed with normal diet for 12 months and 7 months, respectively.  Total RNA samples were extracted from liver tumor tissues. We compared relative liver tumor gene expression levels across these mice.

first: Yuki

last: Matsushita

first: Satoshi

last: Kawamura


title: RNAseq time course for mature hiPS-CMs induced to proliferate with 4 cell cycle factors

city: Houston

first: Tamer

last: Mohamed

state: TX

address: 6770 Bertner Avenue

institute: Baylor College of Medicine

summary: The regenerative capacity of the heart after myocardial infarction (MI) is limited. Our previous study showed that ectopic introduction of Cdk1/CyclinB1 and Cdk4/CyclinD1 complexes (4F) promotes cardiomyocyte proliferation in 15-20% of infected cardiomyocytes in vitro and in vivo and improves cardiac function after MI. Here, we aim to identify the necessary reprogramming stages during the forced cardiomyocyte proliferation with 4F on a single cell basis. Temporal bulk RNAseq of mature hiPS-CMs treated with either LacZ or 4F adenoviruses revealed full cell cycle reprogramming in cardiomyocytes after 48 h post-infection with 4F, which was associated with sarcomere disassembly and metabolic reprogramming.

overall_design: we conducted temporal bulk RNAseq on 60-day-old mature hiPS-CMs infected with either LacZ (control) or CDK1, CDK4, CCNB, CCND (4F) adenovirus for 24, 48 or 72 h.

first: Riham

last: Abouleisa


title: Safety and preliminary efficacy of allogeneic bone marrow-derived multipotent mesenchymal stromal cells for systemic sclerosis: a single-centre, open-label, dose-escalation, proof-of-concept, phase 1/2 study

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

summary:
Background: Systemic sclerosis (SSc) is a chronic autoimmune disease. We tested the safety of a single intravenous injection of intrafamilial allogeneic bone marrow-derived mesenchymal stromal cells (BM-MSC) to treat severe SSc.
Methods: We conducted the first prospective, monocentric, dose-escalation, phase I/II clinical trial investigating the feasibility and safety of a single allogeneic BM-MSC infusion in 20 severe SSc patients who were refractory or had a contraindication to conventional immunosuppressive therapy or autologous hematopoietic stem cell transplant. Patients were assigned to an infusion of either 1x10^6 BM-MSC/kg or 3x10^6 BM-MSC/kg obtained from 20 independent intrafamilial donors. Primary endpoint was the rate of grade ≥ 3 Severe Adverse Events (SAE; NCI Common Terminology Criteria for Adverse Events (v5.0)) in the first 10 days post-BM-MSC infusion. Secondary endpoints included adequacy of BM-MSC production, medium-term SAE, as well as clinical and immunological response.
Findings: No Grade 3 ≥ SAE occurred in the first 10 days following MSC infusion in the 20 SSc patients. A significant improvement in modified Rodnan Skin Score (p<0.0001) was observed after BM-MSC infusion, which peaked at 3 months and was sustained for 1 year. No changes in health-related quality of life or pulmonary function were observed. CD8pos T-Cell and NK cell counts slightly increased after infusion (p<0.05) and two patients developed de novo donor-specific anti-HLA. Circulating TGF-β level at baseline was significantly higher in non-responder compared to responder patients (p<0.05). A pattern of low IDO activity, CCL2 production, and HLA-DR expression in BM-MSC batches under in vitro stimulation by IFN-beta was associated with a lack of clinical response in recipient SSc patients.
Interpretation: A single infusion of allogeneic BM-MSC transplant was safe in severe SSc patients and triggered short-term disease modifying effects. Clinical response was associated with both the recipients biological features and the functional properties of infused BM-MSC.

overall_design: An aliquot of passage #1 BM-MSC derived from 17 healthy donors were collected prior to infusion in the recipient and cryopreserved analyzed for RNA sequencing.

first: Dominique

last: Farge

first: Inés

last: Colmegna

first: HanChen

last: Wang


title: HK-2 cell cultured with normal glucose, high glucose, dapagliflozin, metformin and vildagliptin

city: Zhengzhou

first: Yi

last: Song

address: 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

summary: To investigate the differential expressed circRNAs, and even their biological functions in human proximal tubular epithelial (HK-2) cells induced by normal glucose, high levels of glucose and treatment of dapagliflozin, metformin and vildagliptin.

overall_design: HK-2 cells were cultured in DMEM medium supplemented with 10% fetalfoetal bovine serum, and 100 U/mLU/ml penicillin, and 0.1 mg/mLl streptomycin at 37°C ℃ under humidified air with 5% CO2. After synchronized by culturing in DMEM for 24 h, the cells were treated with normal glucose (5.6mM), high glucose (30.0 mM) for 24 h, then treated with Dapagliflozin (2.5 μM), Metformin (5 mM), Vidagliptin (150 μM) for 48 h in 6-well plates.  All groups were repeated three times.

first: Feng

first: Fengjuan

last: Huang


title: Transcriptome (RNA-Seq) of the stable overexpression of lncRNA XLOC013218 U251 cells

city: Guangzhou

first: Ningbo

last: Xu

state: Guangdong

address: NO.253 Gongye Avenue, Haizhu District

department: Department of Neurosurgery

institute: Southern Medical University

summary: We present RNA-Seq data obtained from U251 control cells and U251 cells with stable overexpression of lncRNA XLOC13218 to identify differentially expressed genes. The discovery of long non-coding RNAs (lncRNAs) has improved the understanding of development and progression in various cancer sub-types. However, the role of lncRNAs in temozolomide (TMZ) resistance in glioblastoma (GBM) remains largely undefined. In this present study, the differential expression of lncRNAs were identified between U87 and U87TR (TMZ-resistant) cells. LncRNA XLOC013218 (XLOC) was drastically upregulated in TMZ-resistant cells and was associated with poor prognosis in glioma. Overexpression of XLOC markedly increased TMZ resistance, promoted proliferation, and inhibited apoptosis in vitro and in vivo. In addition, RNA-seq analysis and gain-of-function or loss-of-function studies revealed that PIK3R2 was the potential target of XLOC. Mechanistically, XLOC recruited Specificity Protein 1 (Sp1) transcription factor and promoted the binding of Sp1 to the promoters of PIK3R2, which elevated the expression of PIK3R2 in both mRNA and protein levels. Finally, PIK3R2-mediated activation of the PI3K/AKT signaling pathway promoted TMZ resistance and cell proliferation, but inhibited cell apoptosis. In conclusion, these data highlight the vital role of XLOC/Sp1/PIK3R2/PI3K/AKT axis in GBM TMZ resistance.

overall_design: The RNA-Seq libraries were constructed from cytoplasmic RNA without polyA-selection. Three independent biological replicates were made for U251 control cells and U251 cells with stable overexpression of lncRNA XLOC13218.

first: Jian

last: Zhou

first: Wenhui

last: Tang

first: Hongbo


title: A Transcriptomic Analysis of Neuropathic Pain in the Spinal Cord after Nerve Injury

city: Changsha

first: Changsheng

state: Hunan

address: 87 Xiangya Road

department: Department of Anesthesiology

institute: Xiangya Hospital, Central South University

summary: Neuropathic pain is a troublesome pathological condition without suitable treatments. In this study, we performed RNA sequencing (RNA-seq) analysis to reveal transcriptomic profiles of spinal cord from chronic constriction injury (CCI) rats.

overall_design: Spinal cord mRNA profiles of sham and 12-hour, 1-day, 3-day, 7-day and 14-day CCI rats

first: Yu

last: Zhang

first: Shiwei

last: Jiang


title: A Transcriptomic Analysis of Neuropathic Pain in the Anterior Cingulate Cortex after Nerve Injury

summary: Neuropathic pain is a troublesome pathological condition without suitable treatments. In this study, we performed RNA sequencing (RNA-seq) analysis to reveal transcriptomic profiles of Anterior Cingulate Cortex (ACC) from chronic constriction injury (CCI) rats. We found 1628 differentially expressed genes (DEGs) were mainly involved in the inflammatory and immune process. Besides, cytokine signaling and other cell-defense related pathways mainly contribute to the occurrence and development of neuropathic pain. Then we classified the DEGs based on the time trend. Our results suggested that chemokines played a vital role in pain, and moreover, CCL5, CXCL9 and CXCL13, compared with CCL2, CCL3, CCL4, CCL6 and CCL7 had different time-dependent manners. In a word, targeting chemokines is of great significance to explore specific mechanisms and develop suitable drugs for neuropathic pain.

overall_design: ACC mRNA profiles of sham and 0.5-day, 1-day, 3-day, 7-day and 14-day CCI rats


title: Plasma exosome microRNA sequencing of Legg-Cavé-Perthes disease

city: Nanning

first: Qian

state: Guangxi

address: Shuangyong road 22

institute: Guangxi Medical University

summary: We performed the miRNA-seq analysis of 3 plasma exosomes from Legg-Cavé-Perthes patients and 3 plasma exosomes from healthy volunteers based on the Illumina Hiseq 2500 platform and obtained data of 6 samples.

overall_design: Plasma exosomal miRNA profiles of 3 Legg-Cavé-Perthes patients and 3 healthy volunteers.

first: Boxiang

last: Li

first: Chengshen

last: Lin

first: Xianxiang

last: Chen

first: Tiantian

first: Jianhong

last: Liu

first: Yun

first: Rongbin

last: Lu

first: Shijie

last: Liao

first: Xiaofei

last: Ding


title: Liver gene expression profile of wild type, liver-specific PTEN KO, SCAP KO and PTEN/SCAP double KO mice.

city: Tsu city

first: Naoto

last: Fujiwara

state: Mie

address: 2-174 Edobashi

institute: Mie University

summary: Nonalcoholic steatohepatitis (NASH), a severe form of nonalcoholic fatty liver disease, is characterized by hepatic steatosis and hepatocellular injury and progresses to cirrhosis and hepatocellular carcinoma. Sterol regulatory element-binding proteins (SREBPs) are  master regulators of lipogenesis. Liver-specific PTEN knockout (KO) mice show constitutive upregulation of SREBP through PI3K-Akt pathway activation, leading to spontaneous fatty liver and subsequent HCC development. SREBP cleavage-activating protein (SCAP) plays a critical role in SREBP activation. We sought to determine the impact of SREBP inhibition on NASH and HCC development. To this end, we additionally inhibited SREBP pathway in liver-specific PTEN mice by ablating SCAP and generated liver-specific PTEN/SCAP double KO (DKO) mice. However unexpectedly, inhibition of SCAP/SREBP pathway markedly exacerbated liver injury (5weeks), fibrosis (5months), and carcinogenesis (7 months) in PTEN KO mice. To elucidate the mechanisms of liver injury in liver-specific PTEN/SCAP DKO mice, we conducted transcriptome analyses of the livers.

overall_design: PTEN F/F, SCAP F/F and PTEN/SCAP F/F mice were crossed to Alb-Cre mice to generate liver-specific PTEN KO, SCAP KO and PTEN/SCAP DKO mice, respectively. Wilt type, liver-specific PTEN KO, SCAP KO and PTEN/SCAP DKO mice were fed with normal diet for 5 weeks, and total RNA samples were extracted from liver tissues. We compared relative liver gene expression levels across these mice.

first: Satoshi

last: Kawamura

first: Yujin

last: Hoshida

first: Hayato

last: Nakagawa


title: Glucose metabolic profiles evaluated by PET associated with molecular characteristic landscape of gastric cancer

city: Seoul

first: Jong-Il

last: Kim

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: Although FDG-PET is widely used in cancer, its role in gastric cancer (GC) is still controversial due to variable [18F]fluorodeoxyglucose ([18F]FDG) uptake. Here, we investigate the molecular landscape of GC and its association with glucose metabolic profiles noninvasively evaluated by [18F]FDG PET. Based on a genetic signature, PETscore, representing [18F]FDG avidity, was developed by imaging data acquired from thirty patient-derived xenografts (PDX). Five genes, PLS1, PYY, HBQ1, SLC6A5, NAT16, were identified for the PETscore, which was validated in independent cohorts by qRT-PCR and RNA-sequencing. By applying the PETscore on the Cancer Genome Atlas (TCGA), a significant association between glucose uptake and tumor mutational burden as well as genomic alterations was identified in GC. Our findings suggest that molecular characteristics are underlying the diverse metabolic profiles of GC. Diverse glucose metabolic profiles may apply to precise diagnostic and therapeutic approaches for GC.

overall_design: RNA sequencing(RNA-seq) data of thirty gastric cancer PDXs (training set) were analyzed for identification of a genetic signature representing [18F]FDG avidity. RNA-seq data of fifteen patients who were paired with 15 PDX cases in the training set were utilized for estimation of SUVmax prediction based on the genetic signature. RNA-seq data of eight patients (validation set) with PET results were used for validation of FDG avidity prediction.

first: Han-Kwang

last: Yang

first: Hyuk-Joon

last: Lee

first: Seong-Ho

last: Kong

first: Yun-Suhk

last: Suh


title: PLD1 promotes tumor invasion by regulation of MMP-13 expression via phosphorylation of NF-kB in bladder cancer

city: Tsukuba

first: Yoshiyuki

last: Nagumo

address: 1-1-1 Tennodai

department: Urology

institute: University of Tsukuba

summary: Invasion of bladder cancer (BC) cells from the mucosa into the muscle layer is canonical for BC progression while phospholipase D isoform 1 (PLD1) is known to mediate development of cancer through phosphatidic acid (PA) production. We therefore used in silico, in vitro and in vivo approaches to detail the effect of PLD1 on BC invasion. In BC patients, higher levels of PLD1 expression were associated with poor prognosis. PLD1 knockdown significantly suppressed cellular invasion by human BC cells and matrix metalloproteinase-13 (MMP-13) was observed to be an invasion mediator gene. In our mouse bladder carcinogenesis model, the development of invasive BCs was suppressed by PLD1 knockout and a global transcriptomic analysis in this model indicated MMP-13 as a potential tumor invasion gene with NF-kB (nuclear factor-kB) as its transcription regulator. Furthermore, PA administration increased both MMP-13 expression and NF-kB p65 phosphorylation levels. Collectively, we demonstrate that PLD1 promotes tumor invasion of BC by regulation of MMP-13 expression via phosphorylation of NF-kB p65. Our results suggest that PLD1 is a potential therapeutic target to prevent progression in BC patients.

overall_design: RNA sequencing was performed using the bladders from the wild-type and PLD1-knockout mice. Bladders were extracted from sacrificed animals at baseline and after 8, 12 and 16 weeks of treatment. All experiments were performed using triplet samples.

first: N

last: Yoshiyuki

first: K

last: Shuya

first: T

last: Kozaburo

last: Satoshi

first: C

last: Ichiro

first: S

last: Masanobu

first: H

last: Akio

last: Hiromitsu

last: Takahiro

first: Mathis

last: BJ

first: F

last: Yuji

last: Hiroyuki


title: VPC-13822 - A Novel Nonsteroidal Drug for the Treatment of Castration Resistant Prostate Cancer by Blocking the Binding Function-3 of the Human Androgen Receptor.

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

summary: Inhibition of the alternative target site Binding Function-3 (BF3) of the androgen receptor (AR) with small molecules may represent a novel and viable option for treating castration-resistant disease. In vitro transcription assays and microsome stability experiments were used to characterize the latest and most optimized AR BF3 inhibitor compound VPC-13789 to determine its anti-AR activity and pharmacokinetic properties. VPC-13789 selectively inhibited AR-mediated transcription with an IC50 value of 0.2 μM and effectively supressed the growth of androgen-stimulated LNCaP cell line with an IC50 of 0.32 μM while having no effect on AR-negative PC3 cells.  We have further synthesized a pro-drug of VPC-13789 (VPC-13822) with improved solubility and bioavailability. The VPC-13822 pro-drug was evaluated for 4 weeks in mice xenograft LNCaP castration resistant model. When administered orally, VPC-13822 significantly reduced PSA production and tumor volume in this prostate cancer model. No signs of generic toxicity of the candidate compound were observed. Taken together, these results establish a novel class of orally available AR inhibitors with a completely distinct mode of action with a potential utility to treat drug-resistant forms of prostate cancer.

overall_design: Polyadenylated RNA profiles of LNCaP cells treated with treated with ethanol (ETOH) plus DMSO, or dihydrotestosterone (DHT) plus either DMSO (Control), Enzalutamide, or VPC-13789, in three biological replicates, obtained using BGISeq500 platform.

first: Ayse

first: Nathan

last: Lack


title: Activation of Nkx2.5 Transcriptional Program is Required for Adult Myocardial Repair

city: Melbourne

first: Akriti

last: Varshney

state: Victoria

address: Wellington Rd

institute: Monash University

summary: We show that cardiac-specific RNA-sequencing studies reveal a disrupted embryonic Nkx2.5 transcriptional profile despite histologically normal, Nkx2.5 loss-of-function adult myocardium. Yet, adult nkx2.5-/- fish exhibit an impaired ability to recover following ventricular apex amputation as illustrated by retention of fibrin and collagen in the injured area. Complex network analyses illuminate that Nkx2.5 is required to mount a proliferative response for cardiomyocyte renewal and to provoke proteolytic pathways necessary for sarcomere disassembly. Moreover, direct Nkx2.5 targets embedded in these distinct gene regulatory modules coordinate appropriate, multi-faceted injury responses. Altogether, our findings support a previously unrecognized, Nkx2.5-dependent regenerative circuit that invokes myocardial proliferation and dedifferentiation to ensure effective regeneration in the teleost heart.

overall_design: We harnessed both new RNA-Seq and our prior DamID data to reveal that the developmental molecular profile regulated by Nkx2.5 is perturbed in the adult nkx2.5-deficient myocardium. Moreover, our multi-variate network analysis underlines Nkx2.5 as a vital regulator of CM renewal, functioning to promote cell cycle re-entry and to maintain proteolysis genetic modules.

first: Carmen

last: de Sena-Tomás

first: Angelika

middle: G

last: Aleman

first: Caitlin

last: Ford

first: Di

last: Yao

first: Jamie

middle: K

last: Harrington

first: Leonor

last: Saúde

first: Mirana

last: Ramialison

first: Kimara

last: Targoff


title: PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics (Chromatin)

city: New York

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

summary: ARID2 is an essential subunit of the SWI/SNF PBAF chromatin remodeler and is highly mutate in melanoma. To elucidate the role of ARID2 in melanoma biology and chromatin structure we utilized CRISPR Cas9 methodology to generate isogenic ARID2 WT and KO melanoma clonal cell lines. We further map the genomic localization of several SWI/SNF subunits, open and repressed chromatin markers, and multiple transcription factors to characterize how loss of the PBAF subcomplex alters chromatin accessibility and the melanoma transcription factor network. Finally, we characterized the transcriptional changes produced by PBAF depletion.

overall_design: Chromatin characterization of ARID2 KO cell lines

first: Saul

last: Carcamo

first: Elena

last: Grossi

first: Christie

last: Nguyen

first: Dan

last: Hasson


title: PBAF complex deficiency in melanoma mediates BAF occupancy and transcription factor dynamics

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

overall_design: Refer to individual Series


title: Effects of fibrolamellar carcinoma-associated DNAJB1-PRKACA in HEK293T cells

city: Ithica

first: Praveen

last: Sethupathy

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

summary: Fibrolamellar carcinoma (FLC) is a type of primary liver cancer that commonly arises in adolescents and young adults in a background of normal liver tissue and has an overall poor prognosis due to lack of effective chemotherapeutic agents. The DNAJB1-PRKACA gene fusion (DP) has been reported in the majority of FLC tumors, however its exact oncogenic mechanisms are unclear. Given the paucity of cellular models, in particular FLC tumor cell lines, we hypothesized that engineering the DP fusion gene in HEK293T cells will provide insight into the oncogenic mechanism of the fusion gene. We used CRISPR/Cas9 to engineer HEK293T clones expressing DP fusion gene (HEK-DP) and performed transcriptomic, proteomic, and mitochondrial studies to characterize this cellular model. Transcriptomic analysis of HEK-DP cells revealed a significant increase in LINC00473 expression similar to primary FLC samples.  Proteomic analysis identified mitochondrial proteins as well as proteins in other subcellular compartments which interact with DP. HEK-DP cells demonstrated significant mitochondrial fission which suggests a role for DP in altering mitochondrial dynamics. Our results support the use of the HEK-DP cells as a novel model for elucidating the oncogenic mechanisms underlying DNAJB1-PRKACA-associated FLC pathogenesis and as a platform for high-throughput drug targeting of DNAJB1-PRKACA protein.

overall_design: Normal and FLC-affected livers were sequenced and differential analysis was performed.

first: Khashayar

last: Vakili


title: Gene expression profiling of dynamic paracrine senescence in human fibroblasts

city: Madrid

first: Ignacio

last: Palmero

state: Madrid

address: Arturo Duperier, 4.

institute: CSIC

summary: Cellular senescence can be transmitted to neighbouring cells in a paracrine manner through different mechanisms, including soluble factors released by senescent cells. To understand the dynamic regulation of paracrine senescence, here we investigated gene expression profiles in normal human fibroblasts (IMR90) exposed to conditioned medium generated by an inducible model of fibroblast Oncogene-Induced Senescence (IMR90-ER:RAS) at different time points after induction of senescence.

overall_design: mRNA expression profiles were obtained from human IMR90 primary fibroblasts exposed to conditioned medium from IMR90-ER:RAS fibroblasts at different times after senescence induction with 4-hydroxy-tamoxifen (4-OHT). Each sample was analyzed in duplicate by RNA-Seq using Illumina HiSeq.

first: Irene

last: López-Antona


title: Defects in secondary cell-wall synthesis mitigate the effects of lincomycin on early chloroplast development

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

summary: Lincomycin (LIN)-mediated inhibition of protein synthesis in chloroplasts prevents greening of seedlings, represses the activity of photosynthesis-related genes in the nucleus including LHCB1.2, and induces the phenylpropanoid pathway, resulting in production of anthocyanins. In genomes uncoupled (gun) mutants, LHCB1.2 expression is maintained in the presence of LIN or other inhibitors of early chloroplast development. In a screen using concentrations of LIN lower than those employed to isolate gun mutants, we have identified happy on lincomycin (holi) mutants. Several holi mutants show increased tolerance to LIN, exhibiting de-repressed LHCB1.2 expression and chlorophyll synthesis in seedlings. The mutations responsible were identified by whole-genome SNP mapping, and most were found to affect the phenylpropanoid pathway. However, LHCB1.2 expression appears not to be directly regulated by phenylpropanoids, as indicated by metabolic profiling of mutants. The most potent holi mutant is defective in a subunit of cellulose synthase encoded by IRREGULAR XYLEM3, and comparative analysis of this and other cell-wall mutants establishes a link between secondary cell-wall integrity and tolerance to LIN, possibly involving altered ABA metabolism or sensing.

overall_design: Examination of differential gene expression in the Arabdidopsis thaliana irx3-2 mutant compared to wild type grown on MS or on MS supplemented with Lincomcycin


title: CTCF Functions as an Insulator for Somatic Genes and a Structural Regulator for Pluripotent Genes during Reprogramming

first: ya

middle: wei

last: song

address: 190 Kai Yuan Avenue, Science Park

department: South China Institute for Stem Cell Biology and Regenerative Medicine

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences


title: Analysis of gene expression profile in photoreceptor-like cells derived from fibroblasts

status: Public on Apr 04 2022

city: Tokorozawa

first: Yuko

last: Seko

state: Saitama

address: 4-1 Namiki

institute: NRCD

summary: To clarify disease-specific profiles, we employed DNA microarray analysis  using induced photoreceptor-like cells derived from fibroblasts.

overall_design: Using induced photoreceptor-like cells by CRX, RAX, NeuroD, and OTX2, we employed DNA microarray analysis to compare expression levels of disease-related genes in fibroblasts.


title: The miRNA expression profiles of serum microvesicles in acute ischemic stroke patients and  healthy controls using high-throughput sequencing

city: Chengdu

first: Junli

last: Hao

address: No. 783, Xindu Avenue

institute: Chengdu Medical College

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: The serum microvesicles of five acute ischemic stroke (AIS) and healthy controls was purified using Ribo™ Exosome Isolation Reagent (C10110-2, RIBOBIO, Guangzhou, China) and analyzed by flow cytometry and nanoparticle tracking analysis (NTA).The miRNA  expression profiles of serum microvesicles of five acute ischemic stroke (AIS) and healthy controls were detected by RNA-seq using llumina HiSeqTM 2500.
Results: Using an optimized data analysis workflow, 732 miRNA species were detected in total. The levels of 51 individual miRNA species were significantly different between AIS patients and healthy controls.
Conclusions: Our study represents the first detailed analysis of miRNA expression profiles of serum microvesicles in AIS and healthy  controls, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of miRNA content in serum microvesicles. We conclude that RNA-seq based non-coding RNA characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

first: Jie

last: Yang


title: In vivo CRISPR screening identifies ISL2 as a tumor suppressor and regulator of metabolic gene expression in pancreatic cancer (RNA-Seq)

city: Chicago

first: Meric

last: Kinali

address: Robert Lurie Biomedical research Building 303 E Superior St

department: Ob/gyn

institute: Northwestern University

summary: Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest cancers with no targeted or personalized therapeutics. PDAC cells reprogram their transcriptional and metabolic state to sustain their energetic needs in the nutrient-poor tumor microenvironment. Identifying molecular regulators of PDAC growth is a critical step towards an improved understanding of the disease and new therapeutic approaches. We employed in vivo CRISPR screening in an orthotopic PDAC model to identify transcription factors (TFs) and chromatin regulators (CRs) whose inhibition promotes aggressive growth of PDAC cells in vivo. The screening identified a previously uncharacterized ISL LIM homeobox 2 (ISL2) gene as a candidate tumor suppressor among some anticipated growth modulators. We confirmed that depletion of ISL2 leads to enhanced cell proliferation and tumor growth in vitro and in vivo. Conversely, the exogenous expression of ISL2 or CRISPR-mediated epigenetic upregulation of the endogenous loci led to reduced cell proliferation, supporting the hypothesis that ISL2 is a candidate tumor suppressor. Importantly, we find that ISL2 is a nuclear, chromatin-associated transcription factor that is epigenetically silenced through DNA methylation in a significant fraction of PDAC tumors. Critically, higher DNA methylation of ISL2 or its reduced expression correlates with poor patient survival. Mechanistically, ISL2 binds to thousands of genes, and its depletion increases antioxidant capacity, oxidative phosphorylation (OXPHOS) and fatty acid metabolism. Critically, ISL2 depleted cells have heightened stemness potential, and we find PPAR as a critical modulator of cell proliferation in ISL2 depleted cells. Notably, ISL2 depleted cells are sensitive to small molecule inhibitors of mitochondrial complex I  in vitro and in vivo. Collectively, these findings nominate ISL2 as a putative tumor suppressor candidate whose inactivation leads to an aggressive PDAC growth through increased mitochondrial metabolism and antioxidant capacity, which creates a potentially exploitable therapeutic vulnerability.

overall_design: mPanc96 and PDX366 cell lines that are either WT or KO for ISL2 gene were used for RNA-seq experiment. Each conditin has 2 replicates. In total, 8 samples were analyzed.

first: Harun

last: Cingoz

last: Ozturk

first: Mazhar

last: Adli


title: In vivo CRISPR screening identifies ISL2 as a tumor suppressor and regulator of metabolic gene expression in pancreatic cancer

overall_design: Flag tagged ISL2 expressing mPanc96 cells were targeted by Flag Ab and H3K27ac Ab for CHIP seq with two replicates.


title: Treatment of Novel Patient-Derived Xenograft and Cell Line Models with PI3K/AKT/mTOR Inhibitors Revealed Treatment Response Heterogeneity in NF2-Associated Schwannoma

city: beijing

first: zhao

last: fu

address: No. 6 Tiantan Xili Dongcheng District

institute: Beijing Neurosurgical Institute

summary: Treatment of multiple intracranial schwannomas in patient with neurofibromatosis type 2 (NF2) is extremely unsatisfactory and innovative therapeutic approaches are urgently needed. The lack of clinically relevant NF2 models has severely hampered drug discovery in this rare disease. Here, we report for the first time the establishment and characterization of patient-derived xenograft (PDX) and cell line models of NF2-associated schwannoma, which retain the gene mutations and transcriptome profile, and recapitulate the morphological and histopathological features with the patient tumors, retain patient NF2 mutations, and maintain gene expression profiles resembling the patient tumor profiles with the preservation of multiple key signaling pathways commonly dysregulated in human schwannoma. Using expression profiling, we found that the PI3K/AKT/mTOR networks are elevated in NF2-associated vestibular schwannomas, as well as in PDX models.

overall_design: 9 NF2-associated schwannoma samples were analysed: three primary  tumour samples,three patient-derived xenografts in grown in nude mice, and three established immortalized cell lines

first: Fu

last: Zhao

first: Pi-nan

last: Liu

first: jing

last: zhang


title: Improvement of dicarboxylic acid production with Methylorubrum extorquens by reduction of product reuptake

city: Frankfurt

first: Laura

last: Pöschel

state: Hessen

address: Theodor-Heuss-Allee 25

department: Microbial Biotechnology

institute: Dechema Forschungsinstitut

summary: In the past, two dicarboxylic acid products, namely mesaconic acid and 2‑methylsuccinic acid, were successfully produced by Methylorubrum extorquens AM1 with heterologous thioesterase YciA, but the yield was reduced by product reuptake. In our study we conducted comprehensive research on the uptake mechanism of those dicarboxylic acid products. To identify potential import factors, we performed transcriptome analysis of a strain harboring plasmid pCM160_RBS_yciAHI and an empty vector control strain. Samples were taken and analyzed at different timepoints throughout cultivation. However, we could not identify genes that were clearly upregulated in stationary growth phase compared to early sampling points in the exponential growth phase and which were annotated as potential transporters. When specifically analyzing the time-dependent expression levels of dctA homologs and kgtP (suggested as targets in previous studies) and comparing them with a control strain, we found slightly increased levels only for dctA1. After concluding that the transcriptome analysis was obviously no appropriate approach to identify relevant transport factors, we chose a straightforward mutant selection approach using a cytotoxic dicarboxylic acid.

overall_design: Examination of M. extorquens AM1 harboring pCM160_RBS_YciAHI (="P") and M. extorquens AM1 harboring pCM160 (empty vector control="L") in three replicates, respectively

first: Markus

last: Buchhaupt


title: Analysis of the genomic composition of phage YerA41

city: Helsinki

first: Mikael

last: Skurnik

address: Yliopistonkatu 4, 00100 Helsinki, Finnland

department: Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program,

country: Finland

institute: Faculty of Medicine, University of Helsinki

summary: Genomic material isolated from purified phage YerA41 lysate was shown to contain RNA. YerA41 phage lysate was RNase treated to remove phage-external RNA and total RNA was then isolated from the phage preparate using Qiagen Rneasy mini kit. The isolated RNA was sequenced to elucidate its origin. The results suggested that the RNA originated from intact ribosomes of the host bacterium that contaminated the phage lysate.

sample_organism:
Yersinia ruckeri
Yersinia phage YerA41

platform_organism:
Yersinia ruckeri
Yersinia phage YerA41

overall_design: RNA was isolated from two separate phage lysates in triplicate

first: Tobias

last: Kerrinnes

first: Christina

last: Homberger

first: Jörg

last: Vogel


title: Gene signature profiles in lung tisses of wild type mice or Has2 heterozygous deficient mice stimulated with ovalbumin

first: Takumi

last: Kiwamoto

address: 1-1-1 Tennoudai

department: Pulmonary Medicine

summary: Background: HAS2 is a member of the gene family encoding hyaluronan synthase 2 (HAS2) which can generate high molecular weight hyaluronan (HMW-HA). Although we previously reported that HAS2 is a novel candidate gene for susceptibility to adult asthma., little is known about whether HAS2 dysfunction affect eosinophilic airway inflammation.  Objective: We therefore hypothesized that attenuation of HAS2 will enhance eosinophilic airway inflammation.  Methods: C57BL/6 wild type (WT) mice, Has2 heterozygous deficient (Has2+/−) mice were used in eosinophilic airway inflammation model which induced by ovalbumin (OVA). Quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to detect Has2 and HA binding protein mRNA expression levels. Lung tissue and lavage fluid (BALF) were analyzed for inflammation and various cytokines and chemokines. Airway resistance was measured using forced oscillation technique. gene expression analyses were also performed to elucidate further pathogenesis.  Results: The expression levels of Has2 mRNA was significantly decreased in OVA stimulated Has2+/− (Has2+/−-OVA) mice. Has2+/−-OVA mice also displayed significant reduce of CD44, and TGF-beta1 mRNA expression. BALF eosinophil number, levels of various Th2 cytokines and chemokines in BALF, and airway responsiveness were significantly increased in Has2+/−-OVA mice compared with similarly treated WT mice. ILK Signaling and PKA signaling were downregulated significantly more in Has2+/−-OVA mice compared with similarly treated WT mice.  Conclusions: Has2 dysfunction induce more intense allergic eosinophilic airway inflammation and increase of airway hyper responsiveness with impairment of HAS2-CD44-TGF-beta signaling. Modulating HAS2 signaling might provide novel therapeutic targets for intractable bronchial asthma patients.

overall_design: 12 strand-specific RNA libraries for high-throughput sequencing were prepared (3 from the lungs of the wild type mice treated with saline, 3 from the lungs of the Has2+/- mice treated with saline, 3 from the lungs of the wild type mice sensitized and interanasaly stimulated with ovalbumin, and 3 from the lungs of the Has2+/- mice stimulated with ovalbumin using the Illumina Stranded mRNA Sample Preparation Kit with 500ng of total RNA according to manufacturer’s instructions.

first: Yoshiya

last: Tsunoda

first: Masashi

last: Matsuyama

first: Nobuyuki

last: Hizawa