title: Impact of Obesity on Day-Night Differences in Cardiac Metabolism

city: Birmingham

first: Martin

last: Young

state: Alabama

address: 703 19th Street S

institute: University of Alabama at Birmingham

summary: An intrinsic property of the heart is an ability to rapidly and coordinately adjust flux through metabolic pathways in response to physiologic stimuli (termed metabolic flexibility). Cardiac metabolism also fluctuates across the 24-hr day, in association with diurnal sleep-wake and fasting-feeding cycles. Although loss of metabolic flexibility has been proposed to play a causal role in the pathogenesis of cardiac disease, it is currently unknown whether day-night variations in cardiac metabolism are altered during disease states. Here, we tested the hypothesis that diet-induced obesity disrupts cardiac “diurnal metabolic flexibility”, which is normalized by time-of-day-restricted feeding. Chronic high fat feeding (20-wk) induced obesity in mice, abolished diurnal rhythms in whole body metabolic flexibility, and increased markers of adverse cardiac remodeling (hypertrophy, fibrosis, and steatosis). RNAseq analysis revealed that 24-hr rhythms in the cardiac transcriptome were dramatically altered during obesity; only 22% of rhythmic transcripts in control hearts were unaffected by obesity. However, day-night differences in cardiac substrate oxidation were essentially identical in control and high fat fed mice. In contrast, day-night differences in both cardiac triglyceride synthesis and lipidome were abolished during obesity. Next, a subset of obese mice (induced by 18-wks ad libitum high fat feeding) were allowed access to the high fat diet only during the 12-hr dark (active) phase, for a 2-wk period. Dark phase restricted feeding partially restored whole body metabolic flexibility, as well as day-night differences in cardiac triglyceride synthesis and lipidome. Moreover, this intervention partially reversed adverse cardiac remodeling in obese mice. Collectively, these studies reveal diurnal metabolic inflexibility of the heart during obesity specifically for non-oxidative lipid metabolism (but not for substrate oxidation), and that restricting food intake to the active period partially reverses obesity-induced cardiac lipid metabolism abnormalities and adverse remodeling of the heart.

overall_design: Mice were fed either a control diet or a high fat diet for 20 weeks, after which hearts were isolated at 6 distinct times of the day. Following RNA isolation, RNAseq was performed.

first: Lamario

last: Williams


title: Sequencing of cDNAs derived from RNA transcripts from nine adult Xenopus tropicalis tissues

status: Public on Apr 09 2021

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

country: USA

institute: Cincinnati Children's Hospital and Medical Center

type: Expression profiling by high throughput sequencing

overall_design: Total RNA extracted from nine adult Xenopus tropicalis tissues using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep.

first: David

last: Hill

first: Praneet

last: Chaturvedi


title: Selective inhibition of CDK7 reveals the influence of CDK7 on psoriatic CD4+ T cells

city: Xi’an

first: Lin

last: Yiting

state: Shaanxi

address: 127 Changlexi Road

department: dermatology

country: China

institute: Xijing hospital

summary:
Purpose: The goals of this study are to compare the differential gene of psoriatic CD4+ T cells treated with THZ1 and DMSO
Methods: RNA sequencing of psoriatic CD4+ T cells which treated with THZ1 (10 nM) or DMSO

overall_design: Overall differential gene expression through RNA sequencing comparing THZ1-treated psoriatic CD4+ T cells with DMSO-treated psoriatic CD4+ cells

first: Yiting

last: Lin

first: Bing

last: Li

first: Gang

last: Wang


title: Experimental and clinical assessment of angiogenesis-related parameters inpatients with juvenile idiopathic arthritis-associated uveitis

city: Muenster

first: Karoline

last: Walscheid

address: Hohenzollernring 74

country: Germany

institute: Department of Ophthalmology and Ophtha-Lab at St. Franziskus-Hospital

summary: Introduction: In chronic and treatment-resistant cases of juvenile idiopathic arthritis-associated uveitis (JIAU), alterations of the iris vasculature may be observed clinically. We sought to investigate this phenomenon by combining clinical and laboratory analyses.  Methods: Iris tissue (IT), aqueous humor (AH) and serum samples from patients with clinically inactive JIAU (n=30) or acute anterior uveitis (AAU; n=18), and primary open angle glaucoma (POAG; n=20) were obtained during ocular surgery. Samples were analyzed by RNA-sequencing (RNA-Seq), qRT-PCR, liquid chromatography, high–definition mass spectrometry technique (LC-MS), Western-Blot (WB), and LEGENDplex analysis. Pattern of iris vasculature in JIAU patients was assessed qualitatively via fluorescein and indocyanine green angiography (FLA/ICGA).  Results: RNA-Seq of IT showed significantly differential expression (DE) of 136 genes between JIAU and POAG, of which 15 were associated with angiogenesis. qRT-PCR, performed to validate RNA-Seq results, showed significant upregulation of the angiogenesis-related genes Kdr, Angpt-1, Tie-1, Tie-2 and Mmrn2 in IT (JIAU vs POAG). LC-MS of IT revealed a total number of 56 DE proteins (JIAU vs POAG), of which asporin, lumican and decorin were associated with angiogenesis and showed increased (p>0.05) expression on WB analysis. LEGENDplex analysis showed upregulation of ANGPT-2 in AH from JIAU compared to AAU and POAG, whereas VEGF was upregulated in AAU. Iris vascular leakage, hypoperfusion and neovascularization were observed by FLA/ICGA in JIAU patients with treatment-refractory complicated course of uveitis.  Conclusion: Angiogenesis-related genes and proteins are upregulated in the iris tissue of JIAU patients, correlating with increased vascular permeability, hypoperfusion, and neovascularization of the anterior uveal tissue in chronic and complicated JIAU.

overall_design: JIAU (study group): 4 samples; POAG (control group): 4 samples

first: Lena

last: Wildschütz

first: Doreen

last: Ackermann

first: Maren

last: Kasper

last: Busch

first: Solon

last: Thanos

first: Dirk

last: Bauer

first: Monika

last: Stoll

first: Simone

last: König

first: Arnd

last: Heiligenhaus


title: Responses to Moritella viscosa in skin and spleen of Atlantic salmon

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

summary: Bacterial pathogen Moritella viscosa, the causative agent of winter ulcer, causes heavy losses in Atlantic salmon aquaculture. The study compared responses in salmon reared under normal condition (G100) and fish exposed to hypoxia - 60% saturation of dissolved oxygen - at early life (G60). G60 showed lower survival after challenge. Analyses were performed in the most affected tissues: skin and spleen

overall_design: The M. viscosa challenge trial was performed at the Aquaculture Research Station in Tromsø, Norway.  Atlantic salmon (AquaGen strain) was smoltified by the following light regime: 6 weeks of 18 h darkness and 6 h light (winter), followed by 6 weeks of 24 h light (summer). After smoltification the fish, mean weight 80 gr, was transferred to seawater in 900 l circular tanks, 325 fish per tank at 10oC and acclimated for 5 days before bath challenge (stagnant oxygenated water, density 58 kg/m3, duration 1 hour, bacterial dose 10e7 cfu/ml) with M. viscosa (LFI5006/2). Samples were collected before challenge, at day 0, and at the end of the challenge experiment. Mortality was registered for 36 days and all dead fish were scored for wounds. Verification of M. viscosa as cause of death was done by isolation of the pathogen from head kidney samples of a selected number of fish on blood agar with 2% NaCl. At termination all surviving fish from the two tanks were scored for wounds, and 30 fish from each tank were sampled for blood (plasma, erythrocytes), gill, skin, head kidney and spleen on RNAlater.

first: Lill-Heidi

last: Johansen


title: Mechanistic understanding of the combined immunodeficiency in complete human CARD11 deficiency

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: British Columbia

address: A5-122 950 W 28th Avenue

department: Pediatrics

country: Canada

institute: The University of British Columbia

summary: From lymphoblastoid cell lines derived from two homozygous CARD11-deficient patients and two heterozygous parents of the first patient, we performed differential expression analysis, gene set enrichment, and pathway analyses by RNA-Seq to demonstrate impaired activation of critical immune pathways.

overall_design: Transcriptome profiling of lymphoblastoid cell lines derived from 2 homozygous CARD11-deficient patients and 2 heterozygous parents in technical triplicate for 4 individuals, with or without stimulation (4hrs with 50ng/mL PMA + 1uM Ionomycin).

first: Henry

middle: Y

last: Lu

first: Mehul

last: Sharma

first: Ashish

middle: A


city: Wako

first: Junko

last: Ueda

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

type: Methylation profiling by genome tiling array

summary: Bipolar disorder (BD) is a severe mental disorder characterized by repeated mood swings.  Although genetic factors with small effect sizes are collectively associated with the pathophysiology of BD, the underlying molecular mechanisms, especially how environmental factors affect the brain genome, remain largely unknown. We revealed neuronal cell-type-specific, pathophysiology-related DNA methylation changes in the prefrontal cortex (PFC) of BD patients, highlighting the importance of the neural epigenome for understanding BD.

overall_design:
Promoter-wide profiling of DNA methylation in human neuroblastoma cells cultured with mood stabilizers.
In total 11 samples; 5 reference files (different conditions) and 6 drug treated files (different conditions).


overall_design:
Promoter-wide profiling of DNA hydroxymethylation in prefrontal cortex of healthy controls.
In total 5 samples; 1 reference samples, 2 neuronal nuclei samples, 2 non-neuronal nuclei samples.


overall_design:
Promoter-wide profiling of DNA methylation in profrontal cortex with patients with bipolar disorder.
In total 278 samples; 2 reference files, 34 files from neuronal nuclei of prefrontal cortices of bipolar disorder (replicated), 34 files from nonneuronal nuclei of prefrontal cortices of bipolar disorder (replicated) files, 35 files from  neuronal nuclei of prefrontal cortices of control (replicated), 35 files from  nonneuronal nuclei of prefrontal cortices of control (replicated).


title: Expression data from mouse heart treated with 2-methyl-2-thiazoline

status: Public on Apr 10 2021

city: Kyoto

first: Masahiro

last: Nishi

address: Kajii-cho 465, Kawaramachi Hirokoji, Kamigyo

department: Cardiology

institute: Kyoto prefectural university of medicine

summary:
2-methyl-2-thiazoline preserves left ventricular systolic function and decreases infarct size in heart after ischemia/reperfusion injury with ameliorated oxidative stress.
We used microarrays to detail the global program of gene expression underlying cardioprotective effect of 2-methyl-2-thiazoline.

overall_design: Left ventricule tissue from 10-week-old C57/BL6 mouse treated with 2-methyl-2-thiazoline was collected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the gene expression data to understand the cardioprotective mechanism by 2-methyl-2-thiazoline.

first: Takehiro

last: Ogata


title: Small RNA-Seq in epididymis of wild type and Alkbh3-/- mice

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

type: Non-coding RNA profiling by high throughput sequencing

summary: Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA). The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

overall_design: Examination of small RNA difference in epididymis between wild type and Alkbh3-/- mice

first: Hongsheng

last: Wang

first: Guanzheng

last: Luo

first: Bin

last: Shen


title: Small RNA-Seq in ALKBH3 stable over expression and control HeLa cells

summary: Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs (15~50 nt) in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA). The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

overall_design: Examination of small RNA difference in ALKBH3 stable over expresion and control HeLa cells


title: Bdellovibrio RNA seqence (Klebsiella pneumoniae)

city: Ulsan

first: Hansol

last: Im

address: UNIST gil 50st

country: South Korea

institute: Ulsan National Institute of Science and Technology

summary: The evaluating the response of Bdellovibrio bacteriovorus HD100 with specific prey (Klebsiella pneumoniae)

overall_design: Bdellovibrio RNA seqeunce was prepared as described at 'Attack-Phase Bdellovibrio bacteriovorus Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth'  Total samples are 21 (Triplicate samples for 7 different conditions)  Reference samples are annotated as 'Bdellovibrio with HEPES' (1,2,3) and Actual samples are named as 'Bdellovibrio predated Klebsiella pneumoniae' (1,2,3)

first: Sooin

last: Choi

first: Robert

middle: J

last: Mitchell


title: Cyproheptadine, an epigenetic modifier, exhibits anti-tumor activity by reversing the epigenetic silencing of IRF6 in urothelial carcinoma

status: Public on Apr 08 2021

city: Chia-Yi

first: Yu Ming

last: Chuang

address: 168 University Road,Min Hsiung

department: Department of Biomedical Science

country: Taiwan

institute: National Chung Cheng University

summary: To investigate the effect of cyproheptadine treatment on bladder cancer cells, expression profile was compared in BFTC905 cells treatment DMSO vs 55µM CPH.

overall_design: BFTC 905 bladder cancer cells were treated with DMSO (control) or 55µM CPH (treatment).

first: Michael

middle: W

last: Chan

first: Chin

last: Li

first: Hsiao-Yen

last: Hsieh

first: Ru-Inn

last: Lin

first: Yu-Ming


title: Quantitative Analysis of Transcriptomes of Control and BP-3 exposure embryos (zebrafish) by RNA-sequencing

city: Wuhan, Hubei, China

first: Jing

address: Qingnian Road, Qiaokou, Hankou

department: Department of Pediatric Surgery

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary:
Purpose: The goals of this study are to quantitatively  compare the expression difference of  embryos incubated with or without benzophenone-3（BP-3） at the transcriptome level and find the underlying mechanism how could BP-3 impede the development of enteric nervous system.
Methods:  Intestinal RNA profiles of 5dpf Wide Type (WT) and BP-3 exposure groups of zebrafish embryos were generated by paired-end sequencing, in triplicate, using Illumina HiSeqTM 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level. The PossionDis algorithm was applied to perform differential gene detection and screened |log2 (FoldChange)| > 1 & qvalue<0.05 as the DEGs. Gene Set Enrichment Analysis (GSEA) comparing WT and BP-3 exposure groups was performed by GSEA software (version 4.0.03). A nominal p-value < 0.05 and false discovery rate (FDR) q-value < 0.25 were considered statistically significant for GSEA analyses.
Results: The PossionDis algorithm was applied to perform differential gene detection and screened |log2 (FoldChange)| > 1 & qvalue<0.05 as the DEGs. RNA-seq data confirmed 159 up-regulated and 73 down-regulated genes in BP-3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process and MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis.
Conclusions: Our study represented the first detailed analysis of BP-3 exposure zebrafish intestinal transcriptomes, with biologic replicates, generated by RNA-sequencing technology. Our results showed that 159 genes were up-regulated and 73 were down-regulated  in BP-3 exposure groups. Some MAPK/ERK signaling pathway related terms were enriched in molecular function and biological process. MAPK/ERK signaling pathway reached notable enrichment based on KEGG analysis.

first: Xinyao

last: Meng


title: RNAseq of wild-type and VHL-deficient CD8+ subsets

city: La Jolla

first: Ananda

last: Goldrath

state: CA

address: 9500 Gilman Dr

institute: UCSD

summary: Adoptive T cell therapies hold great promise in cancer treatment, but low overall response rates in patients with solid tumors underscore remaining challenges in realizing the potential of this cellular immunotherapy approach. Promoting CD8+ T cell adaptation to tissue residency represents an underutilized but promising strategy to improve tumor-infiltrating lymphocyte (TIL) function. Using mice lacking von Hippel Lindau (VHL) in CD8+ T cells and RNA-sequencing (RNA-seq), we identified tissue-resident memory (TRM)-like TIL in mouse models of malignancy. Additionally, we found that VHL-deficient TIL exhibited a core TRM signature despite an exhaustion-associated phenotype. These results reveal a key role for VHL/HIF axis in controlling the formation of a TRM CD8+ T cell subset in primary and secondary tumors that resists functional exhaustion and mediates strong anti-tumor responses.

overall_design: 8 samples, 2-3 biological replicates with five mice each, Spleen and TIL CD8+ T cell subsets

first: Ilkka

last: Liikanen


title: RNAseq of KMT2D and KDM6A human lymphoblastoid cell lines

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

summary: RNA-seq of lymphoblastoid cell lines from KMT2D/MLL2 and KDM6A patients.

overall_design: Human lymphoblastoid cell lines from KMT2D and KDM6A patients and controls were grown to a count of 10^6 and pelleted. RNA was extracted by Zymo Research Direct-zol RNA MiniPrep Kit. RNA-seq libraries were prepared using Nugen mRNA. Sequencing was performed on an Illumina NovaSEQ6000 (150bp PE). Processed reads are raw counts after aligning reads to the human genome (hg38) using STAR aligner (v2.7.3a) and computing counts using quant mode.

first: Rwik

last: Sen

first: Tamim

middle: H

last: Shaikh

first: Kristin

last: Artinger


title: piRNA-30473 contributes to tumorigenesis by regulating RNA m6A-methylation in DLBCL

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

type: Methylation profiling by high throughput sequencing

summary: N6-methyladenosine (m6A), the most abundant modification on eukaryote messenger RNA (mRNA), functions in various fundamental bioprocesses. However, the role of m6A in diffuse large B-cell lymphoma (DLBCL) remains poorly understood. Piwi-interacting RNAs (piRNAs), a novel class of small non-coding RNAs, have been documented to be involved in epigenetic regulation of cancer. Here, we reported that piRNA-30473, which expression supported the aggressive phenotype of DLBCL and was correlated with poor prognosis. Moreover, our data indicated that WTAP (m6A mRNA methylase) was downregulated by piRNA-30473 and played a critical oncogenic role in DLBCL. piRNA-30473 or WTAP depletion also reduced proliferation and induced cell cycle arrest, but not apoptosis in DLBCL cells. In “human-in-mouse” xenograft DLBCL models, inhibition of piRNA-30473 led to a significant reduction in tumor volume compared with control. Furthermore, integrating transcriptome and m6A-seq analyses revealed that WTAP through enhancing m6A levels in mRNA transcripts of its critical target gene HK2 and thereby triggering corresponding signaling cascades in DLBCL. Our study highlights the functional importance of m6A modification machinery in DLBCL, and provides profound insights into the molecular mechanism underlying tumorigenesis by revealing a previously unrecognized mechanisms of gene regulation in DLBCL.

overall_design: m6A-seq in SU-DHL-8 cells with or without WTAP knockdown.

first: Bingzong


title: Promoter-wide profiling of DNA methylation changes in bipolar disorder

first: Junko

last: Ueda

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

overall_design: Refer to individual Series


title: Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos.

city: Shanghai

first: Chuan

last: Chen

address: 1239 Siping Road

institute: Tongji University

type: Genome binding/occupancy profiling by high throughput sequencing


title: Identification of miRNAs that mediate protective function of anti-cancer drugs during white matter ischemic injury

status: Public on Apr 07 2021

city: Portland

first: Selva

last: Baltan

state: OR

address: 3181 S.W. Sam Jackson Park Rd.

department: Anesthesia and Perioperative Medicine (APOM)

institute: Oregon Health and Science University

summary:
Anti-cancer drugs, CX-4945 and MS-275 provide protection to white matter injury in part through miRNAs expression regulation.
Optic_nerve_nanostring_file_Raw_Data.xls

overall_design: In this study, we treated mouse optic nerve with two anticancer drugs, CX-4945 and MS-275, after oxygen glucose deprivation (OGD) followed miRNAs profiling on Nanostring platform

first: Sylvain

last: Brunet

first: Chinthasagar

last: Bastian

first: Ajai

last: Tripathi

first: Hung

last: Nguyen

first: Helen

last: Liu

first: Ranjan

last: Dutta


title: Single cell transcriptome analysis of adult murine lung airway epithelium after NAPH-induced injury

city: Hangzhou

first: Ming

last: Jiang

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

summary: To comprehensively study how club cells response to airway epithelial injury, we performed single cell transcriptomic analysis of the normal and NAPH injured lung samples. Our analysis reveals that a previously undescribed pathway promoting mucous metaplasia that involves VEGFa and its receptor KDR. Our single cell RNA sequencing analysis revealed that VEGFR2 (also known as FLK1 or KDR) is expressed in club cell subpopulations. Loss of KDR, its ligand VEGFa, or downstream MEK/ERK causes excessive differentiation of club cells into mucous cells (mainly goblet cells) during development and regeneration following Naphthalene (NAPH) challenge.

overall_design: We performed single cell transcriptomic sequencing of flow purified Epcam+ cells via 10X Genomics platform

first: Jianwen

last: Que


title: Genome Wide Chromatin Interaction Analysis with Hi-C in Mouse Embryonic Stem Cells

city: Shenzhen

first: JING

last: LUO

email: luoj17@lzu.edu.cn, luojing9520@163.com

address: No 7,Pengfei Road,Dapeng District

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

summary: We select three identified Sox2 associated enhancers (E1, E2 and E3), representing different distal interaction categories, to further explore their biological effects and how this diversity influence gene transcription. Enhancer-deletion is constructed via CRISPR/Cas9 system in mouse embryonic stem cells (mESCs). Results indicate that these associations show quantitative regulation without causing dramatic changes in gene expression and phenotype faultiness. E1 potentially speeds up cell cycle and restrains nerve differentiation and involves in cardiac development, which has been validated in vivo. In contrast, the E2 has potential effect on nervous system function and lipid metabolism. E3 functions in ion transport and metabolism which might play essential role in the pluripotent maintenance. Further, integrated with the Hi-C analysis, enhancer-deletion associated genes show dynamic promoter-enhancer interactions also.

overall_design: Two expreimental repeats represent wild type and E1-E3 enhancer knock out cells were used to generate ten Hi-C library.

first: Lei

last: Huang

first: Qing

last: Li

first: Qitong


title: Effects of fatty acids EPA and oleic acid on responses of Atlantic salmon adipocytes to polyinosinic:polycytidylic acid

first: Aleksei

last: Krasnov

summary: EPA might have a special and unique role in the immune system of Atlantic salmon, especially when exposed to viral infection. Adipose tissue is an endocrine organ that secretes various adipokines involved in metabolic regulation and in inflammatory responses. This study investigates the role of EPA during a simulated viral infection in salmon adipocytes.

platform_organism:
Oncorhynchus mykiss
Salmo salar

overall_design: In vitro cultured adipocytes isolated from Atlantic salmon were enriched with either oleic acid (OA) or EPA through the growth media, stimulated with polyIC and sampled at 24h or 96h.

first: Tone-Kari

last: Østbye

first: Marta

last: Mira Bou


title: The epigenetic Transcriptional factor FVE orchestrates cytoplasmic SGS3-DRB4-DCL4 activities to promote transgene RNA silencing in Arabidopsis

city: college station

first: Di

last: Sun

state: TX

institute: TAMU

summary: We examined global expression profiles of 5-day-old fve-8 seedlings compared to parental line (E5-4) using illumina sequencing

overall_design: Examination of RNA and small RNA (19-24 nt) expression and sRNA expression in fve-8 and its WT (E5-4).


title: Transcriptional profiling of Bone Marrow Derived Dendritic Cells (BMDC) stimulated with zymosan or bacterial spent medium

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: We reported transcriptional characterization of BMDCs stimulated  by filter-sterilized spent medium of Parabacteroides goldsteinii ASF519 (ASF519 SSM) alone or in comination with zymosan. We identified that ASF519 SSM-induced differentially expressed genes have a wide association with the regulation of immune functions, cell communication, apoptosis. We observed that ASF519 SSM induced transcriptomic changes towards immune tolerance, such as a dramatic induction of tolerogenic Il10, lipocalin-2(Lcn2) and indoleamine 2, 3-dioxygenases (Ido1/2), and a reduction of the co-stimulatory molecule Cd40 and inflammatory cytokines, including Il12b, Il23a, and Il1f9 (or Il-36 gamma).

overall_design: Bulk RNA sequencing of BMDCs post stimulation with either ASF519 SSM or uninoculated bacterial broth alone, or in combination with zymosan.

first: Martina

middle: S

last: Corsi

first: Tao

last: Xu

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

summary: Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.

overall_design: Perform the chromatin interaction assay ChIA-PET, ChIA-Drop, H3K27ac ChIPseq and RNAseq to define genome-wide ecDNA-mediated chromatin interactomes and to characterize their functional impact on transcription programs in cancers.

first: Yanfen

last: Zhu

first: Harianto

last: Tjong

first: Che

last: Wong

first: Amit

last: Gujar

first: Chia

middle: L

first: Roel

last: Verhaak


title: RNA-Seq from wheat-Th. elongatum translocation line Zhongke 1878

city: Beijing

first: Xianrui

last: Guo

state: Beijing

address: No.1 West Beichen Road,Chaoyang District, Beijing

institute: Institute of Genetics and Developmental Biology

summary: To screen the transcripts from Th. elongatum 7EL, we inoculated the spikes of translocation line Zhongke 1878 with Fusarium graminearum. We performed full-length transcriptome sequencing after 96 hours. To detect the expression level, we performed RNA-Seq on Zhongke 1878 after 12h, 24h, 48h and 96h.

overall_design: Samples from different spikes of Zhongke 1878 were used in the study. The high-quality, full-length cDNAs was synthesized from total RNA by using a SMARTer™ PCR cDNA Synthesis Kit by Berry Genomics Co. Ltd, China. Sequenced transcripts were mapped to Chinese Spring reference genome using the software GMAP. The unmapped transcripts were extracted. For next generation sequencing, the cDNA libraries were constructed following Illumina standard protocols and sequenced with Illumina HiSeq 2500 by Berry Genomics Co. Ltd, China. Sequenced reads were trimmed using Trimmomatic (version: 0.36), then mapped to the screened transcripts using hisat2 (version: 2.0.0-beta) and the FPKM value were calculated using StringTie (version:1.3.3).

first: Fangpu

last: Han


title: Expression profiles of TREM-1 high and TREM-1 low expressing monocytes

city: Amsterdam

first: Manon

last: Wildenberg

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Amsterdam UMC

summary: The expression of Triggering Receptor Expressed on Myeloid cells (TREM)-1 has been described as a predictive marker for anti-Tumor Necrosis Factor (TNF)-α monoclonal antibody (mAb) therapy responsiveness in patients with inflammatory bowel disease (IBD). Here we investigated expression of TREM-1 specifically in CD14+ monocytes in relation to anti-TNF response. The pretreatment TREM-1 expression levels of CD14+ monocytes of Crohn’s disease (CD) patients were predictive of outcome to anti-TNF mAb therapy, with low TREM-1 expression associated with response to anti-TNF. FACSorting of CD14+ monocytes with different TREM-1 levels showed that differentiation towards regulatory CD206+ M2 type macrophages by anti-TNF was suppressed in CD14+ monocytes with high TREM-1 expression. Activity of the Fcγ-Receptor and autophagy pathway, both necessary for M2 type differentiation and the response to anti-TNF, were decreased in CD14+ monocytes with high expression of TREM-1. We confirmed that the activity of the Fcγ-Receptor pathway was decreased in the CD patients that did not respond to anti-TNF therapy and that it was negatively correlated with TREM-1 expression levels in the CD patient cohort. In conclusion, our results indicate that TREM-1 expression levels in CD14+ monocytes associate with decreased autophagy and FcγR activity resulting in decreased differentiation to M2 type regulatory macrophages upon anti-TNF mAb treatment, which may explain anti-TNF non-response in IBD patients with high expression levels of TREM-1.

overall_design: Monocytes were isolated from healthy blood donor buffy coats (n=13). Cells were stained for expression of TREM-1, and sorted by flow cytometry into separate TREM-1 high (upper 30% of expressio range) and TREM-1 low (lowest 30% of expression range) populations.

first: Pim

last: Koelink


title: Attrition of X chromosome inactivation in aged hematopoietic stem cells

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

summary: During X chromosome inactivation (XCI), the inactive X chromosome (Xi) is recruited to the nuclear lamina at the periphery of the nucleus. Beside X chromosome (X chr) reactivation resulting in a highly penetrant aging-like hematopoietic malignancy, little is known about XCI in aged hematopoietic stem cells (HSCs) . Here, we demonstrate that LaminA/C defines a distinct repressive nuclear compartment for XCI in young HSCs, and its reduction in aged HSCs correlates with an impairment in the overall control of XCI. Integrated omics analyses reveal higher variation in gene expression, global hypomethylation and significantly increased chromatin accessibility on the X chr in aged HSCs. In summary, our data support the role of LaminA/C in the establishment of a special repressive compartment for XCI in HSCs, which is impaired upon aging.

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) was performed using 3 young and 3 aged C57BL/6 mice derived long-term Hematopoietic stem cells (Lt-HSCs).


title: Resistance to BET inhibitors in lung adenocarcinoma is mediated by casein kinase phosphorylation of BRD4

city: Vancouver

first: William

last: Lockwood

address: 675 West 10th Avenue

department: Integrative Oncology

institute: BC Cancer

summary: Targeting the epigenome to modulate gene expression programs driving cancer development has emerged as an exciting avenue for therapeutic intervention. Pharmacological inhibition of the bromodomain and extraterminal (BET) family of chromatin adapter proteins has proven effective in this regard, suppressing growth of diverse cancer types mainly through downregulation of the c-MYC oncogene and its downstream transcriptional program. While initially effective, resistance to BET inhibitors (BETi) typically occurs through mechanisms that reactivate MYC expression. We have previously shown that lung adenocarcinoma (LAC) is inhibited by JQ1 through suppression of FOSL1, suggesting that the epigenetic landscape of tumor cells from different origins and differentiation states influences BETi response. Here, we assessed how these differences affect mechanisms of BETi resistance through the establishment of isogenic pairs of JQ1 sensitive and resistant LAC cell lines. We found that resistance to JQ1 in LAC occurs independent of FOSL1 while MYC levels remain unchanged between resistant cells and their JQ1 treated parental counterparts. Furthermore, while epithelial-mesenchymal transition (EMT) is observed upon resistance, TGF- induced EMT did not confer resistance in JQ1 sensitive LAC lines, suggesting this is a consequence, rather than a driver of BETi resistance in our model systems. Importantly, siRNA knockdown demonstrated that JQ1 resistant cell lines are still dependent on BRD4 expression and we found that phosphorylation of BRD4 is elevated in resistant LACs, identifying casein kinase 2 (CK2) as a candidate protein mediating this effect. Inhibition of CK2, as well as downstream transcriptional targets of phosphorylated BRD4 - including AXL and activators of the PI3K pathway - synergize with JQ1 to inhibit BETi resistant LAC. Overall, this demonstrates that the mechanism of resistance to BETi varies depending on cancer type, with LAC cells developing JQ1 resistance independent of MYC re-activation, and identifying CK2 phosphorylation of BRD4 as a potential target to overcome resistance in this cancer.

overall_design: Two lung adenocarcinoma cell lines initially sensitive to JQ1 were treated with escalating doses of the drug until resistant cells were selected (Resistant). In parallel, the parental cells were cultured in vehicle as a control (DMSO). In addition, control cells were treated with JQ1 for 6hours. All treatment conditions were done in triplicate before RNA was extracted and profiled.


title: Transcriptomic alterations upon HSP90 inhibition in human LN229 and T98 glioblastoma cells in vitro

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

summary:
Purpose: Characterization of transcriptomic alterations upon HPS90 inhibition in human LN229 and T98G glioblastoma cells in vitro.
Methods: LN229 and T98G glioblastoma cells were treated with 10 nM of the HSP90 inhibitor NW457 or the vehicle control for 24 h, and total RNA was subjected to 3' RNA sequencing.
Results: Distinct transcriptomic alterations were observed, dominated by a transcriptional upregulation of the heat shock response.
Conclusion: HSP90 inhibition resulted in distinct transcriptomic alterations and a clear upregulation of the heat shock response.

overall_design: RNAseq analysis of human LN229 and T98G glioblastoma cells. HSP90 inhibitor treatment (10 nM NW457 for 24 h) was compared to the vehicle control.

first: Michael

last: Orth

first: Kirsten

last: Lauber


title: Gene expression and m6A profiling for AGS cells with sh-NC or sh-YTHDF1 [RNA-seq and MeRIP-seq]

first: Xiao-Yu

last: Chen

state: Shanghai

address: Yishan Road 600, Shanghai, China.

department: Department of Gastroenterology

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

summary: N6-methyladenosine (m6A) RNA methylation is implicated in the progression of multiple cancers via influencing mRNA modification. Intersection of RNA-seq, Methylated RNA immune-precipitation (MeRIP)-seq, co-immunoprecipitation, RNA pull-down and MeRIP-PCR were used to identify YTHDF1- modified USP14 and its m6A levels in GC cells. Intersection assays revealed that YTHDF1 promoted USP14 protein translation in an m6A-dependent manner. Our data suggested that m6A reader YTHDF1 facilitated tumorigenesis and metastasis of GC by promoting USP14 protein translation and might act as a clinical therapy for GC.

overall_design: To identify candidate downstream genes of YTHDF1, RNA m6A profiling and RNA-seq analysis was implemented in AGS cells with sh-NC or sh-YTHDF1.

first: Rui

last: Liang

first: You-Cai

last: Yi

first: Hui-Ning

last: Fan

first: Ming

first: Jing

last: Zhang

first: Jin-Shui


title: Lgr6 marks epidermal stem cells with a nerve-dependent role in wound re- epithelialization

city: Philadelphia

first: Panteleimon

last: Rompolas

address: 421 Curie Blvd., BRB II/III Room 1014

department: Dermatology

institute: University of Pennsylvania

summary: Stem cells support the lifelong maintenance of adult organs but their specific roles during injury are poorly understood. Here, we demonstrate that Lgr6 marks a regionally restricted population of epidermal stem cells that interact with nerves and specialize in wound re-epithelialization. Diphtheria toxin-mediated ablation of Lgr6 stem cells delays wound healing, and skin denervation phenocopies this effect. Using intravital imaging to capture stem cell dynamics after injury, we show that wound re-epithelialization by Lgr6 stem cells is diminished following the loss of nerves. This induces the recruitment of other stem cell populations, including hair follicle stem cells, which partially compensate to mediate the wound closure. Single-cell lineage tracing and gene expression analysis reveal that the fate of Lgr6 stem cells is shifted towards differentiation following the loss of their niche. We conclude that Lgr6 epidermal stem cells are primed for injury response and interact with nerves to regulate their fate

overall_design: mRNA profiling of FACS-sorted untreated or denervated Lgr6-GFP+-Tomato+-Itga6+ mouse dorsal epidermal stem cells

first: Sixia

last: Huang

first: Paola

last: Kuri

first: Yann

last: Aubert

first: Megan

last: Brewster

first: Ning

last: Li

first: Olivia

last: Farrelly

first: Gabriella

last: Rice

first: Hyunjin

last: Bae

first: Stephen

last: Prouty

first: Tzevte

last: Dentchev

first: Wenqin

last: Luo

first: Brian

middle: C

last: Capell


title: Identification of potential plasma biomarkers in early-stage nasopharyngeal carcinoma-derived exosomes based on RNA sequencing

city: Fuzhou

first: Ye

middle: wang

last: zhong

state: Fujian

address: No.420, Fuma Road

department: Department of Radiation Oncology

institute: Fujian Medical University Cancer Hospital & Fujian Cancer Hospital

summary:
Purpose：Early diagnosis of nasopharyngeal carcinoma (NPC) is vital to improve the prognosis of these patients. However, early diagnosis of NPC is typically challenging.Therefore, we explored the roles and mechanisms of exosomes in plasma of patients with early-stage NPC.
Methods: Exosomes in plasma were extracted by ultra-high-speed centrifugation.Western blot and transmission electron microscopy (TEM) were used to verify the purity of exosomes. The sequencing data (6 plasma samples from healthy volunteers vs. 6 NPC plasma samples) were analyzed by principal component analysis (PCA), DESeq2, gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG), and TargetScan. The differentially expressed miRNAs (DEmiRNAs) were obtained from the dataset (GSE118720) downloaded from the Gene Expression Omnibus (GEO) repository. Additionally, the datasets downloaded from the GEO database (GSE12452, GSE13597, GSE53819, GSE64634) were used to predict the target genes and functions of hsa-miR-1301-3p. qPCR was applied to verify the differences in the expressions of hsa-miR-1301-3p between 10 normal plasma and 10 NPC plasma samples.
Results:Western blot, TEM, and Nanoparticle Tracking Analysis showed adequate purity of the extracted exosomes. RNA-seq analysis revealed 21 upregulated miRNAs, and 10 downregulated miRNAs in plasma exosomes of early-stage NPC patients. GO analysis showed that the target genes of DEmiRNAs were mainly enriched in DNA synthesis and transcription regulation. KEGG analysis revealed that DEmiRNAs were mainly enriched in PI3K-Akt and MAPK signaling pathways. Moreover, the expression of hsa-mir-1301-3p was verified to be significantly upregulated in enlarged samples of plasma exosomes.
Conclusions:We identified several DEmiRNAs extracted from tumor-derived exosomes between normal plasma and early-stage NPC plasma. Bioinformatics analyses indicated that these DEmiRNAs may be related to NPC development. Our study may provide novel insights into underlying biomarkers and mechanisms of plasma exosomes in early-stage NPC.

overall_design: The RNA sequence of 6 plasma samples from healthy volunteers vs. 6 NPC plasma samples

first: Chuanben

last: Chen

first: Wei

last: Zheng

first: Wangzhong

last: Ye


title: Primary intestinal myofibroplast transcriptomic profiles upon the LPS stimulation vs PBS controls across embryonic development (E14.5) and adulthood.

city: Adelaide

first: Susan

last: Woods

state: Select State

address: Level 5 South, SAHMRI building, North Terrace

department: School of Medicine

country: Australia

institute: The University of Adelaide

summary: The intestinal stroma provides a microenvironment for immune cells activation. Upregulated Toll-like receptor 4 (TLR4) in the intestinal epithelium is has key roles in necrotizing enterocolitis among premature infants. However, the involvement of stroma in excessive inflammation is yet to be investigated. To characterize the immature stroma, intestinal stromal cells were collected from the small intestines of embryonic day 14.5 (E14.5) and adult mice and treated with lipopolysaccharide and a global mRNA sequence analysis of differentially expressed transcripts was performed. TLR4 was expressed at lower levels in embryonic stromal cells than adult. CD14 expressed in flow CD11b+CD45+ stromal cells was identified as a key inducer for TLR mediated inflammatory signals. Embryonic stroma induced differentiation of monocytes into a higher proportion of CD11bhighCD11chigh mononuclear phagocytes (MPs), which have lower CD103 expression than adult stoma. Co-culture of inflamed embryonic stroma with LPS induced increased phagocytotic activity of MPs, which was markedly reduced following CD14 knock down. In summary, the immature intestinal stroma hyper activates inflammatory signals through CD14, producing a high proportion of CD11bhighCD11chigh MPs, which could lead to subsequent aberrant immune activation.

overall_design: We compared primary intestinal myofibroplast transcriptomic profiles upon the LPS stimulation vs PBS controls across embryonic development (E14.5) and adulthood.

first: Mari

last: Ichinose

first: Nobumi

last: Suzuki

first: Tongtong

last: Wang

first: Yoku

last: Hayakawa

first: Patrick

last: Hughes

first: Daniel

last: Worthley


title: Multiple IL-17 family cytokines signaling through IL-17RA drive inflammatory pathways in psoriasis

city: Ballerup

first: Maxim

middle: Alexandre Xavier

last: Tollenaere

address: Industriparken 55

department: Advanced Biologics

country: Denmark

institute: LEO Pharma

summary: The IL-23/IL-17 immune axis is of central importance in psoriasis. However, the contribution of IL-17 family cytokines other than IL-17A to drive skin inflammation in psoriasis has not been fully established. To further elucidate the role of individual IL-17 family cytokines in psoriasis, we investigated their expression and localization in psoriasis skin at the mRNA and protein level. Moreover, we investigated the gene expression signatures induced by individual IL-17 family cytokines in human skin ex vivo as well as modulation of responses induced by the combination of IL-17 family cytokines in human keratinocytes by brodalumab, a human monoclonal antibody targeting the IL-17RA, versus the IL-17A blocking antibody ixekizumab.     We demonstrate that IL-17A, IL-17AF, IL-17F and IL-17C are expressed at increased levels in psoriasis lesional skin and induce inflammatory gene expression signatures in human skin ex vivo that correlate with those observed in psoriasis. Furthermore, we show that brodalumab, in contrast to ixekizumab, fully blocks gene expression responses induced by the combination of IL-17A, IL-17AF, IL-17F and IL-17C in human keratinocytes.     These findings suggest that inhibition of several IL-17 family cytokines, e.g. by targeting of the IL-17RA receptor, could be a favored mechanism to obtain a profound suppression of the inflammatory processes in psoriasis and thereby achieve high levels of skin clearance and sustained efficacy in patients with psoriasis.

overall_design: 60 human skin samples separated into 11 groups treated with Il17 variants and 1 untreated control group

first: Josephine

last: Hebsgaard

first: David

last: Ewald

first: Paola

last: Lovato

first: Sandra

last: Garcet

first: Xuan

last: Li

first: Steven

middle: D

last: Pilger

first: Minna

last: Tiirikainen

first: Malene

last: Bertelsen

first: James

middle: G

last: Krueger

first: Hanne

last: Norsgaard


title: YBX3 mediates the metastasis of nasopharyngeal carcinoma via PI3K/AKT signaling

city: China

first: Xiaoqin

last: Fan

state: Guangdong

address: Sungang West Road

department: Institute of Translational Medicine

institute: Shenzhen Second People's Hospital

summary: The metastasis of nasopharyngeal carcinoma (NPC) is a complex process associated with oncogenic dysfunction, the deciphering of which remains a challenge and requires more in-depth studies. Y-box protein 3 (YBX3) is a DNA/RNA binding protein associated with gene transcription, DNA repair and the progression of various diseases. However, whether and how YBX3 affects the metastasis of NPC remains unknown. Thus, in this study, we aimed to investigate the role of YBX3 in the metastasis of NPC and determine its underlying mechanism. Interestingly, it was found that the expression of YBX3, which was associated with NPC metastasis, was upregulated in the clinical NPC tissues and cell lines using solid experimental evidences. Moreover, we found that knockdown of YBX3 expression by lentivirus shRNA significantly suppressed NPC cells migration in vitro and metastasis in vivo. Mechanistically, RNA sequencing results suggested that the genes regulated by YBX3 were significantly enriched in cell adhesion molecules, cAMP signaling pathway, calcium signaling pathway, focal adhesion, PI3K-Akt signaling pathway, Ras signaling pathway, Rap1 signaling pathway, NF-κB signaling pathway, and Chemokine signaling pathway. Of these, PI3K-Akt signaling pathway contained the most genes. Accordingly, YBX3 knockdown decreased the activation of PI3K/AKT signaling, thereby inhibit epithelial-to-mesenchymal transition and MMP1. These results have demonstrated that YBX3 are involved in the metastasis of NPC through regulating PI3K/AKT signaling pathway, and serve as a potential therapeutic target for patients with NPC.

overall_design: In this study, we applied RNA sequencing in nasopharyngeal carcinoma cells of YBX3-shRNA 5-8F cells and YBX3-control 5-8F cells.

first: Xina

last: Xie

first: Guohui

last: Nie


title: Inhibition of the mRNA-binding protein IGF2BP1 suppresses proliferation and sensitizes neuroblastoma cells to chemotherapeutics

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Gain at chromosome 17q21 in neuroblastoma and is associated with a poor prognosis, independent of MYCN amplification status. Several potential proto-oncogenes have been identified in this region, one of them - insulin-like growth-factor-2 mRNA binding protein (IGF2BP1) – is expressed at high levels in stage 4 tumors, and associated with overall lower patient survival. Here, we demonstrate that down-regulation of IGF2BP1 activity, either by transcript silencing or chemical inhibition, suppresses neuroblastoma cell growth. Furthermore, the combination of IGF2BP1 inhibition along with commonly used chemotherapeutics that broadly affect DNA synthesis, or cyclin-dependent kinase (CDK) inhibitors that disrupt signal transduction, have a synergistic effect on the suppression of neuroblastoma cell proliferation.

overall_design: Total 6 samples were analyzed; 3 replicates each for SK-N-AS RNA shScramble control and SK-N-AS RNA shIGF2BP1.

first: Jason

middle: M

last: Biegel

first: Mayura

last: Dhamdhere

first: Shuang

last: Gao

first: Chethana

middle: P

last: Gowda

first: Vladimir

last: Spiegelman


title: 1α,25-Dihydroxyvitamin D3 encapsulated in Nanoparticles Prevents Venous Neointimal Hyperplasia and Stenosis in Porcine Arteriovenous Fistulas

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

overall_design: 1α,25-Dihydroxyvitamin D3  vs. vehicle

first: Sreenivasulu

last: Kilari

first: Avishek

middle: K

last: Singh

first: Chuanqi

last: Cai

first: Chenglei

last: Zhao

first: Michael

last: Simeon

first: Edwin

last: Takahashi

first: Elazer

middle: R

last: Edelman

first: Hyunjoon

last: Kong

first: Thanila

last: Macedo

first: Ravinder

first: Matthew

last: Urban

first: Rajiv

last: Kumar


title: Integrated Transcriptomic Analysis of the miRNA-mRNA Interaction Network in Thin Endometrium [RNA-Seq]

city: hefei

first: lu

last: zong

state: anhui

address: lujiang road

institute: Anhui Provincal Hospital

summary: Although the thin endometrium (TE) has been widely recognized as a critical factor in implantation failure, the contribution of miRNA-mRNA regulatory network to the development of disease aetiology remains to be further elucidated. This study performed an integrative analysis of the miRNA-mRNA expression profiles in the thin and adjacent normal endometrium of 8 patients with intrauterine adhesion to construct the transcriptomic regulatory networks. A total of 1093 differentially expressed genes (DEGs) and 72 differentially expressed miRNAs (DEMs) were identified in the thin adhesive endometrium of the TE group compared with the control adjacent normal endometrial cells. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that DEGs and the target genes of DEM were significantly enriched in angiogenesis, cell growth regulation and Wnt signalling pathway. Multiple hub genes (CAV1, MET, MAL2, has-mir-138, ARHGAP6, CLIC4, RRAS, AGFG1, has-mir-200, and has-mir-429) were identified by constructing the miRNA-mRNA regulatory networks. Furthermore, a miRNA-mRNA-pathway-function analysis was conducted, and the hub genes were enriched in the FoxO signalling pathway, cell growth regulation, inflammatory response regulation and regulation of autophagy pathways. Our study is the first to perform integrated mRNA-seq and miRNA-seq analyses in the thin adhesive endometrium and the control adjacent normal endometrial cells. This study provides new insights into the molecular mechanisms underlying the formation of thin endometrium.

overall_design: thin adhesive endometrium and the control adjacent normal endometrial cells of 8 patients with intrauterine adhesion.The thin endometrium RNA and adjacent normal endometrial RNA respective pooled equally, and reverse transcribed into cDNAs using the QuantiTect Reverse Transcription Kit.

first: Shengxia

last: Zheng

first: Lu

last: Zong

first: Ye

last: Meng

first: Bo

last: Xu


title: Integrated Transcriptomic Analysis of the miRNA-mRNA Interaction Network in Thin Endometrium [miRNA-seq]

overall_design: thin adhesive endometrium and the control adjacent normal endometrial cells of 8 patients with intrauterine adhesion.The thin endometrium RNA and adjacent normal endometrial RNA respective pooled equally,Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:   1) 3'-adaptor ligation;   2) 5'-adaptor ligation;   3) cDNA synthesis;   4) PCR amplification;   5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).   The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq per the manufacturer's instructions.


title: Moringa isothiocyanate-1 regulates Nrf2 and NF-κB Pathway in response to LPS-driven sepsis and inflammation

city: Piscataway

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: Moringa Isothiocyanate-1 (MIC-1) purified from moringa (Moringa oleifera Lam) seed extract (MSE) has been previously proved to modulate anti-inflammatory and antioxidant activities. However, the molecular mechanism remains poorly understood, particularly nothing is known about its effect on Lipopolysaccharide (LPS) induced sepsis/inflammation. Hence, we investigated whether MIC-1 can decrease acute inflammation in the LPS-induced acute inflammation/sepsis model in mice. Mice were treated orally with MIC-1 for three days before the intraperitoneal injection of LPS. MIC-1 treatment resulted in a dramatic improvement in the histopathological signs of inflammation in the liver, kidney, spleen, and colon and a significant reduction of the LPS-induced sepsis. Moreover, MIC-1 treatment significantly reduced the expression of inflammatory markers in all these organs. We also performed transcriptome analysis in vitro and in vivo in LPS induced macrophages and liver with/without MIC-1 treatment.  Interestingly, there is an upregulation of inflammatory/immune response genes in LPS induced macrophages/liver, and there is downregulation of same set of genes after treating with MIC-1. Our results together indicate that MIC-1 reduces sepsis/inflammation through NF-κB and Nrf2 mediated anti-inflammatory/antioxidant signaling pathways. Research has demonstrated that chronic low-grade tissue inflammation and oxidative stress are essential factors in the development of metabolic disorders. Therefore, MIC-1 could be a new natural therapeutic strategy to treat metabolic syndrome.

overall_design: Mouse data comprising RNA-Seq from 18 samples was obtained: 9 samples from the liver (3 saline control replicates, 3 LPS treated replicates, 3 LPS+10uM MIC-1 treated replicates) and 9 samples from macrophages (3 saline control replicates, 3 LPS treated replicates, 3 LPS+10uM MIC-1 treated replicates).

first: Badi

last: Sailaja

first: Rohit

last: Aita


title: Integrated Transcriptomic Analysis of the miRNA-mRNA Interaction Network in Thin Endometrium

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

overall_design: Refer to individual Series


title: Macrophages in Crohn’s disease creeping fat are predominantly inflammatory and produce calprotectin

first: Manon

last: Wildenberg

summary: Crohn’s disease is characterized by transmural inflammation and therefore the mesenteric immune compartment has gained interest. However, its significance in Crohn’s disease is largely unclear. Macrophages are plastic cells that adapt their phenotype to environmental stimuli resulting in inflammatory and regulatory macrophage subsets. Hence, their distribution can reflect the overall nature of an immune infiltrate. We show that mesenteric macrophages contain two populations, characterized as CD11b-high and CD11b-dim. The CD11b-dim population is characterized by expression of regulatory markers CD206, CD200R, CD163, PD-L2, CD32. CD11b-high macrophages display an IFNγ induced signature and produce high levels of calprotectin. CD11b-dim and CD11b-high populations were comparable between Crohn’s disease and other indications in expression pattern, but the CD11b-high population was strongly overrepresented in this patient group.

overall_design: CD11b-high macrophages were isolated from the mesentery of patients undergoing bowel resection (n=12). CD11b-low macrophages were isolated from the same patients (n=10, remaining patients did not yield sufficient number of cells).

middle: E

first: Felicia

last: Bloemendaal


title: Dickkopf 1 Impairs Sensitivity to PD-1 Blockade through CD8+ T Cell Inactivation in dMMR/MSI Colorectal Cancer

city: Guangzhou

first: Qiaoqi

last: Sui

address: Dongfeng East Road 651

institute: Sun Yat-sen University Cancer Center

summary: Dickkopf 1 (DKK1) could promote tumor progression by suppressing immunity. Therefore, we investigated whether DKK1 influence prognosis and sensitivity to PD-1 blockade in colorectal cancers (CRCs) with defective DNA mismatch repair genes (dMMR) or microsatellite instability (MSI). We found that elevated DKK1 expression was associated with recurrence and dismissed CD8+ T cell infiltrations, and patients with high serum DKK1 had poor anti-PD-1 response. RNA interference or neutralization of DKK1 in CRCs enhanced CD8+ T cell cytotoxicity, and down-regulation of T-bet and E2F1 following GSK3β activation was detected in DKK1-treated CD8+ T cells. In organoid-lymphocyte co-culture model, apoptosis proportions were elevated after individual neutralization of both PD-1 and DKK1, and the combined neutralization resulted in further increases. In conclusion, DKK1 suppresses tumor immunity in dMMR/MSI CRCs by inactivating CD8+ T cells through GSK3β/E2F1/T-bet axis. DKK1 neutralization may improve the sensitivity to PD-1 blockade in dMMR/MSI CRCs.

overall_design: We obtained tumor tissues and serum of dMMR/MSI CRCs. DKK1 expression and immune status of 80 cases were evaluated by immunohistochemistry, while serum DKK1 of another 43 cases receiving PD-1 blockade were measured by ELISA. Control and DKK1 knockdown CT26 cells were grafted in BALB/c mice, or co-cultured with T cells in vitro. Organoids of dMMR CRCs were co-cultured with T cells, treated with DKK1, anti-DKK1 and mock. PD-1 neutralizations were given to some of those models. To assess cytotoxicity of T cells, apoptosis assays and flow cytometrys were used. RNA sequencing on CD8+ T cells were performed to investigate downstream of DKK1 and underlying mechanism.

first: Dingxin

last: Liu

first: Kai

last: Han

first: Guochen

first: Wu

last: Jiang

first: Leen

last: Liao

first: Jinghua

last: Tang

first: Yuan

last: Li

first: Lingheng

first: Qingjian

last: Ou

first: Binyi

last: Xiao

first: Yihong

last: Ling

first: Jiewei

last: Chen

first: Zexian

first: Zhixiang

last: Zuo

first: Zhizhong

last: Pan

first: Jian

first: Muyan

last: Cai

first: Penghui

last: Zhou

first: Peirong

last: Ding


title: Expression data from mesenchymal stem and progenitor cells freshly isolated from human bone marrow

city: Essen

first: Yi-Yang

state: NW

address: Hufelandstraße 55

institute: University Hospital Essen

summary: Murine models of myeloid neoplasia show how leukemia infiltration alters the mesenchymal stem and progenitor cells to reinforce malignancy at the expense of healthy hematopoiesis. However, little is known about the bone marrow architecture in humans. We used global gene expression analyses to analyze mesenchymal stem and progenitor cells from AML patients and compared with mesenchymal stem and progenitor cells from the non-leukemic donor.

overall_design: Bone marrow mesenchymal stem and progenitor cells were isolated from either first diagnosed acute myeloid leukemia patients or non-leukemic donors with surface marker CD45-CD235a-CD31-CD271+CD146+

first: Maher

last: Hanoun

first: Yiyang


title: Improved persistence and expanded TPEX formation in Regnase-1 KO CAR T cells is TCF-1-dependent

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary:
transcriptional profiling was performed on Regnase-1 KO CAR and Regnase-1 TCF-1 DKO CAR T cells isolated 7days after co-transfer into tumor bearing mice.
TCF-1 deficiency in Regnase-1 KO CAR T cells led to reduced long-term persistence and memory-like phenotype.

overall_design: In total 10 samples were analyzed: (KO CAR n=5; DKO CAR n=5)

first: Zheng

last: Wenting

first: Yogesh

last: Dhungana

first: Geiger

last: Terrence


title: DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RRBS]

city: Ghent

first: Jeroen

last: Galle

address: Coupure Links 653

department: Dept. Of Mathematical Modelling, Statistics and Bioinformatics

country: Belgium

institute: Ghent University

summary:
Song learning in zebra finches is a prototypical example of a complex learned behavior, yet knowledge on the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 dph and 65 dph).
We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA (hydroxy)methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age dependent gene expression was found for various transcription factors (i.a. OTX2, AR and FOS) involved in neurodevelopment. Additionally, genomic regions featured by age dependent differential methylation in differentially expressed genes were significantly enriched for specific transcription factor binding motifs. Incomplete dosage compensation was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life.
In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.

overall_design: For each sex per time point (1 day post hatch (dph), 20dph, 65dph and adult), 3 independent biological replicates were sequenced, resulting in a total of 24 samples. To increase power, each of these biological replicates consisted of a pool of DNA of 3 telencephalons in equal proportions.

first: Jolien

last: Diddens

first: Louis

last: Coussement

first: Carolina

last: Frankl-Vilches

first: Gaurav

last: Majumdar

first: Steyaert

last: Sandra

first: Sita

last: ter Haar

first: Galle

last: Jeroen

first: Ellen

last: De Meester

first: Sarah

last: De Keulenaar

first: Criekinge

last: Wim van

first: Charlotte

middle: A

last: Cornil

first: Jacques

last: Balthazart

first: Annemie

last: Van Der Linden

first: Tim

last: De Meyer

first: Wim

last: Vanden Berghe


title: DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RNA-Seq]

overall_design: For each sex per time point (1 day post hatch (dph), 20dph, 65dph and adult), 3 independent biological replicates were sequenced, resulting in a total of 24 samples. To increase power, each of these biological replicates consisted of a pool of RNA of 3 telencephalons in equal proportions.


title: The use of autologous peritoneum for mucosal replacement following ileal neobladder construction: a novel technique in a porcine model

city: Beijing

first: Jie

address: Qing Hua Yuan

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Background:The transposed intestinal segments maintain their absorptive and secretive functions which may lead to metabolic disorders after ileal neobladder construction. The aim of this study was to develop a novel technique to reduce the complications of orthotopic urinary diversion in a porcine model.
Methods: An ileal neobladder procedure was performed in eight female pigs. Four pigs (experimental group) received mucosal replacement of the neobladder using autologous peritoneum, while the other four pigs (control group) received a normal U-shaped ileal neobladder. After three months, the neobladder was evaluated using IVU, cystograms and cystoscopy. Blood biochemistries, urine samples and venous gas analyses were obtained preoperatively and postoperatively. The neobladder was then harvested to assess pathological findings.
Results: The mean (range) operating time was 248 (224-287) min in the control group and 325 (296-360) min in the experimental group. All animals but one from the experimental group survived to the designated endpoints. Postoperative IVU revealed that the urinary tracts were patent and that there was no hydronephrosis or dilated ureter. Cystograms demonstrated a spherical neobladder. Cystoscopy showed a smooth neobladder wall. Histological analysis revealed that the peritoneum-ileal seromuscular flap surface was lined with the urothelial layers. Transcriptome comparison showed the maximum similarity between mucosa of neobladder from experimental group and mucosa of normal bladder.
Conclusions: The novel technique is shown to be feasible and reproducible in a porcine model. The imageological, histological, and transcriptometric analyses all confirmed that autologous peritoneum can be used as a natural biological reconstruction material.

overall_design: We conduct the mRNA-seq from 2 replicates of mucosa of neobldder from experimental group (MN-exp), 2 replicates of mucosa of normal bladder (MNB), 2 replicates of mucosa of neobladder from control group (MN-ctrl), and  2 replicates of normal peritoneum(NP).

first: Biao

last: Chen

first: Xia

first: Wenjia

last: Wang

first: Zhiqiang

last: Song

first: Shuaijun

first: Haoyu

last: Ji

first: Fangyuan

last: Zhang

first: Jianchen

last: Wu

first: Shengwen

last: Li


title: RORa is required for neutrophil migration

status: Public on Apr 06 2021

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

summary: We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited

overall_design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control

first: Alan

middle: Y

last: Hsu

first: Sheng

last: Liu

first: Jun

last: Wan


title: Obese Insulin Resistant Humans with Compensatory Hyperinsulinemia Dissociate Lipolysis from Glycemia as Possible Adaptive Response to Fatness

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

summary: High blood levels of free fatty acids link obesity with type-2 diabetes, but this connection remains poorly understood. We have investigated lipolysis and glucose homeostasis in recently diagnosed obese type-2 diabetics; in obese insulin resistant non-diabetic subjects (obese-IR) matched for age, sex, body composition and fasting insulin levels; and in healthy lean individuals. Our results show that obese-IR dissociate lipolysis from glycemic control, revealing that the action of compensatory hyperinsulinemia on blood glucose is not mediated by reduced lipolysis. In the obese adipose tissue free fatty acids and glycerol levels were elevated in spite of high local levels of insulin or lactate; correlated with adipocyte size and metabolic inflammation, with reduced adipose tissue mRNA levels of genes implicated in beta-adrenergic signaling, de-novo lipogenesis, and increased expression of genes implicated in adipose tissue hyperplasia. These results shed light on the nature of the interaction between lipolysis and glucose homeostasis and indicate an possible adaptive response to fatness.

overall_design: To undersrand the mechanisms driving elevated levels of FFA and glycerol in the obese groups we have performed genome-wide RNASeq analysis of RNA preparations from abdominal subcutaneous adipose tissues of Lean, Obese-IR, and Obese-T2D subjects

first: Emanuel

last: Fryk

first: Josefin

last: Olausson

first: Karin

last: Mossberg

first: Martin

last: Schmelz

first: Li-Ming

last: Gan

first: Alessandro

last: Provenzani

first: Barbara

last: Becattini

first: Giovanni

last: Solinas

first: Per-Anders

last: Jansson


title: Intestinal organoids and transcriptional response to T3

city: Lyon

first: Michelina

last: Plateroti

address: 28 rue Laennec

country: France

institute: Cancer Research Center of Lyon

summary: The aim of the study was to analyse the impact of T3 treatment on intestinal stem and progenitor cells using mouse organoids as model system

overall_design: Transcriptome from organoids maintained in control condition or treated with 10-7M T3 were analyzed by RNA-seq by Illumina NextSeq 500


title: Cancer-associated exportin-6 upregulation inhibits the transcriptional repressive and anticancer effects of nuclear profilin-1

city: Saint Louis

first: Jieya

last: Shao

address: 660 South Euclid Ave

institute: Washington University in St. Louis

summary: Aberrant expression of nuclear transporters and altered subcellular localization of their cargo proteins are increasingly recognized as drivers and therapeutic targets of cancer.  Here, we report that exportin-6, a nuclear exporter specific for actin/profilin-1, is upregulated in a broad range of cancers and associated with poor prognosis.  Exportin-6 loss triggers antitumor effects in breast cancer cells in a profilin-1-dependent fashion.  Nuclear profilin-1 interacts with the Super Elongation Complex (SEC), a positive transcriptional regulator of pro-cancer genes including MYC.  Exportin-6 loss, by increasing nuclear profilin-1, inhibits SEC-dependent transcription and sensitizes breast cancer cells to inhibition of BET domain proteins.  Thus, exportin-6 upregulation is a previously unrecognized cancer addiction that reduces the transcriptional inhibitory and anticancer activities of nuclear profilin-1.

overall_design: Duplicate results of RNA-seq using breast cancer MCF-7 cell line stably expressing exportin-6 (wild type or RNAi-resistant) and infected with shRNAs targeting firefly luciferase or exportin-6.

first: Arshag

last: Mooradian


title: The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3′-UTRs of yeast mitochondrial mRNAs

city: Goettingen

first: Katharina

middle: Bettina

last: Hofmann

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

summary: Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5′ capping and 3′ polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3′-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3′-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.

overall_design: We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to systematically generate transcriptome-wide protein binding profile for Rmd9 in the yeast Saccharomyces cerevisiae.

first: Hauke

last: Hillen

first: Dmitry

last: Markov

first: Ireneusz

last: Wojtas

middle: B

first: Michael

last: Lidschreiber

first: Andrew

middle: T

last: Cowan

first: Julia

last: Jones

last: Temiakov

first: Patrick

last: Cramer

last: Anikin


title: Long read sequencing of nuclear RNAs from human coronary artery smooth muscle cells

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

summary: To study isoforms of nuclear RNAs, including CARMN lncRNA, we performed Oxford Nanopore long-read sequencing of RNAs isolated from the nuclear fraction of human coronary artery smooth muscle cells.

overall_design: We perfomed Oxford Nanopore long read sequencing (MinION) on 2 biological replicates of RNAs isolated from nuclear fraction of HCASMCs.

first: Francesca

last: Vacante

first: Mukesh

last: Lalwani

first: Thomas

last: Williams

first: Matthew

last: Bennett

middle: H

last: Baker


title: Adenylate kinase 4 Promotes the expression of Inflammatory Genes in Macrophages via Hif-1a

city: Taipei

first: Shi-Chuen

last: Miaw

address: No.1 Jen Ai road section 1

institute: National Taiwan University, College of Medicine

summary: Macrophages comprise the first line of defense against various pathogens. Classically activated macrophages (M1), induced by IFNg and LPS, express a high level of inflammatory cytokines and contribute to inflammatory processes. By contrast, alternatively activated macrophages (M2) are induced by IL-4/IL-13, produce IL-10, and display anti-inflammatory activity. Adenylate kinase 4 (Αk4), an enzyme that transfers phosphate group among ATP/GTP, AMP, and ADP, is a key modulator of ATP and is involved in maintaining the homeostasis of cellular nucleotides which is essential for the function of cells. However, its role in regulating the function of macrophages is not fully understood. Here we report that the expression of Ak4 is induced in M1 but not M2 macrophages. Suppressing the expression of Ak4 in M1 macrophages with shRNA enhances the production of ATP. RNA-seq analysis identifies several inflammation-related genes, including Il1b, Il6, Tnfa, Nos2 and Hif1a, as downstream targets of Ak4. We further demonstrate that Ak4 and Hif1a form a positive feedback loop in sustaining the expression of the inflammation-related genes. Our data depict a potential mechanism linking energy consumption and inflammation in macrophages.

overall_design: Total M1 macrophages mRNA profile of scramble and Ak4 shRNA KD


title: DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon

first: Jeroen

last: Galle


title: Expression data from Hoxb13+ Prostate Luminal Epithelial Cells

city: New York

first: Charles

last: Drake

state: New York

address: 650 W. 168th Street

department: Medicine

country: Mexico

institute: Columbia University

summary:
A subpopulation of prostate luminal epithelial cells has been previously reported to be sufficient to regenerate prostatic architecture following consecutive rounds of androgen deprivation/repletion. This functional characteristic suggest prostate luminal epithelial cells as the putative cell-of-origin for castration-resistant prostate cancer - which more notizable fenotype is the lack of response to androgen deprivation thereapy.
We used microarrays to profile the androgen-induced transcripts in luminal prostate epithelial cells involved in a cycle of prostate regression/regeneration in Hoxb13-rtTA|TetO-H2BGFP transgenic mice.

overall_design: Twelve-week-old male Hoxb13-GFP mice carrying the Hoxb13-rtTA transgene and a Tetracycline operator–Histone 2B-Green Fluorescent Protein (TetO-H2BGFP), which results in GFP expression restricted to luminal epithelial Hoxb13+ cells, were castrated via bilateral orchiectomy.  A cycle of prostate regression/regeneration was induced by allowing murine prostates to regress for six weeks to reach the fully involuted state. Following euthanization, prostate luminal epithelial cells were FACS sorted for RNA extraction and hybridization on ClariomD (MTA-1.0) Affymetrix microarrays. We sought to obtain homogeneous populations of luminal epithelial cells at each treatment group (untreated, n=3; ADT, n=3; and ADT+TR, n=4) in order to increase the resolution of expression profiles. To that end, we isolated luminal epithelial cells based on their expression of the GFP fluorescent protein, their positive expression of CD24, intermediate expression of CD49f, and negative expression of the immune markers CD45, F4/80, and CD11b cells. Biological replicates of each treatment group (n≥3), were compared.

first: Zoila

last: Lopez-Bujanda


title: Single cell RNA-seq analysis of endothelial cells (HUVEC) treated with IL1b and TGFb2 as a model of endothelial to mesenchymal transition (EndMT)

summary: Endothelial-to-mesenchymal transition (EndMT) is a dynamic biological process involved in pathological vascular remodeling. However, the molecular mechanisms that govern this transition remain largely unknown. To study EndMT in vitro, human umbilical vein endothelial cells (HUVEC) were treated with transforming growth factor-β2 and interleukin-1β, leading to a decrease of endothelial markers as well as an increase of mesenchymal markers and EndMT regulators after 7 days. Single-cell RNA-seq was carried out to study the dynamics of the transition.

overall_design: Single-cell RNA-sequencing were performed in untreated and treated (IL1b+TGFb2) HUVEC at 0, 3 and 7 days using 10X Genomics.

first: Axelle

last: Caudrillier

first: Shiau-Haln

last: Chen

first: Ross

last: Dobie

first: Beth

last: Henderson

first: Richard

middle: S

last: Taylor

first: Neil


title: 4C analysis of MN1-ETV6 translocations

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary: We show that translocations place regulatory regions in close proximity to MN1 and enhance gene expression

overall_design: Chromatin conformation capture (4C) in two human AML cell lines with MN1-ETV6 translocation and two control cell lines

first: Simone

last: Riedel

first: Hongbo

last: Xie


title: Whole genome bisulfite sequencing of E13.0 and E13.5 Tex14 mutant, heterozygote and wild-type murine female germ cells

city: San Francisco

first: Bikem

last: Soygur

state: California

address: 35 Medical Center Way, Parnassus, RMB, PodB, 913D

department: Obstetrics, Gynecology & Reproductive Sciences

institute: UCSF

summary: Meiosis is critical to generating oocytes however, the mechanisms regulating the switch from mitotic primordial germ cells (PGCs) to meiotic germ cells are poorly understood in females. We showed that the onset of meiosis in the fetal murine ovary propagates via intercellular bridges between developing germ cells by using Tex14 mutant (Tex14-/-) mice. Tex14-/- germ cells, which lack intercellular bridges, initiates meiosis prematurely and they more rapidly extinguish pluripotency-associated transcripts (such as Dppa3) upon entering meiosis. Considering the involvement of Dppa3 in methylation process as well as the importance of epigenetic reprogramming for gamete formation and meiosis, we isolated Tex14 wild-type, heterozygous and mutant germ cells from E13.0 and E13.5 ovaries for whole genome bisulfite sequencing. We compared how methylation differs between age-matched wild-type/heterozygous controls and mutants. We find that DNA methylation across the genome is not affected in Tex14 mutant germ cells however, promoters of Germline Reprogramming Responsive (GRR) genes and younger L1 genes are hypomethylated. These results suggest that cytoplasmic sharing via intercellular bridges slows and coordinates the cell state transition from pluripotency to meiosis potentially by diluting regulatory factors of epigenetic reprogramming.

overall_design: E13.0 and E13.5 Oct4-GFP+ female germ cells from single Tex14 mutant, heterozygote or wild-type embryos were purified by fluorescence-activated flow cytometry (8,611 cells from wild-type; 9,944 cells from heterozygote; 4,371 cells from mutant at E13.0 and 3,224 and 8,606 cells from heterozygotes; 3,710 and 10,371 cells from mutants at E13.5). Sequencing was completed for whole-genome analysis as well as specifically for GRR genes and LINE1 elements.

first: Rebecca

last: Jaszczak

first: Diana

last: Laird


title: Intercellular bridges coordinate the transition from pluripotency to meiosis in mouse fetal oocytes

city: San Francisco, CA

middle: Garrett

address: 35 Medical Center Way, Room 913D

summary:
Purpose: Investigate the transcriptomes of Tex14 heterogygous sample (with intercellular bridges intact) compared to Tex14 homozygous mutant (lacking intracellular bridges) to ascertain what effects the loss of cytoplasmic sharing has on mitotic to meiotic mouse ovary
Methods: Single cell RNA sequencing libaries were created from embryonic day 13.5 mouse ovaries from Tex14 +/- and Tex14 -/- samples. Three Tex14+/- and two Tex14-/- E13.5 ovaries were pooled. Libaries were creating using 10X Chromium Single Cell 3' (v2 Chemistry) library kits per 10X posted protocols. Samples were sequenced on HiSeq 4000 (Illumina) with paired-end sequencing parameters: Read1, 98 cycles; Index1, 14 cycles; Index2, 8 cycles; and Read2, 10 cycles. Tex14+/- sample had 23,567 mean reads per cell, and Tex14-/- had 19,735 mean reads per cell. Since 10X Genomics recommends an average of 60k raw reads per cell, we submitted our two libaries for deeper sequencing. Our second sequencing run was done on a Novaseq S2 flowcell with the following parameters: Read 1 Length 26bp; Index 1 Length 8bp; Index 2 Length 0bp; Read 2 Length: 98 bp. Follwing deeper sequencing, Tex14+/- sample had 55,744 mean reads per cell, and Tex14-/- had 41,117 mean reads per cell. Cells which passed quality control metrics were further analyzed.
Results: We used CellRanger v2.1.0 to align the sequenced data to the 10X Genomics pre-built mm10 genome. We mapped about 300,000,000 sequence reads for each shallowly sequenced library, and 750-800,000,000 reads for the deeply sequenced libraries. We used Seurat v3 to keep high quality cells, excluding cells which did not all of the following metrics: genes expressed in at least 3 cells, fewer than 25,000 unique fragments (to exclude cell doublets), greater than 200 genes expressed (to exclude GEMS with no cells), and cells with 7.0% or less mitochondrial gene expression. After quality control exclusion, cell counts for the gene by cell matrices are as follows: tex14 het shallow, 12260 cells; tex14 ko shallow, 14715 cells; tex14 het deep, 11794 cells; tex14 ko deep, 13982 cells.
Conclusions: Our study represents the first single cell RNA sequencing experiment conducted on fetal mouse ovaries lacking intracellular bridges. We observed that the absence of Tex14 did not alter the transcriptional composition of ovarian somatic cells, but specifically attenuated the level of pluripotency-associated transcripts as germ cells enter meiosis.

middle: J


title: ETS1 ChIP-seq in human monocytic THP-1 cells

city: Kuopio

first: Carsten

last: Carlberg

address: Yliopistonranta 1D

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: ChIP-seq for ETS1 in THP-1 cells after stimulation with the the natural VDR ligand 1,25-dihydroxyvitamin D3 (1,25(OH)2D3)

overall_design: THP-1 cells were treated for 24 h with 100 nM 1,25(OH)2D3 or vehicle before ChIP assay

first: Sabine

last: Seuter

first: Antonio

last: Neme


title: The loss of CARMN regulates vascular smooth muscle cell phenotype and accelerates the development of atherosclerosis in mice.

first: Julie

last: Rodor

summary: We investigated the function of CARMN lncRNA, located immediately upstream of the miRNAs miR-143 and miR-145, as critical regulator of vSMC phenotypes in vitro and the consequence of its loss during the development of atherosclerosis in vivo. We hypothesized that loss of CARMN is a primary event controlling the functional switch towards pro-atherogenic vSMC phenotypes and accelerates the development of the plaques in vivo.

overall_design: RNA sequencing was performed on primary Human Coronary Arterial Smooth Muscle Cells (HCASMCs), under basal (0.2%FBS) or stimulated with PDGF-ββ (20 ng/mL), scratch stimulus or loaded with methyl-β-cyclodextrin (MBCD) (10ng/ml) exposed to either CARMN depletion via GapmeR (GapCARMN) or GapmeR control (GapCTR). Each treatment was done in triplicates.

first: Francesca

last: Vacante

first: Andrew

last: Baker


title: Genome-wide DNA Methylation and Transcriptome Analysis of Non-invasive and Invasive Melanoma Cell Lines

city: Dunedin

first: Jyoti

last: Motwani

state: Otago

address: PO Box 56

department: Department of Pathology

country: New Zealand

institute: University Of Otago

summary:
This SuperSeries is composed of the SubSeries listed below.
Motwani, J., Roger, E. J.,  Stockwell, P.A.,  Baguley, B.C., Macaulay, E.C. , Eccles, M.R. (2020). Integrated transcriptome and DNA methylome analysis of invasive and non-invasive melanoma cell lines identifies widespread coding and long non-coding RNA expression differences, yet comparatively few differences in DNA methylation

overall_design: Refer to individual Series


title: Genome-wide DNA Methylation and Transcriptome Analysis of Non-invasive and Invasive Melanoma Cell Lines (RRBS)

summary: Melanoma is a very aggressive type of skin cancer, which renders it difficult to treat because of extensive heterogeneity frequently observed in melanoma tumours. Here we hypothesized that gene expression and DNA methylation differences would correlate with invasiveness in melanoma cells. To address this question, we carried out genome-wide transcriptome and methylome investigations in non-invasive and invasive groups of melanoma cell lines.

overall_design: We generated methylation profiles of 12 cell lines (10 samples + 2 technical replicates) which included non-invasive cell lines, invasive cell lines and melanocyte cell lines

first: Mike

last: Eccles


title: Genome-wide DNA Methylation and Transcriptome Analysis of Non-invasive and Invasive Melanoma Cell Lines (RNASeq)

overall_design: We generated  gene expression profiles of 12 cell lines which included non-invasive cell lines, invasive cell lines and melanocyte cell lines


title: Transcriptome analysis reveals the contribution of glia -derived cues for maintenance of microglia identity in rhesus macaques

city: Rijswijk

first: Raissa

last: Timmerman

address: Lange Kleiweg 161

department: Alternatives

institute: Biomedical Primate Research Centre

summary: We analyzed the transcriptomes of different primary microglia cultures from adult rhesus macaques, and compared them with those of ex vivo microglia

overall_design: Primary microglia cultured with M-CSF, IL-34, M-CSF + TGFb, IL-34 + TGFb (n=4). Primary microglia cultured with serum + M-CSF, serum (4days) + different serum-free wash out regimes (4, 11 and 18 days), and serum-free medium (22 days) (n=4). Primary microglia cultured with serum + M-CSF, with serum for 4 days and subsequently cultured in serum-free medium for 11 days, and microglia cultured in spheres together with oligodendrocytes and radial glia (n=4). Freshly isolated microglia (ex vivo) (n=4)

first: Jeffrey

last: Bajramovic


title: Integrative analysis of transcriptomic data for the identification of biomarkers associated with T-cell activation in preterm birth

city: Seoul

first: Do Young

last: Hyeon

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

institute: Seoul National University

summary: Preterm birth (PTB), defined as birth at less than 37 weeks of gestation, is a major determinant of neonatal mortality and morbidity. Early diagnosis of the PTB followed by protective treatments is essential to reduce neonatal adverse outcomes. However, due to the redundant nature of clinical conditions with other diseases, PTB-associated clinical parameters are poor predictors of the PTB. It has been thus needed to identify molecular biomarkers with high accuracy in diagnosis of PTB. Here, we performed mRNA sequencing analysis of PTB patients and full-term birth (FTB) controls in Korean population and identified differentially expressed genes (DEGs) between PTB and FTB, as well as cellular pathways represented by the DEGs. By integrating two previous gene expression profiles generated from different ethnic groups, we then identified the core T-cell activation pathway associated with the PTB, which was shared among all previous datasets, and selected the three representative DEGs (CYLD, TFRC, and RIPK2) of the core pathway as biomarker candidates for the PTB. We finally confirmed the dysregulations of the biomarker candidates and the core T-cell activation pathway in an independent cohort. Our results suggest that CYLD, TFRC, and RIPK2 can serve as reliable biomarkers for the PTB.

overall_design: Total RNA expression profiles of 5 full-term birth controls (FTB) and 5 preterm birth patients (PTB) were examined by Illumina NextSeq500.

first: Young

last: Kim

first: Daehee

last: Hwang


title: Short term fasting changes the hepatic miRNAome in  rainbow trout, Oncorhynchus mykiss

city: Houston

first: Kyle

middle: Ryan

last: Navel

state: Texas

address: 2575 W. Bellfort Ave. Ste 270

department: Sales

country: USA

institute: LC Sciences

summary:
Purpose: Next-generation sequencing (NGS) of small RNAs allows transcriptome level analysis of the miRNAome. The goals of this study are to identify differentially regulated hepatic miRNAs in response to a short term fast using small RNA next generation sequencing. Specific quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods were used to validate optimal high-throughput data analysis, and in silico prediction to identify bona fide target pathways regulated by differentially regulated miRNAs following this fasting stressor.
Method: Small RNA sequencing was performed using four randomly selected samples from each treatment group were used for sequencing. The quality of total RNA was confirmed by RNA Integrity Numbers greater than 9.0 using an Agilent Technologies 2100 Bioanalyzer. Nucleotide fractions (15-50) of small RNA were isolated from the total RNA using polyacrylamide gel electrophoresis and were ligated to a 30 adapter followed by a 50 adapter (Illumina, San Diego, CA, USA). The small RNA ligated to the adaptors was reverse transcribed to cDNA, PCR amplified and gel purified. The gel-extracted cDNA was used for library preparation, which was further used for cluster generation on Illumina's Cluster Station before sequencing using Illumina GAIIx. Raw sequence data was obtained from image data using Illumina's Sequencing Control Studio software version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's Real-Time Analysis version 1.8.70 (RTA v1.8.70). The ACGT101-miR v4.2 pipeline (LC Sciences) was used to analyze sequenced data. Sequences with low Q scores, reads mapped to mRNA, RFam, Repbase and piRNA database were deleted and unique families were generated from identical sequences. These filtered unique sequences were then mapped to fish pre-miRNA and miRNA using miRBase or to the rainbow trout genome (Berthelot et al., 2014) to identify conserved miRNA following ACGT-101 User's Manual. Unique or novel miRNAs were identified after the BLAST performed against fish miRNAs from miRbase database (release 21) and published miRNAs from rainbow trout (Mennigen et al., 2016). The miRNAs that do not match any sequences in the specified databases and have the propensity of forming hairpin structure with the extended sequences at the mapped positions were classified as unique miRNAs. These unique miRNAs were further classified into different groups depending on the mappable reads to selected miRNAs in miRbase. Differentially expressed miRNAs were identified using the statistical software R (Version 3.2.2) package DESeq2 for one-way ANOVA comparison of all three treatment groups. Real-time RT–PCR validation was performed using SYBR Green assays
Results: 11 miRNA differentially regulated by fasting. 4 miRNAs are downregulated with fasting. 7 miRNAs are upregulated with fasting.
Conclusions: Our study represents the first detailed analysis of the rainbow trout miRNAome in response to nutritional stimuli. Specifically, we here identify common hepatic miRNAs differentially regulated by refeeding following a short-term fast (2d), as well as miRNAs differentially regulated in the postprandial state depending on the dieatary stimulus (no carbohydrates compared to >20% dietary carbohydrates)

overall_design: Hepatic miRNA profiles of 4-day fasted and control trout were generated by deep sequencing, in three replicates per experimental group, using Illumina GAIIx.

first: D

last: Kostniuk

first: B

last: Culbrt

first: K

last: Gilmur

last: Zhang

first: C

last: Martniuk

first: J

last: Menngen


title: RNA m6A methylome of Caenorhabditis elegans

city: Mexico City

first: David

last: Valle-Garcia

address: Av. Insurgentes Sur 3877, La Fama, Tlalpan

institute: National Institute of Neurology and Neurosurgery

summary: One of the most abundant RNA modifications is N6-methyladenosine (m6A). RNA from all forms of life, including viruses, contain m6A. This modification has been detected in many types of RNAs, such as mRNA, ribosomal RNA, long non-coding RNAs, small nuclear RNAs and microRNAs. Diverse set of proteins have been characterized to methylate, demethylate and specifically bind to this modification in different organisms.     C. elegans is a unique model organism with abundant m6A modification, although its genome does not code for orthologs of the well characterized m6A methyltransferase METTL3/METTL14 complex or the demethylases FTO or ALKBH5. Furthermore, orthologs of the YTH family m6A reader proteins seem to be absent from the worm genome as well.     To gain insights into how this modification is installed in this organism, we set out to identify enzymes that contribute to the abundant level of m6A in C. elegans. We designed a targeted RNAi screen by which the expression of 22 candidate putative RNA methyltransferase genes are knocked down. We measured global RNA methylation level by HPLC-MS/MS analysis after two generations of RNAi-mediated knock down. The knock down of two candidate methyltransferases resulted in a decrease in global m6A level in total RNA. The first methyltransferase, F33A8.4, is an ortholog of the human ZCCHC4 gene. The second methyltransferase, C38D4.9, is an ortholog of the human METTL5 gene.    In order to determine if ZCCHC4 or METTL5 are involved in the deposition of m6A at the mRNA level, m6A-RIP-seq experiments were performed in mRNA derived from WT (N2), ZCCHC4 KO, METTL5 KO and ZCCHC4/METTL5 dKO C. elegans embryos.

overall_design: m6A-RIP-seq of mRNA derived from C elegans embryos

first: Valle-Garcia

last: David

first: Sendinc

last: Erdem

first: Shi

last: Yang