title: Molecular Assessment of Rejection and Injury in Lung Transplant Biopsies

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

summary: Improved understanding of lung transplant disease states is essential because failure rates are high, often due to chronic lung allograft dysfunction. However, histologic assessment of lung transplant transbronchial biopsies (TBBs) is difficult and often uninterpretable even with 10 pieces. All 242 single-piece TBBs produced reliable transcript measurements. Paired TBB pieces available from 12 patients showed significant similarity but also showed some sampling variance. Alveolar content, as estimated by surfactant transcript expression, was a source of sampling variance. To offset sampling variation, for analysis we selected 152 single-piece TBBs with high surfactant transcripts. Unsupervised archetypal analysis identified four idealized phenotypes (archetypes) and scored biopsies for their similarity to each: normal, T cell-mediated rejection (TCMR; T cell transcripts), antibody-mediated rejection (ABMR)-like (endothelial transcripts), and injury (macrophage transcripts). Molecular TCMR correlated with histologic TCMR. The relationship of molecular scores to histologic ABMR could not be assessed because of the paucity of ABMR in this population. Molecular assessment of single-piece TBBs can be used to classify lung transplant biopsies and correlated with rejection histology. Two or three pieces for each TBB will probably be needed to offset sampling variance.

overall_design: We prospectively studied whether microarray assessment of single TBB pieces could identify disease states and reduce the amount of tissue required for diagnosis. Following strategies successful for heart transplants, we used expression of rejection-associated transcripts (annotated in kidney transplant biopsies) in unsupervised machine learning to identify disease states.


title: Monocyte-to-macrophage differentiation is defined by gain and loss of DNA methylation at transcription factor binding sites

status: Public on Aug 17 2019

city: Leiden

first: Koen

last: Dekkers

country: Netherlands

institute: Leiden University Medical Center

summary: Macrophages and their precursors monocytes play a key role in inflammation and chronic inflammatory disorders. Monocyte-to-macrophage differentiation and activation programs are accompanied by significant epigenetic remodeling where DNA methylation associates with cell development and identity. Here we show that confined local gain and loss of DNA methylation at transcription factor binding sites as a key characteristic of macrophage identity. Using the Illumina 450k array with a paired epigenome-wide analysis in combination with public whole-genome sequencing data we found that differential DNA methylation was typically highly localized to single CpGs or very short regions that are enriched for lineage specific enhancers. Furthermore, differentially methylated CpGs were located at sites characterized by increased binding of transcription factors known to be involved in monocyte-to-macrophage differentiation including C/EBP and ETS for gain and AP-1 for loss-of-methylation. Our study highlights subtle, highly localized remodeling of DNA methylation at regulatory regions as key in understanding cell differentiation and, potentially, disease mechanisms.

overall_design: Bisulphite converted DNA from the 24 samples (from 4 donors: monocytes, macrophages, M(LPS+IFNγ), M(IL-4), M(oxLDL), M(acLDL)) were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

middle: F

first: Annette

middle: E

last: Neele

first: J

middle: W

last: Jukema

first: Bastiaan

middle: T

last: Heijmans

first: Menno

middle: P

last: de Winther


title: RNA-seq analysis of spleen and liver tissue from wild-type and SXR/PXR knockout mice exposed to PCB-153 or vehicle

city: Irvine

first: Riann

middle: Jenay

last: Egusquiza

state: CA

address: 4311 Natural Sciences II

country: USA

institute: University of California, Irvine

type: Expression profiling by high throughput sequencing

summary: Purpose: to investigate transcriptomal differences between wild-type and SXR/PXR knockout mice and the impact of PCB-153 exposure to both strains to help reveal the mechanism behind the phenotype of hemolytic anemia observed in SXR knockout mice exposed to PCB-153

overall_design: Wild-type and SXR/PXR knockout mice were exposed to approximately 54µg/kg/day of PCB-153 or vehicle (DMSO) perinatally until 4 weeks of age. Liver and spleen tissues sections were flash frozen then rapidly homogenized in Trizol reagent. Total RNA was isolated by chloroform extraction. RNA-seq libraries were prepared with the Illumina TruSeq stranded mRNA library prep kit. Two separate libraries were made for the liver and spleen samples and sequenced on the HiSeq4000 with 1 library per flow cell lane.

middle: J

first: Bruce

last: Blumberg


title: RNA sequence of CD49f-positive mesenchymal populations in dermis of neonatal mice

status: Public on Aug 16 2019

city: Beijing

first: Zhigang

last: Yang

address: 33 Ba-Da-Chu Rd.

country: China

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: We defined CD49f-high, CD49f-low and CD49f-neg mesenchymal subpopulations in the dermis. Transcriptome analysis revealed that CD49fhigh cells highly express gene regulatory network of neural crest cells, while CD49flow cells were enriched with melanocyte lineage development and maintenance related genes. The identity and function of above cell populations were further verified by lineage tracing.

overall_design: Skin mesenchymal subpopulations with different expression level of CD49f were FACS sorted and sequenced.

first: Ran

last: Xiao


title: lncRNA  expression of in NPC and para carcinoma tissues

city: Guangzhou

first: Wei

last: Zhang

state: Guangdong

address: 651 Dongfeng East Road

institute: Sun Yat-sen University

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

summary: Nasopharyngeal carcinoma is a common epithelial carcinoma with high occurrence and metastatic rates in Southern China. The assessment of the metastatic potential of NPC is vital for determining prognosis and treatment, and more targeted treatments are needed for NPC.To identify  new biomarkers to evaluate metastatic potential of NPC, a comparative genomic expression profiling of NPC tumors and para-carcinoma tissues  were assayed by Arraystar human lncRNA array 2.0

overall_design: We designed this experiment to screen for lncRNAs whose expressions are dyregulated in NPC tissues.

first: Qiannan

last: Guo

first: Weixiong

last: Xia

first: Fang

last: Zheng

first: Jianing

last: Chen

first: Di

last: Huang

first: Linxiaoxiao

last: Ding

first: Xing

first: Yanqun

last: Xiang

first: Herui

last: Yao


title: An integrated molecular diagnostic report for heart transplant biopsies using an ensemble of diagnostic algorithms

first: Jessica

last: Chang

summary: We previously reported a microarray-based diagnostic system for heart transplant endomyocardial biopsies (EMBs), using either 3-archetype (3AA) or 4-archetype (4AA) unsupervised algorithms to estimate rejection. The present study aimed to examine the stability of machine-learning algorithms in new biopsies, compare 3AA vs. 4AA algorithms, assess supervised binary classifiers trained on histologic or molecular diagnoses, create a report combining many scores into an ensemble of estimates, and examine possible automated sign-outs. Algorithms derived in cohort 331 performed similarly in new biopsies despite differences in case mix. In the combined cohort, the 4AA model, including a parenchymal injury score, retained correlations with histologic rejection and DSA similar to the 3AA model. Supervised molecular classifiers predicted molecular rejection (AUCs>0.87) better than histologic rejection (AUCs<0.78), even when trained on histology diagnoses. A report incorporating many AA and binary classifier scores interpreted by one expert showed highly significant agreement with histology (p<0.001), but with many discrepancies as expected from the known noise in histology. An automated random forest score closely predicted expert diagnoses, confirming potential for automated sign-outs.Molecular algorithms are stable in new populations and can be assembled into an ensemble that combines many supervised and unsupervised estimates of the molecular disease states. (ClinicalTrials.gov NCT02670408).

overall_design: We studied 889 EMBs from 454 transplant recipients at eight centers: the initial cohort (N=331) and a new cohort (N=558). Published 3AA algorithms derived in cohort 331 were tested in cohort 558; the 3AA and 4AA models were compared; and supervised binary classifiers were created.


title: Expression profile of select glucose and lipid metabolic genes mediated by STIM1 knockout in SMMC7721 cells

city: Chongqing

first: Huakan

last: Zhao

state: State...

address: Xinqiao Street 183, Shapingba district

department: Clinical Medicine Research Center

institute: Xinqiao Hospital, Third Military Medical University

summary: To investigate the altered glucose and lipid metabolic genes after STIM1 knockout in SMMC7721 cells. STIM1 knockout SMMC7721 cells were constructed by CRISPR/Cas9. The cells mentioned above were cultured in DMEM supplemented with 10% (v/v) FBS at 37°C in 5% CO2. When the cells grow to 60~70% confluent, Total RNA was extracted by using Trizol (TAKARA, Japan). Reverse transcription was performed from 1μg total RNA using PrimeScript™ RT reagent Kit with gDNA Eraser (TAKARA), Quantitative real-time PCR were performed (CFX386, BioRad) with 40 cycles at 95 °C for 10 seconds, 59 °C for 20seconds and 72°C for 30 seconds.

overall_design: In the study presented here, Widetype (WT), STIM1 knockout (STIM1 KO)-SMMC7721 cells were used to acquire expression profiles of a total of 49 unique genes related to glucose and lipid metabolism.

first: Yongsheng

last: Li


title: Microarray of Aspergillus fumigatus wild type and ΔcrpA grown at different zinc concentrations.

status: Public on Aug 15 2019

city: Sungbuk-gu

first: HYEWON

last: SEO

state: Seoul

address: Anam-dong

country: South Korea

institute: Korea university

summary: Gene expression profiling of Aspergillus fumigatus comparing controls grown at normal zinc concentration of aspergillus minimum media (77uM), low (1uM) and high (500uM) zinc concentrations.

overall_design: Three experiment conditions : Zinc 77uM vs. Zinc 1uM. Vs. 500uM, Two strains : wild type vs. ΔcrpA

first: Cheol-Won

last: Yun

first: Hyewon

last: Seo

first: Suzie

last: Kang

first: Yong-Sung

last: Park


title: Silencing ferrochelatase in breast cancer cells MDA-MB-231

city: Berlin

first: Wolfgang

last: Kemmner

state: Berlin

address: Lindenberger Weg 80

department: ECRC

country: Germany

institute: Max-Delbrueck-Center

summary:
Aim was to identify novel targets of protoporphyrin-IX (PpIX) after silencing Ferrochelatase (FECH) enzyme. PpIX is a light sensitive metabolite of heme synthesis. Generation of PpIX is increased if FECH activity is suppressed. Here, silencing of FECH leads to down-regulation of PpIX, measured by a decrease of PpIX-specific fluorescence.
PpIX is a photosensitizer used for photodynamic treatment of various carcinomas. Increasing PpIX leads to apoptosis of tumor cells.

overall_design: Breast cancer cells were treated in four different ways: A) No treatment group; B) No siRNA, only 0.1mM 5-ALA; C) 15nM FECH siRNA + 0.1mM 5-ALA; D) 15nM Allstar control siRNA + 0.1mM 5-ALA.


title: Gene expression profiling using extracted RNA from MLL-AF9/Mn1wt and MLL-AF9/Mn1null cells

city: Hannover

first: Amit

last: Sharma

address: Carl neuberg str-1

department: Hematology

institute: Hannover Medical School

summary: We evaluated the function of Meningioma 1 (MN1), a cofactor of HOXA9 and MEIS1, in murine MLL-r leukemia by CRISPR-Cas9 mediated deletion of MN1. MN1 was required for in vivo leukemogenicity of MLL-r murine and human AML cells. Loss of MN1 inhibited cell cycle and proliferation, promoted apoptosis and induced differentiation of MLL-r cells. Expression analysis and chromatin immunoprecipitation with sequencing demonstrated that MN1 primarily maintains active transcription of HOXA9 and HOXA10, which are critical downstream genes of MLL, and their target genes like BCL2, MCL1 and Survivin.

overall_design: CRISPR-Cas9 mediated deletion of MN1

first: Michael

last: Heuser


title: Human FcγRIIa mediates osteoclastogenesis through a novel noncanonical pathway independent of RANKL and inflammatory cytokines

city: Suzhou

first: Xiao-Ming

last: Gao

address: 199 Ren’ai Road

department: Institute of Biology and Medical Sciences, School of Biology and Basic Medical Sciences,

institute: Soochow University

summary: Under physiological conditions, osteoclasts (OCs) are generated from monocytic osteoprecursors under the stimulation of RANKL and M-CSF, requiring co-stimulatory signals from Fc receptor common γ chain (FcRγ) or DNAX-activated protein 12. It has been proposed that immune complexes (ICs) directly potentiate RANKL-mediated osteoclastogenesis by triggering FcγR-coupled Fcγ receptors (FcγRs), thereby linking IC accumulation and pathological osteolysis under various disease conditions. However, whether ICs possess pro-osteoclastogenic potential independent of RANKL is unknown. Here we demonstrate that IgG ICs alone can drive the differentiation of human blood monocytes into nonclassical OCs (NOCs) phenotypically and functionally distinguishable from RANKL-induced classical OCs (COCs). This novel noncanonical osteoclastogenesis pathway is triggered by full crosslinking of human FcγRIIa (hFcγRIIa), or co-ligation of hFcγRIIa and TLR4, and signals through the Src family kinase-STAT5 axis without inducing the expression of NFATc1, a master transcription factor for the previously described osteoclastogenesis pathways. Surprisingly, IgG ICs strongly overrule the generation of COCs driven by RANKL in vitro. More importantly, TRAP+ OCs found in the inflammatory joint tissues of hFcγRIIa-transgenic mice with collagen-induced arthritis bear the NFATc1- phenotype. Our results unmask the “double faces” of IgG ICs in health and disease, and suggest a novel and important pathway for ICs contributing to pathological bone erosion in inflammatory arthritis.

overall_design: Monocytes were pre-incubated either with cell culture medium (Medium), LFIC (10μg/ml) or cIgG (10 μg/ml) for 24 hrs.After wash-out, cells were harvested and processed into RNA extraction.

first: Qiao

last: Zhong


title: Heme metabolism confronts urinary pathogens at the urothelium

city: New York

first: Atlas

last: Khan

state: NY

address: 1150 St Nicholas Ave, 408B

institute: Columbia University

summary: The kidney and bladder expresses a variety of powerful defense mechanisms to limit urinary infection including iron scavenging, a process called "nutritional immunity". We previously demonstrated that bladder and kidney epithelia generates the archetype of the urinary iron defense, a lipocalin called NGAL which binds Enterochelin, a bacterial siderophore. However, because urinary bacteria can evade the bacteriostatic effects of NGAL by modifying Enterochelin and by producing additional siderophores, other mechanisms of "nutritional immunity" are anticipated. To study the defense in the kidney, we used a cell type specific method of RNA isolation in mouse (adapted from Gay et al, Oregon). A promiscuous form of phosphoribosyltransferase (UPRT) was cloned into the Rosa26 locus using a floxed-stop design which we activated in a cell specific fashion with Atp6v1b1-Cre. Thiouracil was introduced 12hr and 24hrs after urinary tract infection. Isolation of RNA directly from intercalated revealed synthetic (Npas1-Bmal1-Alas), transport (Hrg1, Flvcr1) and metabolic enzymes (Hmox1) of heme metabolism. Hmox1 was detected in the kidney with a luciferase based reporter (Contag et al, Stanford) after infection. CO production was detected in vivo and in AtpCre-mTmG FACS isolated intercalated cells in vitro using a novel metal-based probe synthesized at Columbia (adapted from Liu et al, China). Urinary bacteria (UPEC) with heme transport mutations were not competitive in the colonization of the kidney but conversely were markedly stimulated by iron, suggesting bacterial-host competition for heme capture and metabolism. In fact, infection upregulated both heme synthetic and metabolic genes, suggesting that CO production is induced by infection. Exposure to CO terminated the growth of UPEC. In sum, we have identified an unusual iron trafficking system in the collecting ducts that mirrors the nutritional requirements of UPEC to achieve pyelonephritis. Many of these components are specific to the intercalated cells, consistent with the notion that these cells defend the urinary tract from infection.

overall_design: Examining cell-specific transcriptional profile of urinary tract infection (UTI) mouse model, compared to controls, in kidney intercalated cells using thio-uracil RNA labeling technique

first: Katherine

last: Xu

first: Tian

middle: H

last: Shen

first: Nicholas

last: Tatonetti

first: Krzysztof

last: Kiryluk

first: Jonathan

last: Barasch


title: BCL6 confers KRAS-mutant NSCLCs resistance to BET inhibitors

first: Lingyun

last: Zheng

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

summary: We report that OTX015 upregulates BCL6 in KRAS-mutant NSCLC cells. Considering that both BCL6 and BET proteins regulate target genes by affecting transcription, we performed an RNA-seq experiment to identify downstream genes which response to OTX015. Retinal mRNA profiles of A549 cells treated with DMSO (0.1% for 6 hr) and OTX015 (1 μM for 6 hr) were generated by deep sequencing, in triplicate, using the SOLiD v4 sequencing platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows-Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT-PCR validation was performed using TaqMan and SYBR Green assays.

overall_design: Retinal mRNA profiles of A549 treated with 1μM OTX015 for 6 hr or not were generated by deep sequencing, in triplicate, using the Illumina HiSeq 2500 sequencing platform.


title: Transcriptomic analysis of IPF lung-associated and normal peripheral blood T cells

city: Los Angeles

first: David

last: Habiel

address: 8700 Beverly Blvd

institute: Cedars-Sinai Medical Center

summary: Lung explant derived T cells were sorted from mechanically dissociated IPF lung explants and compared to CD4+ T cells magnetically sorted from the peripheral blood of normal donors.

overall_design: Each sample was sequenced in triplicates, n=3 IPF and n=3 normal.

middle: M

first: Cory

last: Hogaboam


title: Elevated H3K27ac in aged skeletal muscle tissue drives a fibrogenic conversion of muscle satellite cells

first: Jiajian

last: Zhou

address: No. 2 Lujing Road, Yuexiu District,

department: Dermatology Hospital

institute: Southern Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: A variety of epigenetic alterations impairs functions of cells and tissues during aging, but it is not known if epigenetic alterations are associated with aging muscle. Here, we examined the changes of a panel of histone marks and found H3K27ac (an active enhancer mark) is markedly increased during aging in human skeletal muscle tissues. Our integrated analysis showed that enhancer activation during muscle aging is associated with the up-regulation of extracelluar matrix (ECM) genes, which may result in stiffness of the niche environment of satellite cells (SCs). An age-related fibrogenic conversion of geriatric SCs was observed through differential gene expression analysis. In mice, treatment of aging muscles with JQ1, an inhibitor of enhancer activation reverted the ECM up-regulation and fibrogenic conversion of SCs, suggesting that ECM increase in aging muscle is indeed a result of enhancer activation. The study here not only uncovered a novel aspect of muscle aging that is associated with enhancer remodeling but also highlighted JQ1 as a potential treatment approach for restoring SC function in aging muscle.

overall_design: 3 ChIP-seq experiments were performed

first: Huating

last: Wang

first: Hao

last: Sun

first: Karl

middle: K

last: So


title: LSD1 maintains mammary luminal cell differentiation and suppresses luminal breast cancer cell invasion

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

summary: LSD1 (KDM1A) is a histone demethylase that plays both oncogenic and tumor suppressor roles in breast cancer. However, the exact contexts under which it plays these opposite roles remain largely elusive. By characterizing its role in normal and cancerous luminal mammary epithelial cells (MECs), here we show that LSD1 is essential for maintaining differentiation and survival of luminal cells. LSD1-inhibition by both genetic and pharmacological approaches increases invasion of luminal breast cancer cells. Mechanistically, we find LSD1 interacts with GATA3 and their common target genes are highly related to breast cancer. LSD1 positively regulates GATA3 expression and represses that of TRIM37, a histone H2A ubiquitin ligase and breast cancer oncoprotein. LSD1-loss leads to reduced expression of several cell junction genes (e.g., CDH1, VCL, CTNNA1), possibly via TRIM37-mediated repression. Collectively, our data suggest LSD1 largely plays a tumor suppressor role in luminal breast cancer and the increased MEC invasiveness associated with LSD1-inhibition can be blocked via TRIM37-inhibition.

overall_design: Total RNA obtained from MCF7 cells treated with either LSD1 siRNA, or GATA3 siRNA, or ESR1 siRNA compared to that from MCF7 cells treated with nonspecific control siRNA.

first: Xin

last: Hu


title: Tumor intrinsic PRMT5 inhibition through MTAP loss predicts response to the first-in-class type I PRMT inhibitor, GSK3368715

city: Collegeville

first: Satyajit

last: Rajapurkar

state: PA

address: 1250S. Collegeville Rd.

institute: GlaxoSmithKline LLC

summary: Type I Protein Arginine Methyltransferases (PRMTs) catalyze asymmetric dimethylation of arginine (ADMA) residues on numerous protein substrates to modulate their activity. Type I PRMTs and many of their substrates have been implicated in human cancers, suggesting that inhibiting Type I PRMT activity offers a tractable approach for therapeutic intervention. The current report describes GSK3368715 (EPZ019997), a potent, reversible Type I PRMT inhibitor with anti-tumor activity against human cancer cells both in vitro and in vivo. GSK3368715 reduces ADMA on numerous substrates and concomitantly increases monomethyl (MMA) and symmetric dimethyl arginine (SDMA) levels. Inhibition of PRMT5, the major type II PRMT, attenuates this induction and produces synergistic antiproliferative effects in combination with GSK3368715 in cancer cells. PRMT5 activity is inhibited by 2-methylthioadenosine (MTA), a naturally occurring metabolite that accumulates in tumor cells deficient for the enzyme Methylthioadenosine Phosphorylase (MTAP). MTAP deletion in cancer cell lines correlates with sensitivity to GSK3368715, indicating a sufficient degree of PRMT5 inhibition from MTA accumulation to achieve a tumor cell-intrinsic combination. These data provide the rationale to explore MTAP status as a biomarker strategy for patient selection to maximize the anti-tumor activity of GSK3368715.

overall_design: Paired-end sequenced RNA-seq data from 5 pancreatic cancer cell lines. HuPT4, BxPC3, Capan-2, PANC08.13 have been sequenced with 2 replicates, containing GSK3368712 (treated) and control (DMSO) samples. PANC03.27 has isogenic MTAP CRISPR knockout and parental samples with 2 replicates, each containing GSK3203591, GSK3368712 and a combination of the two (Combo) treatments.

first: Andy

last: Fedoriw


title: MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Müller glia in mice

status: Public on Aug 14 2019

city: Seattle

first: Thomas

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structure

institute: University of Washington

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

overall_design: Refer to individual Series


title: Gene expression profiling in patients with a kidney transplantation

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

summary: Microarrays were used to analyze the gene expression in peripheral blood and kidney allograft biopsies from patients with a kidney transplantation to get more insight in the molecular mechanisms underlying the different clinical phenotypes of kidney transplant rejection.

overall_design: 117 peripheral blood samples and 95 kidney allograft biopsies were used for genome-wide gene expression analysis. The updated Banff 2017 classification was used for diagnosis of the samples. Total RNA extracted from blood and biopsies was used to analyze mRNA expression via Affymetrix Human U133 Plus 2.0 arrays.

first: Elisabet

last: Van Loon

first: Stéphane

last: Gazut

first: Saleh

last: Yazdani

first: Evelyne

last: Lerut

first: Henriette

last: de Loor

last: Coemans

first: Laure-helene

last: Noel

first: Lieven

last: Thorrez

first: Leentje

last: Van Lommel

first: Frans

last: Schuit

first: Ben

last: Sprangers

first: Dirk

last: Kuypers

first: Marie

last: Essig

first: Wilfried

last: Gwinner

first: Dany

last: Anglicheau

first: Pierre

last: Marquet


title: Genome-Wide Transcriptome Analysis Reveals Degeneration Progress of Subculture Cordyceps Militaris

city: Zhenjiang

first: Juan

last: YIN

address: Sibaidu Street, Runzhou District, Zhenjiang City, Jiangsu Province

department: School of Biotechnology

institute: Jiangsu University of Science and Technology

summary: The high frequency strain degeneration during subculture seriously restrict the large-scale production of Cordyceps militaris and industrialized process. In the current study, the high-throughput Illumina sequencing was performed on 6 passages subculture C. militaris strains to obtain the divergence of transciptomes in degeneration progress. Then various statistical comparison analysis was further conducted based on the HQ reads to better understand their difference. Over 9015 unigenes and 731 new genes were formed by initial sequence splicing and showed a perfect coverage;3737 ends in 3695 genes were optimized, 2010 at 5’ end (1847 genes ≥ 50 bps) and 1727 at 3’ end (1485 genes ≥ 50 bps); 134783 variants including 126923 SNP variants and 7860 InDelvariants were detected;more than 11304 RNA editing events occurred in total, which yielded 2950 nonsynonymous SNV, 6 stoploss, 5 stopgain and 8343 synonymous SNV; Compared with the first passage strain, the third passage strain exhibited 2498 differentially expressed genes (DEGs) including 1729 up-regulated genes and 769 down-regulated genes, which was higher than other samples. Seventeen enriched gene ontology (GO) terms were identified by GO enrichment analysis and twenty seven enriched pathways were identified by KEGG enrichment analysis, which might be mainly associated with the processing of degeneration. The findings revealed the DEGs involved into the degeneration progress of C. militaris and yielded insights into molecular mechanism of degeneration, which provide the reference for efficiently and artificially producing C. militaris.

overall_design: To obtain the divergence of tranisciptomes in degeneration progress of Cordyceps militaris

last: Yin

first: Zhongzheng

last: Gui


title: MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Müller glia in mice [NanoString]

first: Thomas

last: Reh

summary:
In order to identify the miRNAs in postnatal day 2 (P2) retinal progenitor cells (RPCs), and P8, P11, and adult Müller glia (MG) of the neural retina, we isolated the retinal progenitors from Sox2-CreER: Stopf/f-tdTomato and MG from Rlbp-CreER: Stopf/f-tdTomato mice by means of fluorescent activated cell sorting and analyzed their miRNAs using NanoStrings Technologies®.
We next compared miRNA expression of RPCs with MG. We found that most specific miRNAs decline with glial maturation (RPC miRNAs) while others increase (MG miRNAs). Overexpression of miRNA-25 found in RPCs and inhibition of MG miRNA let-7 can induce a neurogenic potential in MG and initiates a de novo differentiation toward neuronal fates.

overall_design: We used fluorescence activated cell sorting (FACS) to purify adult RPCs (pooled from 8 retina) and MG (P8, P11 and adult, pooled from 52, 32 and 40 retinas respectively), using an RPC and MG specific cre-lox labeling strategy by crossing Sox2-CreER or Rlbp-CreER mice with stopf/f-tdTomato mice. The RNA was extracted from purified MG. The miRNA expression of P2 RPCs and P8, P11 and adult MG were analyzed using NanoStrings® and nCounter Technologies ®.

first: Stefanie

middle: G

last: Wohl

first: Marcus

last: Hooper

middle: A


title: MicroRNAs miR-25, let-7 and miR-124 regulate the neurogenic potential of Müller glia in mice [RNA-Seq]

summary: Müller glial cells (MG) generate retinal progenitor (RPC)-like cells after injury in non-mammalian species, though this does not occur in the mammalian retina. Studies have profiled gene expression in these cells to define genes that may be relevant to their differences in neurogenic potential. However, less is known about differences in micro-RNA (miRNA) expression. In this study, we compared miRNAs from RPCs and MG to identify miRNAs more highly expressed in RPCs, and others more highly expressed in MG. To determine whether these miRNAs are relevant to the difference in neurogenic potential between these two cell types, we tested them in dissociated cultures of MG using either mimics or antagomiRs to increase or reduce expression, respectively. Among the miRNAs tested, miR-25 and miR-124 over-expression, or let-7 antagonism, induced Ascl1 expression and conversion of approximately 40% of mature MG into a neuronal/RPC phenotype. Our results suggest that the differences in miRNA expression between MG and RPCs contribute to their difference in neurogenic potential and that manipulations in miRNAs provide a new tool to reprogram MG for retinal regeneration.

overall_design: Identification of Muller glia-specific and retinal progenitor cell-specific miRNAs. ScRNA sequencing was performed to examine the effects of let7 antagonism, miR-25, miR-124 and the combination of these on Muller glial gene expression and cell fate.


title: Growth Differentiation Factor 11 exacerbates non-alcoholic fatty liver disease in vitro and in vivo

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

summary: Growth differentiation factor 11 (GDF11), also known as bone morphogenetic protein 11 (BMP11) is a member of the Growth differentiation factors (GDFs), a subfamily of proteins belonging to the transforming growth factor-beta (TGF-β) superfamily (Katoh and Katoh 2006).  ). In the past 7-8 years, several high profile studies, showed that systemic restoration of GDF11 levels reverses age-related phenotypes and rejuvenated heart and skeletal muscle in aged mice (Loffredo, Steinhauser et al. 2013, Sinha, Jang et al. 2014), improves insulin sensitivity via restoring pancreatic β-cell function in diabetic mice (Li, Li et al. 2017), and increases proliferation of brain capillary endothelial cells thereby improving the vascular and neurogenic rejuvenation in the brain of aged mice (Katsimpardi, Litterman et al. 2014, Finkenzeller, Stark et al. 2015, Zhang, Guo et al. 2018). Nonetheless, the possible rejuvenation effect of GDF11 was questioned over past years by several other studies. These reports doubted the age-associated decrease of circulating GDF11 level and related phenotypes in the muscle, the heart and the brain (Egerman, Cadena et al. 2015, Rodgers and Eldridge 2015); moreover, restoration of GDF11 levels in old mice had no positive effect on heart structure or function (Smith, Zhang et al. 2015). Increase of GDF11 levels had deleterious effects on aging skeletal muscle regeneration (Egerman, Cadena et al. 2015), suggesting also that supraphysiological levels could lead to cachexia (Hammers, Merscham-Banda et al. 2017).   In the field of liver diseases, GDF11 was shown to exhibit tumor suppressive properties in HCC cells (Zhang, Pan et al. 2018, Gerardo-Ramírez, Lazzarini-Lechuga et al. 2019) and to worsen hepatocellular injury and liver regeneration after liver ischemia reperfusion injury (Liu, Dong et al. 2018). From these controverted studies, it is clear that the systemic effects of GDF11 in health and disease are not yet clearly and fully delineated.   The aim of the present study was to specifically characterize the role of GDF11 in lipid metabolism and in the progression of the NAFLD disease spectrum, which is currently unknown. We thus aimed at investigating the potential effect of GDF11 on lipid droplet formation in human hepatocytes.  Our data strongly suggest that GDF11 supplementation exacerbates, both in presence or absence of FFA, lipid droplet accumulation in two hepatic cell models (HepG2 and Hep3B) by impinging on ALK5/SMAD2/3 dependent signaling pathway.

overall_design: Profiling the transcriptome of hepatocellular carcinoma cells HepG2 treated with GDF11 (24h, 200 nM) for macroH2A1 using RNA-Seq.

first: Manlio

last: Vinciguerra


title: Comparison of microbial communities between conventional MBR system and biofilm MBR system

city: muang

first: Dome

last: Adoonsook

state: ChiangMai

address: Suthep

country: Thailand

institute: Dome

summary: We reported the microbial communities in wastewater between conventional membrane bioreactor (MBR) system and biofilm MBR system using Illumina sequencing.

overall_design: Examination of 2 different types of reactors.

first: A

last: Dome

first: W

last: Aunnop


title: Large-scale serum microRNA profiling for developing an esophageal squamous cell carcinoma detection model

status: Public on Aug 21 2019

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

summary: A serum miRNA combination could be a powerful classifier for the detection of esophageal squamous cell carcinoma.

overall_design: Serum microRNA profiles of 5531 samples, which consist of 566 of esophageal squamous cell carcinoma and 4965 of non-cancer controls.

first: Kazuki

last: Sudo

first: Ken

last: Kato

first: Juntaro

last: Matsuzaki

first: Narikazu

last: Boku

first: Seiichiro

last: Abe

first: Yutaka

last: Saito

first: Hiroyuki

last: Daiko

first: Satoko

last: Takizawa

first: Yoshiaki

last: Aoki

first: Hiromi

last: Sakamoto

first: Shumpei

last: Niida

first: Fumitaka

last: Takeshita

first: Takahiro

last: Fukuda

last: Ochiya


title: Genome-wide DNA methylation analysis of cervical scrapes samples

city: Henan

first: wang

middle: rui

last: jie

state: zhengzhou

address: No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, Henan, China

institute: The Third Affiliated Hospital of Zhengzhou University, Zhengzhou University

summary: Genome-wide DNA methylation profiles in liquid based cytology (LBC) cervical scrapes samples was assessed using the Illumina Infinium Methylation850 BeadChip V1.0B4. The purpose of this study was to  identify new candidate genes that are differentially methylated in squamous cell carcinoma compared to the DNA samples from cervical intraepithelial neoplasia grade (CIN) and normal cervical scrapes.

overall_design: In this study 3 normal cervical samples (HPV negative), 4 samples with CIN lesions (HPV16 positive) and 3 cervical cancer samples (HPV16 positive) were included.

first: RuiJie

last: Wang

first: Ya

last: Li

first: PeiPei

last: Du

first: XiaoAn

last: Zhang

first: XiaoFu

first: GuoMei

last: Cheng


title: Single-cell analysis reveals fibroblast heterogeneity and myofibroblasts in systemic sclerosis-associated interstitial lung disease

city: Pittsburgh

first: Tracy

last: Tabib

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

summary: Myofibroblasts are key effector cells in the extracellular matrix remodeling of systemic sclerosis-associated interstitial lung disease (SSc-ILD), however the diversity of fibroblast populations present in the healthy and SSc-ILD lung is unknown, and has prevented the specific study of the myofibroblast transcriptome.   We sought to identify and define the transcriptomes of myofibroblasts and other mesenchymal cell populations in human healthy and SSc-ILD lungs to understand how alterations in fibroblast phenotypes lead to SSc-ILD fibrosis.

overall_design:
We performed droplet-based single-cell RNA-sequencing with integrated canonical correlation analysis of 13 explanted lung tissue specimens (56,196 cells) from 4 healthy control and 4 SSc-ILD patients, with findings confirmed by cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) in additional samples.

Please note that the control samples (GSM3660644-GSM3660648 in GSE128033) were re-used in the current study (as indicated in the GSM3666096-GSM3666100 sample titles).

***The GEO records contain only processed data (raw counts in sparse matrix format) as raw data is unavailable due to patient privacy concerns.

first: Eleanor

last: Valenzi

first: Melissa

last: Bulik

first: Christina

last: Morse

first: John

last: Sembrat

first: Humberto

last: Trejo Bittar

first: Mauricio

last: Rojas

first: Robert

last: Lafyatis


title: Genome-wide profiling of differentially spliced mRNA resulting from prenatal alcohol exposure in human cerebral cortex

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

summary: Report of alternative splicing events altered by alcohol exposure in human fetal ceebral cortex in late first trimester.

overall_design: Deep sequencing of RNAs extracted from human fetal cortical slices cultured in medium containing 50mM ethanol (sample names: E1, E2) or control medium (sample names: C1, C2) for 24 hours.

first: Shahid

last: Mohammad

first: Alexander

last: Son

first: Aiesha

last: Basha

first: Anna

middle: C

last: Salzberg

first: Masaaki

last: Torii

first: Kazue

last: Hashimoto-Torii


title: Germline NPM1 mutations lead to altered rRNA 2’-O-methylation and cause dyskeratosis congenita (microarray)

status: Public on Aug 13 2019

first: Jonathan

middle: David

last: Lee

address: 3 Blackfan Circle, Rm. 424

institute: BIDMC

summary: We identify nucleophosmin (NPM1) as an essential regulator of 2’-O-methylation on rRNA by directly binding C/D box small nucleolar RNAs (snoRNAs), thereby modulating translation. We demonstrate the importance of 2’-O-Me regulated translation for cellular growth, differentiation and hematopoietic stem cells (HSC) maintenance, and show that Npm1-inactivation in adult HSCs results in bone marrow failure (BMF). We identify NPM1 germline mutations in DC patients presenting with BMF; and demonstrate that they are deficient in snoRNA binding. CRISPR knock-in mice harboring the DC germline NPM1 mutation recapitulate both hematological and non-hematological features of DC. Thus, our findings provide a direct demonstration of the role of 2’-O-Me in the pathogenesis of human disease

overall_design: Microarray analysis of ribosome-bound RNAs (by sucrose gradient ribosome fractionation) was performed to analyze translational program skewing and impermanent due to Npm1 deletion.

first: Daphna

last: Nachmani

middle: D

first: Pier

last: Pandolfi


title: Gene expression profiles of 4-1BB+PD-1-high, 4-1BB-PD-1-high, and PD-1-int tumor-infiltrating CD8 T cells in hepatocellular carcinoma

city: Daejeon

first: Su-Hyung

last: Park

address: 291 Daehak-ro

institute: Korea Advanced Institute of Science and Technology

summary: We report the gene expression profiles of FACS-sorted 4-1BB+PD-1-high, 4-1BB-PD-1-high, and PD-1-int tumor-infiltrating CD8 T cells in hepatocellular carcinoma.

overall_design: Examination of gene expression profiles in 3 distinct subpopulations of tumor-infiltrating CD8 T cells in hepatocellular carcinoma.


title: Spermidine promote the sucrose content in inferior grain and by this improve the grain filling in inferior grain of wheat

city: 咸阳

first: Jian

last: Luo

address: 西北农林科技大学

institute: 西北农林科技大学

summary: Exogenous spermidine promotes starch sugar metabolism in wheat grains, thereby promoting grain filling

overall_design: Analysis of the role of spermidine in grain filling from the perspective of endogenous and exogenous sources

first: Bin

last: Wei


title: A Structural Motif for mRNA Target Recognition by a tRNA Pseudouridine Synthase

city: Cambridge

first: Thomas

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: MIT

summary: We used an in vitro pool based strategy to probe the sequence and structural requirements for mRNA target recognition by the yeast tRNA pseudouridine synthase Pus1.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

platform_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: RNA in vitro transcribed from synthetic oligo pools was pseudouridylated with a source of Pus1 activity. Pseudouridylation was measured using Pseudo-seq, a seqeuncing based technique for identifying Ψs (Carlile et al. Nature 2014).

first: Wendy

middle: V

last: Gilbert


title: Germline NPM1 mutations lead to altered rRNA 2’-O-methylation and cause dyskeratosis congenita

type:
Expression profiling by array
Other


title: 3' Tag RNA-seq analysis of wild type (S. pimpinellifolium accession LA1589) and SUN NIL during tomato fruit development.

city: Athens

first: Biyao

last: Zhang

state: GA

address: CAGT, Rm120, 111 Riverbend RD

department: Horticulture

institute: University of Georgia

summary: This study is to decipher the effect of SUN overexpressed NIL on gene expression during fruit development in tomato. RNA libraries were sequenced through Illumina Nextseq500 at Georgia Genomics and Bioinformatics Core (GGBC) of University of Georgia for 75 bp single end sequencing.  Clean reads were mapped to ITAG3.2. Processed data are normalized into TPM.

overall_design: mRNA profile of three dissected tissues (pericarp, seeds and columella) of 2, 4, 6, 8, 10dpa fruits in wildtype and SUN overexpressed NIL

first: Esther

last: van der Knaap


title: Gene expression profiles of tumor-infiltrating CD8 T cells in hepatocellular carcinoma

summary: We report the gene expression profiles of MACS-sorted tumor-infiltrating CD8 T cells in hepatocellular carcinoma.

overall_design: Examination of gene expression profiles of tumor-infiltrating CD8 T cells in hepatocellular carcinoma.


title: Germline NPM1 mutations lead to altered rRNA 2’-O-methylation and cause dyskeratosis congenita (HITS-CLIP)

overall_design: HITS-CLIP analysis to determine that RNA molecules bound by NPM1 was perform using Trp53-/- and Trp53-/-;Npm1-/- mouse embryonic cells.

first: Anne

last: Bothmer


title: Differential mRNA expression upon 9p21 deletion in HEK TE single-cell derived clones

first: Peihua

last: Zhao

summary: RNA sequencing was performed to identify mRNAs that are dysregulated upon loss of 9p21. Subsequently, the effect on cell transformation was investigated upon knockdown/overexpression of the candidate targets found from the RNA sequencing analysis .

overall_design: HEK TE single-cell derived clones wt or harbouring 9p21 deletion were analyzed for gene expression.

first: Maria

middle: F

last: Baietti

last: Sablina


title: Absence of NKG2D ligands defines human leukaemia stem cells and mediates their immune evasion

city: Amsterdam

first: Mattia

last: Falcone

address: Plesmanlaan 121

department: Oncogenomics

institute: NKI

summary: Patients with acute myeloid leukaemia (AML) often achieve remission yet subsequently die of disease relapse, which is commonly driven by chemotherapy-resistant  leukaemic stem cells (LSCs). LSCs are defined by their capacity to initiate leukaemia in immuno-compromised mice. This precludes an analysis of their interaction with lymphocytes as components of anti-tumour immunity, which LSCs must escape in order to induce cancer7. Here we propose that stemness and immune evasion are closely intertwined in human AML. Using human AML xenograft and syngeneic mouse leukemia models, we show that ligands of the danger detector NKG2D, a critical mediator of anti-tumour immunity by cytotoxic lymphocytes such as natural killer (NK) cells, are generally expressed on bulk AML cells but not on LSCs. Functional LSCs can be isolated by their lack of NKG2D ligand (NKG2DL) expression, even in human AMLs not expressing the conventional LSC marker CD34. NKG2DL expressing AML cells are cleared by NK cells while NKG2DLneg leukaemic cells isolated from the same individuals escape NK cell killing. These NKG2DLneg AML cells show an immature morphology, display molecular and functional stemness characteristics, can initiate serially re-transplantable leukaemia and survive chemotherapy in patient-derived xenotransplants (PDX). Mechanistically, poly-ADP-ribose polymerase 1 (PARP1) negatively regulates NKG2DL and PARP1 inhibition (PARPi) induces NKG2DL surface expression in LSCs. Consequently, co-treatment with PARPi and NK cells suppresses leukaemogenesis in PDX models. Low expression of surface NKG2DL as well as high PARP1 expression are associated with inferior clinical outcome in patients with AML. In summary, our data link the concept of LSCs to immune escape and indicate absence of immunostimulatory NKG2DL as a novel method to identify LSCs across genetic AML subtypes. Moreover, we provide a strong rationale for targeting therapy resistant LSCs by PARP1 inhibition rendering them amenable to NK cell control in vivo.

overall_design: Bone marrow samples of 5 AML patients without CD34-expression were separated by FACS according to NKG2DL-expression and subjected to RNA-Sequencing

first: Simon

last: Raffel

first: Andreas

last: Trumpp


title: 499 GRKO vs WT Single Cell Seq

city: Philadelphia

first: Lexus

last: Johnson

state: Pennsylvania

address: 421 Curie Blvd, 532

department: Radiation Oncology

institute: University of Pennsylvania

summary: Interferon-gamma (IFNG) augments immune function yet promotes T cell exhaustion through PDL1. How these opposing effects are integrated to impact immune checkpoint blockade (ICB) is unclear. We show that while inhibiting tumor IFNG signaling decreases interferon-stimulated genes (ISGs) in cancer cells, it increases ISGs in immune cells by enhancing IFNG produced by exhausted T cells (TEX). In tumors with favorable antigenicity, these TEX mediate rejection. In tumors with neoantigen or MHC-I loss, TEX instead utilize IFNG to drive maturation of innate immune cells, including a PD1+TRAIL+ ILC1 population. By disabling an inhibitory circuit impacting PD1 and TRAIL, blocking tumor IFNG signaling promotes innate immune killing. Thus, interferon signaling in cancer cells and immune cells oppose each other to establish a regulatory relationship that limits both adaptive and innate immune killing. In melanoma and lung cancer patients, perturbation of this relationship is associated with ICB response independent of mutational burden.

overall_design: Immune cells were profiled using single cell RNA sequencing from WT and IFNgR KO 499 tumors

first: Andy

last: Minn


title: B16 vs Res499 Whole Exome Sequencing

summary: Interferon-gamma (IFNG) augments immune function yet promotes T cell exhaustion through PDL1. How these opposing effects are integrated to impact immune checkpoint blockade (ICB) is unclear. We show that while inhibiting tumor IFNG signaling decreases interferon-stimulated genes (ISGs) in cancer cells, it increases ISGs in immune cells by enhancing IFNG produced by exhausted T cells (TEX). In tumors with favorable antigenicity, these TEX mediate rejection. In tumors with neoantigen or MHC-I loss, TEX instead utilize IFNG to drive maturation of innate immune cells, including a PD1+TRAIL+ ILC1 population. By disabling an inhibitory circuit impacting PD1 and TRAIL, blocking tumor IFNG signaling promotes innate immune killing. Thus, interferon signaling in cancer cells and immune cells oppose each other to establish a regulatory relationship that limits both adaptive and innate immune killing. In melanoma and lung cancer patients, perturbation of this relationship is associated with ICB response independent of tumor mutational burden.

overall_design: 2 replicate samples of B16, 3 replicate samples of Res499. All samples from in vivo tumors, tumor cells sorted by FACS and processed for sequencing.

first: Lex


title: Postnatal lipids drive hepatocyte maturation

city: Jerusalem

first: Avner

last: Ehrlich

address: Silberman 3-512, Edmond J. Safra Campus (Givat Ram)

department: Bioengineering

country: Israel

institute: The Hebrew University of Jerusalem

summary: Rodent lipid metabolism and postnatal nutrition is fundamentally different from humans. Therefore, we used embryonic stem cells (hESC) to model hepatic development in human. Pluripotent stem cells reliably produce hepatocytes with neonatal characteristics5. Postpartum was mimicked by the removal of oncostatin M (OSM), lost due to the migration of hematopoietic cells to the bone marrow after birth, and the concomitant addition of oleic acid (OA) and linoleic acid (LA), major components of breast milk.

overall_design: 2 or 3 (9CLA only) Biological repeats (samples) were sequenced, including undifferentiated cells (mTeSR), control (BSA), lipid-only (OA+LA) and in vivo references - fetal human hepatocytes (FHH) and primary human hepatocytes (PHH)

first: Yaakov

last: Nahmias

first: Muneef

last: Ayyash

first: Michal

last: Zimerman

first: Robert

last: Schwartz

first: Matan

last: Hofree


title: Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade

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

overall_design: Refer to individual Series


title: Cancerous inhibitor of PP2A (CIP2A) Constrains Th17 Differentiation by Modulating STAT3 Signaling

city: Turku

first: Ubaid Ullah

last: Sheikh

state: Turku

address: Tykistökatu

department: Turku Centre for Biotechnology

country: Finland

institute: University of Turku

summary: Genome-wide RNA seq data profile gene expression in human CIP2A silenced Th17 cells

overall_design: RNA seq data from 24h polarised human Th17 cells with non-targeting(NT) siRNA and CIP2A targeting siRNA.

first: Mohd

last: Khan

first: Ubaid

last: Ullah

first: Lingjia

last: Kong

last: Moulder

first: Santosh

last: Bhosale

first: Meraj

first: Omid

last: Rasool

first: Zhi

last: Chen

first: Jukka

last: Westermarck

first: Riitta

last: Lahesmaa


title: Characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare)

status: Public on Aug 12 2019

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

type: Methylation profiling by high throughput sequencing

summary: Whole-genome DNA cytosine methylation profiling was used to characterize a knock-down RNA interference line of rice OsNRPD1

overall_design: SRA bioproject PRJNA535389. Genome-wide DNA cytosine methylation profiling of wildtype and OsNRPD1 RNAi plants.

first: Eric

last: Lasserre

first: Pao-Yang

first: Tzuu-fen

last: Lee


title: Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: RNAseq of samples to identify changes in gene expression upon SRSF2 mutation

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Three biological replicates of primary mouse leukemia cells were harvested for RNAseq preparation.

first: Ernesto

last: Guccione


title: RNA-seq data from adult zebrafish caudal fin regeneration

city: LYON

first: Pauline

last: NAUROY

address: 46 Allée d'Italie

department: Institute of Functional Genomics of Lyon

country: France

institute: CNRS - ENS of Lyon

summary: Adult zebrafish are able to regenerate many organs such as their caudal fin in only few days post amputation. To explore the landscape and dynamic of the genes involed in regeneration, we performed a global transcriptomic analysis using RNA-seq during zebrafish caudal fin regeneration.

overall_design: RNAs were extracetd from a pool of 6 adult zebrafish caudal fins before amputation and at 2, 3 and 10 days post amputation. Experiment was performed in triplicates. The experimental design results in a total of 12 samples.

last: Nauroy

first: Benjamin

last: Gillet

first: Sandrine

last: Hughes

first: Florence

last: Ruggiero


title: Spop restrains inflammation-induced emergency hematopoiesis by targeting MyD88 [scRNA-Seq]

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

summary: Examination of the single cell trasncriptional profile of bone marrow sorted LSK 10 days post Poly(I:C) challenge

overall_design: Single-cell RNA-seq libraries of sorted LSK

first: Maria

last: Guillamot

first: Iannis

last: Aifantis


title: Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson’s disease

city: Grand Rapids

first: Sonia

last: George

state: MI

address: 333 Bostwick Ave

institute: Van Andel Research Institute

summary:
Background: Cell-to-cell propagation of α-synuclein (α-syn) aggregates is thought to contribute to the pathogenesis of Parkinson’s disease (PD) and underlie the spread of α-syn neuropathology. Increased pro-inflammatory cytokine levels and activated microglia are present in PD and activated microglia can promote α-syn aggregation. However, it is unclear how microglia influence α-syn cell-to-cell transfer.

Methods: We developed a clinically relevant mouse model to monitor α-syn prion-like propagation between cells; we transplanted wild-type mouse embryonic midbrain neurons into a mouse striatum overexpressing human α-syn (huα-syn) following adeno-associated viral injection into the substantia nigra. In this system, we depleted or activated microglial cells and determined the effects on the transfer of huα-syn from host nigrostriatal neurons into the implanted dopaminergic neurons, using the presence of huα-syn within the grafted cells as a readout.

Results: First, we compared α-syn cell-to-cell transfer between host mice with a normal number of microglia to mice in which we had pharmacologically ablated 80% of the microglia from the grafted striatum. With fewer host microglia, we observed increased accumulation of huα-syn in grafted dopaminergic neurons. Second, we assessed the transfer of α-syn into grafted neurons in the context of microglia activated by one of two stimuli, lipopolysaccharide (LPS) or interleukin-4 (IL-4). LPS exposure led to a strong activation of microglial cells (as determined by microglia morphology and cytokine production) and significantly higher amounts of huα-syn in grafted neurons. In contrast, injection of IL-4 did not change the proportion of grafted dopamine neurons that contained huα-syn relative to controls. RNA sequencing analysis revealed differential gene expression between LPS and IL-4 injected mice; many genes were upregulated in LPS including those involved with the inflammatory response.

Conclusions: The absence or the hyperstimulation of microglia affected α-syn transfer in the brain. Our results suggest that under resting, non-inflammatory conditions, microglia modulate the transfer of α-syn. Pharmacological regulation of neuroinflammation could represent a future avenue for limiting the spread of PD neuropathology.

overall_design: RNA-seq  on mouse striatum injected with PBS, LPS or IL-4


title: Spop restrains inflammation-induced emergency hematopoiesis by targeting MyD88 [Bulk RNA-Seq]

summary: examination of the transcriptional profile of LSK and neutrophils (L6G+)

overall_design: RNA seq of bone marrow sorted LSK and sorted Ly6G+ cells (neutrophils)


title: Changes in skeletal muscle gene expression following castration

status: Public on Aug 11 2019

city: Tallahassee

first: gang

last: wang

state: Florida

address: 319 Stadium Dr

department: The Center for Genomics and Personalized Medicine

institute: Florida State University

summary:
The objective of this study was to identify novel genes whose expression is sensitive to androgen deprivation.
We used microarrays to detail the change in gene expression within the tibialis anterior muscle following castration surgery.

overall_design: Male, C57Bl/6 mice aged 11 weeks were subjected to a sham or castration surgery.  At 18 weeks of age, they were fasted beginning at 1800 hr.  The next morning (~0800 hr), mice were randomized to remain fasted or were allowed to refeed for 30 minutes.  Following the refeeding, all mice were fasted for an additional 4 hr until sacrifice.   At sacrifice, all mice were anesthetized with isoflurane, and the tibialis anterior muscle was extracted and flash frozen in liquid nitrogen

first: Bradley

middle: S

last: Gordon


title: Identification and analysis of long non-coding RNAs reveals regulatory mechanisms responses to heat stress in rainbow trout (Oncorhynchus mykiss)

city: lanzhou

first: jinqiang

last: quan

address: No. 1 Yingmen Village, Anning District

department: College of Animal Science & Technology

institute: Gansu Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: Rainbow trout is a typical cold-water fish, with the intensification of global warming, high temperatures severely restrict the development of aquaculture in summer. Understanding the molecular regulation mechanisms of rainbow trout in response to heat stress will be salutary to alleviate heat stress-related damage. In the present study, we performed transcriptome analysis of liver tissues in rainbow trout under heat stress (24℃) and control (18℃) conditions to identify induced lncRNAs and pathways by heat stress. More than 658 million clean reads and 5,916 lncRNAs were identified from six liver libraries. A total of 927 novel lncRNAs were generated and 428 differentially expressed lncRNAs were screened through stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, the regulatory network of important functional lncRNA-mRNA were constructed. GO and KEGG enrichment analysis of target gene of differentially expressed lncRNAs were performed. Many target genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced under heat stress. Several important regulatory pathways were involved in heat stress, including thyroid hormone signaling pathway, PI3K-Akt signaling pathway, estrogen signaling pathway, etc. This result broadens our understanding of lncRNA associated with heat stress and provides new insights into lncRNA-mediated regulation of rainbow trout heat stress.

overall_design: liver tissues of rainbow trout under heat stress (24C, HS, n=3) and control (18C, CG, n=3) conditions to identify induced lncRNAs

first: Zhe

last: Liu

first: Jinqiang

last: Quan


title: C6orf203 is an RNA-binding protein involved in mitochondrial protein synthesis

status: Public on Aug 10 2019

city: Stockholm

first: Shreekara

last: Gopalakrishna

state: Solna

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: In all biological systems, RNAs are associated with RNA-binding proteins (RBPs), forming complexes that control gene regulatory mechanisms, from RNA synthesis to decay. In mammalian mitochondria, post-transcriptional regulation of gene expression is conducted by mitochondrial RBPs (mt-RBPs) at various stages of mt-RNA metabolism, including polycistronic transcript production, its processing into individual transcripts, mt-RNA modifications, stability, translation, and degradation. To date, only a handful of mt-RBPs have been characterized. Here, we describe a putative human mitochondrial protein, C6orf203, that contains an S4-like domain - an evolutionarily conserved RNA-binding domain previously identified in proteins involved in translation. Our data show C6orf203 to bind highly-structured RNA in vitro and associate with the mitoribosomal large subunit in HEK293T cells. Knockout of C6orf203 leads to a decrease in mitochondrial translation and consequent OXPHOS deficiency, without affecting mitochondrial RNA levels. Although mitoribosome stability is not affected in C6orf203-depleted cells, mitoribosome profiling analysis revealed a global disruption of the association of mt-mRNAs with the mitoribosome, suggesting that C6orf203 may be required for the proper maturation and functioning of the mitoribosome. We therefore propose C6orf203 to be a novel RNA-binding protein involved in mitochondrial translation, expanding the repertoire of factors engaged in this process.

overall_design: Mitochondrial Ribosome profiling RNASeq data of Mitochondrial ribosomal profling from C6orf203 knock-out HEK cells versus wildtype

first: Sarah

last: Pearce

first: Adam

last: Dinan

first: Florian

last: Schober

first: Miriam

last: Cipullo

first: Henrik

last: Spåhr

first: Anas

last: Khawaja

first: Camilla

last: Maffezzini

first: Christoph

last: Freyer

first: Anna

last: Wredenberg

first: Ilian

last: Atanassov

first: Andrew

middle: E

last: Firth

first: Joanna

last: Rorbach


title: Identification of known and novel miRNAs in the apical and basal spikelets of rice Oryza sativa cv. Mahalaxmi

city: Bhubaneswar

first: Birendra

middle: Prasad

last: Shaw

state: Odisha

address: Nalco Square, Besides Kalinga Hospital

country: India

institute: Institute of Life Sciences

summary: The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 22.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ. Beises, the expression of a miRNA in a plant organ may differ depending upon it spatial location. The same is reflected in the NGS data of the apical and basal spikelets of the panicle of the rice cultivar Mahalaxmi.

overall_design: Spikelets of Oryza sativa cv. Mahalaxmi  were  sampled on the 6th days after fertilization from the apical and basal region.  sRNAs were isolated from the apical and basal spikelets. Known and novel miRnAs were identified bioinformatically, and their expression was validated by Northern.

middle: P

first: Tilak

last: Chandra

first: Sagarika

last: Mishra


title: Epigenetic Pathways of HDAC Inhibitor Resistance in Cutaneous T Cell Lymphoma

status: Public on Aug 09 2019

city: Memphis

first: Jared

last: Andrews

state: Tennessee

address: 262 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

summary: Epigenetic changes deregulate gene expression to drive oncogenesis. The reversible nature of these changes enables therapeutic targeting, as in cutaneous T-cell lymphoma (MF/SS), Histone deacetylase inhibitors (HDACi), which alter epigenetic modifications, are effective in ~30% of MF/SS patients. However, there are no markers that predict MF/SS progression or therapy resistance. We hypothesized that epigenetic alterations drive MF/SS progression and promote HDACi drug resistance. Therefore, we profiled the epigenomes and transcriptomes of malignant T cell purified from skin biopsies and peripheral blood from MF/SS patients (N=21) before and after treatment with HDACi, as well as in vitro HDACi-treated CD4+ T cells from healthy donors. Here we report for the first time the epigenome-wide map of acetylation changes in MF/SS patients treated with HDACi, and define the significant differences in regulatory element activity and corresponding transcriptional changes in HDACi-sensitive versus resistant tumors. Our studies identified genes not previously  associated with MF/SS, nor with disease progression or HDACi resistance, and were enriched in pathways that regulate apoptosis (BIRC5), cell cycle (RRM2), and chromosome cohesion (CENPH). We also identified a striking number of genes whose products are involved in cell adhesion and migration, including CCR6, LAIR2, VCAM1, and EPCAM. The mRNA of LAIR2, which encodes a receptor protein secreted by activated T cells that binds collagen and prevents binding of the inhibitory receptor LAIR1, was significantly upregulated in MF/SS tumors that were resistant to HDACi therapy and manifested in both skin and peripheral blood. We also detected elevated levels of LAIR2 protein in the plasma of MF/SS patients with progressive disease. Taken together, these studies defined the first epigenome-wide acetylation landscape of HDACi responsive and resistant MF/SS tumors, identified significantly altered patterns of epigenetic regulation and corresponding gene expression in HDACi resistant MF/SS tumors, and connected them to novel pathways of disease progression, particularly in cell adhesion and migration. These findings may represent novel predictive markers for MF/SS progression that are also targets for future therapeutic development.

overall_design: RNA-seq and ChIP-seq (H3K9/K14ac, H3K27ac) profiling of primary HDACi-treated CTCL peripheral blood and skin samples along with in vitro romidepsin treated healthy control CD4+ T cells.

first: Jacqueline

last: Payton


title: Gene expression profile of uniparous mouse mammary cell luminal progenitor subpopulation FACS-sorted based on expression of CD24CD29CD61

city: Columbus

first: Ramaswamy

last: Bhuvaneswari

state: OH

address: 320 W 10th Ave

department: Internal Medicine, Division of Medical Oncology

institute: The Ohio State University's Wexner Medical Center

summary: We modeled two types of breastfeeding behaviors in wild type FVB/N mice: (1) normal or gradual involution of breast tissue following prolonged breastfeeding and (2) forced or abrupt involution following short-term breastfeeding. To accomplish this, pups were gradually weaned between 28 and 31 days (gradual involution) or abruptly at 7 days postpartum (abrupt involution). FACS was used to relatively quantify mammary epithelial subpopulations. Gene set enrichment analysis was used to analyze gene expression data from mouse mammary luminal progenitor cells. Briefly, single cell suspension of the mammary glands was enriched for lineage-negative (Lin−) epithelial cells excluding the Lin+ cells, specifically hematopoietic (biotinylated CD45 and TER119), endothelial (biotinylated CD31), and immune (biotinylated BP-1) cells. The negatively selected cell population was enriched for luminal epithelium (LE) and mammary stem cell (MaSC)-enriched/basal epithelium (MaSC-enriched). For FACS analysis, Lin− populations were labeled with CD24-PE, CD29-FITC, and CD61-APC while their respective isotypes were used as negative controls. Cell suspensions were incubated with the appropriate antibodies for 30 min on ice. Cells were resuspended in FACS buffer (1 mM EDTA, 1% HI-FBS, and 25 mM HEPES, pH 7.0 in 1× phosphate-buffered saline) and sorted on a FACS BD LSR II Flow Cytometer.

overall_design: 2-3 mice mammary LP tissue isolated from day 28 timepoint were pooled and used for a total of 4 suspensions, 2 AI and 2 GI. P is for AI-LP1, K is for AI-LP2, I is for GI-LP1, and O for GI-LP2. At least 6 mammary glands per mouse were utilized for each replicate.

first: Mustafa

last: Basree

first: Neelam

last: Shinde

first: Gine

last: Sizemore

first: Sarmila

last: Majumder

first: Bhuvaneswari

last: Ramaswamy


title: Regulation of TERT and HKR3 in Hep3B cell lines

city: Seoul

first: Sung Hoon

last: Choi

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Yonsei Liver Center

institute: Yonsei University College of Medicine

summary: The TERT and HKR3 mechanism regulating cell cycle related expression changes remains unknown during HCC progress. We evaluated the relationship between hTERT expression and human kruppel-related 3 (HKR3) and cell cycle-related factors in Hep3B cell lines.

overall_design: NT-Control, HKR3 overexpression and TERT kncokdown in Hep3B cells

first: Jun

middle: Y

last: Park

first: Sung

middle: H


title: Expression data of human peripheral blood leukocytes

status: Public on Aug 08 2019

city: Shanghai

first: Yu

last: Zhao

address: NO528 Zhangheng Road, Pudong district

institute: Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine

summary:
Chronic hepatitis B (CHB) is a huge health burden in China, tongue diagnosis is the premise of personalized treatment of CHB by traditional Chinese medicine(TCM). The modern biological interpretation of pathological TCM tongue coating manifestation is unclear
We performed transcriptional analysis in CHB patients with white tongue coating(WTC) or yellow tongue coating(YTC) to explain the potential inner biological differences

overall_design: After the experts’ tongue image judgment consistency certification, 16 cases of CHB patients with typical light red tongue and WTC, 24 CHB cases with red tongue and YTC were included. 14 healthy controls with normal tongue manifestation, matched with age and gender, were enrolled as control. The peripheral blood samples were collected by TempusTM Blood RNA Tubes (Thermo Fisher Scientific), Affymetrix Human Genome U219 Array plates were used. The quality control data was normalized by the RMA algorithm using Gene Spring Software 11.5 (Agilent). Biological information analysis of DEGs using Ingenuity Pathways Analysis (IPA, Ingenuity systems, Inc., Redwood City, CA, www.ingenuity.com).

first: Yiyang

last: Hu


title: Transcriptome analysis of the effects of cold stress on Panax ginseng embryogenic calli

city: Changchun

first: Tao

last: Zhang

state: Jilin

address: 2888 Xincheng Street

department: College of Chinese Medicinal Material

institute: Jilin Agriculture University

summary: We reported the first study of transcriptome analyses using the Illumina HiSeq4000 platform for low temperature stress on callus of Panax ginseng. In total, over 546,139,358 clean reads were produced and 44,953 unigenes were assembled; Q30 results are above 95%. Differentially Expressed Gene analysis identified 9,435 and 6,345 unigenes which were expressed either higher or lower in treatment group samples(T)  when compared with control group (C). We can find that the differential gene is more expressed in the T_4 vs C_4 group than in the other comparison groups, thus demonstrating that the differential gene expression is more active. Chilling treatment for 2th-6th day, the total saponin content of the treatment group was significantly higher than that of the control group, and reached the maximum on the forth day of treatment, and then gradually decreased. There is a synergistic trend between differential gene expression and saponin content at different treatment times. The accuracy of these de novo sequences was validated by RT-qPCR analysis. A number of transcription factor genes were also filtrated that presumably related to environmental cold stress. These data will enrich our knowledge of triterpenoid saponin biosynthesis and provide a theoretical foundation for molecular research on Panax ginseng.

overall_design: A total of 12 panax ginseng callus samples subjected to low temperature treatment and control treatment were subjected to transcriptome sequencing.

first: Li-min

last: Yang

first: Mei

last: Han

first: Zhongming

first: Lin

last: Cheng

first: Zhuo

last: Sun


title: Pleiotropic impact of DNA-PK in cancer and implications to therapeutic strategies

city: Philadelphia

first: Emanuela

last: Dylgjeri

address: 233 S 10th St

department: Cancer Biology

institute: Thomas Jefferson University

summary: DNA-dependent protein kinase catalitic subunit (DNA-PK) is associated with aggressive disease. DNA-PK plays a role in transcriptional regulation of cancer-relevent pathways but it is not well understood.  This study uses transcriptomic analyses to understand the transcriptional role of DNA-PK in castration resistent prostate cancer (CRPC) upon DNA-PK inhibition

overall_design:
Transcriptional alterations upon DNA-PK inhibition were assessed  through RNA-Seq of C4-2 prostate cancer cells
Transcriptional alterations upon DNA-PK inhibition were assessed  through RNA-Seq of 22RV1 prostate cancer cells

first: Karen

last: Knudsen


title: RNA-seq Analysis of the gene expression regulated by CID755673 in mouse embryonic stem cells

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

summary:
Purpose:The goals of this study is to analyze the candidate genes motified by CID755674 to promote the mouse embryonic stem cell (ESC) self-renewal through RNA-seq approach.
Previously, we found that MEK inhbitior PD0323901 (PD) coporates with protein kinase D inhibitor CID755673 (CID) is able to maitain mouse embryonic stem cell (mESC) self-renewal, we named this conditon is "PC". In order to find out why CID755673 can promote mouse embryonic stem cell self-renewal, we performed RNA-sequence in mESCs treated with PD or PC, and tried to identify the key mechanisms under CID

overall_design: 46C mouse ESCs cultured in 1 µM PD0325901/serum condition in the presence or absence of CID755673 (named PD vs PC)  for 24 hr and then were collected by using Trizol. Two repeat groups were set for each treatment group. These samples were sent to GENERGY BIO (Shanghai, China) company to do deep sequencing by using illumina Hiseq.

first: Shoudong

last: Ye


title: Comparison of gene expression profiles between Dock8+/– and Dock8–/– (tcr)AND Tg DRG (dorsal root ganglion) neurons

city: Fukuoka

first: Takehito

last: Uruno

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary: To examine the genes involved in IL-31-evoked itch sensation, we employed microarray expression profiling and found that 698 genes were expressed at higher levels in the DRG neurons of Dock8–/– (tcr)AND Tg mice (high IL-31 level) than those of Dock8+/– controls (low IL-31 level).

overall_design: DRG neurons from Dock8+/– and  Dock8–/–  (tcr)AND Tg mice were isolated, and their gene expression profiles were compared.

first: Yoshinori

last: Fukui

first: Kazuhiko

last: Yamamura

first: Daiji

last: Sakata


title: Col6a1-/- Mouse Lung

city: Rochester

first: Jared

last: Mereness

address: 204 Robert B. Goergen Hall, Department of Biomedical Engineering, Box 270168

department: Biomedical Engineering

institute: University of Rochester

summary: Collagen 6 (COL6) is known for its role in a spectrum of congenital muscular dystrophies, which are often accompanied by respiratory dysfunction.  However, little is known regarding the function of COL6 in the lung.  We confirmed the presence of COL6 throughout the basement membrane region of mouse lung tissue.  We studied lung structure and organization in a previously described Col6a1-/- mouse, which do not produce detectable COL6 in the lung.  The Col6a1-/- mouse displayed multiple histopathological alveolar and airway abnormalities.  The airspaces of Col6a1-/- lungs appeared simplified, with larger (29%, p<0.01) and fewer (31%, p<0.001) alveoli. These airspace abnormalities included a reduction in IsolectinB4+ alveolar capillaries and Sftpc+ ATII cells. Alterations in lung function consistent with these histopathological changes were evident. Col6a1-/- mice also displayed multiple airway changes including increased branching (59%, p<0.001), increased mucosal thickness (34%, p<0.001) and increased epithelial cell density (13%, p<0.001). Comprehensive transcriptome analysis revealed loss of COL6 is associated with reductions in integrin-paxillin-PI3K signaling in vivo. In vitro, COL6 promoted steady-state phospho-paxillin levels and reduced cell density (16-28%, p<0.05) at confluence. Inhibition of PI3K, or its downstream effectors, resulted in increased cell density to a level similar to that seen on matrices lacking COL6.

overall_design: Col6a1-/-  and wildtype mouse lung

first: Soumyaroop

last: Bhattacharya

first: Thomas

middle: J

last: Mariani

first: John

middle: M

last: Ashton

first: Paolo

last: Bonaldo

first: Alessia

last: Angelin


title: Perinatal Exposure to 2,2’,4’4’ –Tetrabromodiphenyl Ether Impairs Male Reproductive Health in Adult Rats

city: Amherst

first: Alexander

last: Suvorov

state: MA

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

summary: Toxicity of PBDE for male reproductive system was shown in several human and animal studies, however long lasting effects of perinatal exposures on male reproduction are yet poorly understood. In this study pregnant Wistar rats were exposed to 0.2 mg/kg 2,2’,4,4’-tetrabromodiphenyl ether (BDE-47) from gestation day 8 till postnatal day 21 and testis transcriptome was analyzed on postnatal day 120 in offspring. Exposed animals had significant change in testes transcriptome including suppression of genes essential for spermatogenesis and activation of immune response genes. In particular exposed animals had on average 4 fold decreased expression of protamine and transition protein genes in testes suggesting that histone-protamine exchange may be dysregulated in the course of spermatogenesis resulting in exposure legacy transfer to the next generation via aberrant sperm epigenome.

overall_design: Rats were exposed perinataly to vehicle or BDE-47. Total RNA was extracted from testis of 5 control and 5 exposed animals on postnatal day 120 and sequenced with multiplexing on NextSeq500.


city: Cardiff

first: Helen

last: White-Cooper

state: Wales

address: Museum Avenue

department: School of Biosciences

country: United Kingdom

institute: Cardiff University

summary: The transcriptome of  larval carcasses from both wildtype and Nxt1 trans-heterozygotes were assessed by RNA-Seq. A total of 1821 genes were down-regulated and 1339 genes were up-regulated. Down-regulated genes had a higher total intron length and had more introns, while up-regulated genes had a lower total intron length and less introns when compared to the non-differentially expressed genes. The majority of down-regulated genes were involved in the production of circular RNAs (circRNAS). We further investigated circRNA expression in larval carcasses from both wildtype and Nxt1 trans-heterozygotes by sequencing total RNA after RNAseR treatment. RNAseR digests linear RNA and thus enriches for circRNAs. Mock samples without RNAseR treatment were also sequenced. We found that circRNA products of Nxt1-responsive genes are reduced in Nxt1 mutants, although the nascent transcripts of these genes are produced at normal levels.

overall_design: To assess the effect of Nxt1 on circRNA expression, we sequenced and analysed total RNA with and without RNAseR treatment from Nxt1 trans-heterozygotes and wildtype larval carcasses. All samples were sequenced in triplicates. We analysed pre-mRNA:mRNA:circRNA ratios, as well as the different CircRNA structures formed.

first: Katia

last: Jindrich


title: Direct conversion of adult skin fibroblasts to endothelial cells by defined factors

first: Jung-Kyu

last: Han

address: 101 Daehak-ro, Jongro-gu,

department: Internal Medicine

institute: Seoul National University Hospital

summary:
We directly converted mouse adult skin fibroblasts (SFBs) into induced endothelial cells (iECs) by transduction of 5 key factors.
We analyzed the genome-wide gene expression profile of iECs, and compared it with those of negative controls (original SFBs, mock-infected SFBs) or those of positive controls (primary endothelial cells from lungs of mice, MS-1 endothelial cell line).

overall_design: 12 total samples were analyzed.

first: Sung-Hwan

last: Chang

first: Hyun-Ju

last: Cho

first: Saet-Byeol

last: Choi

first: Hyo-Suk

last: Ahn

first: Jaewon

last: Lee

first: Heewon

last: Jeong

first: Seock-Won

last: Youn

first: Ho-Jae

first: Yoo-Wook

last: Kwon

first: Hyun-Jai

first: Byung-Hee

last: Oh

first: Peter

last: Oettgen

first: Young-Bae

last: Park

first: Hyo-Soo

last: Kim


title: Next-generation sequencing of RNA samples from the mice heart of Control, ABHD5-KO and ABHD5-KO transduced with AAV9 expressing HDAC4-NT (AAV9-NT)

city: Phoenix

first: Tobias

last: Jakobi

state: Arizona

address: 475 N. 5th Street

institute: University of Arizona

summary: The purpose of this experiment is to investigate the consequences of ABHD5 deletion in the heart and to evaluate HDAC4-NT gene transfer using AAV9 in ABHD5-KO.

overall_design: RNA profiles of the mRNA samples (heart) of the Control, ABHD5-KO and ABHD5-KO+AAV9-NT were generated by RNA deep sequencing, each in triplicate, using Illumina (2x 150 bp).

first: Z

last: Jebessa

first: Johannes

last: Backs


title: Expression of S-Phase long non-coding RNAs (SPEARs) exert a key transcriptional regulatory role through acH2A.Z activating mark deposition

city: Singapore

first: Vladimir

last: Espinosa Angarica

state: Singapore

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

institute: National University of Singapore

summary: The mechanisms by which epigenetic modifications are established at active genes remain elusive. The present data demonstrate that the appearance of a major epigenetic mark - the acetylated form of H2A.Z - is regulated by cell cycle-specific long noncoding RNAs encoded in regions adjacent to the promoters of active genes. These transcripts, termed Spears (S Phase EArly RNAs) are induced in early S phase: their expression precedes and then controls that of the downstream gene. Spears set the stage for the deposition of the acetylated form of histone H2A.Z by associating with the replacement histone H2A.Z and with the histone acetyl transferase Tip60,. This widespread bimodal interaction uncovers a novel RNA-mediated mechanism for the establishment of cell-specific epigenetic profiles and provides a potentially unifying mechanistic explanation for the accuracy and persistence of epigenetic marks on chromatin.

overall_design: Interaction between H2A.Z and A7:B16 Early RNAs; Interaction betweenTip60 and S-Phase Early RNAs; S-Phase Early RNAs and gene expression.

first: Alexander

middle: K

last: Ebralidze

first: Annalisa

last: Di Ruscio


title: RNA-seq, ChIP-seq and TERRA CHIRT-seq from p53-/- iPS infected with a lentiviral virus carrying a control scrambled shRNA or shRNA against TRF1

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: The mechanisms that regulate pluripotency and cell fate are still largely unknown. Here, we show that the Telomere Repeat Binding Factor 1 (TRF1), a component of the shelterin telomere protection complex, regulates genome-wide binding of polycomb to stem cell and pluripotency genes, thereby exerting vast epigenetic changes that contribute to maintain embryonic stem cells in a naïve state. We further show that TRF1 mediates these effects by regulating TERRA, the long-non-coding RNAs transcribed from telomeres and that are part of the telomeric chromatin. In particular, we find that TERRAs are enriched at polycomb and stem cell genes in pluripotent cells and that TRF1 abrogation results in increased TERRA levels and a higher binding of TERRA to those genes, an event that is coincidental with TRF1-dependent induction of cell-fate programs and loss of the naïve state. These results are consistent with a model in which TERRA recruits polycomb to genes important for pluripotency and differentiation in a manner that is dependent on TRF1. These unprecedented findings explain the long-standing observation that TRF1 is one of the most upregulated genes during induction of pluripotency and it is essential for the induction and maintenance of pluripotency.

overall_design: p53-/- iPS cells were infected with lentivirus encoding a control shRNA or a shRNA against TRF1. After two days selection with puromycin, RNA or chromatin was obtained to perform the next techniques. From RNA-seqs, two independent experiments were performed so 2 different control samples and two different condition samples were analyzed. A single experiment was analyzed for the ChIP-seqs, sending one sample for the control and one for the condition sample. The ChIPs against the following proteins were performed: Suz12, H3K27me3 and TRF1. As control, a mix of the input of the control and the condition samples was sequenced. For the CHIRT-seq against TERRA, the sample from the control condition and the original input were sequenced.

first: Rosa

last: Marión

first: Juan

last: Montero

last: Graña-Castro

first: María

middle: A

last: Blasco


title: Transcriptome analysis of mvaT and mvaU double knockout mutant of Pseudomonas aeruginosa PAO1

city: LOWELL

first: GUOQING

last: LI

address: 220 Pawtucket St

institute: University of Massachusetts Lowell

summary: MvaT and MvaU are two redundant xenogeneic silencing proteins of the H-NS family in Pseudomonas aeruginosa. Previous studies to investigate the physiological consequences of mvaT and mvaU depletion were hampered by activation of Pf4 prophage in the resulting mutants. In this study, an mvaT mvaU double knockout mutant (PAO△TU) was constructed in a strain of PAO1 (Δpf4) devoid of the Pf4 prophage on the chromosome.Transcriptome analysis by GeneChip (Affymetrix) revealed that over 227 genes were found up-regulated in PAO△TU, including several multi-gene loci for type III and type VI protein secretion systems, O-antigen, exopolysaccharide, pili assembly, and many others of unknown functions.

overall_design: We conducted four independent microarray experiments of phage knockout parental strain and mvaT/mvaU double knockout strain of P. aeruginosa PAO1. Strains were grown aerobically in 2YT broth with 300 rpm shaking at 37°C and harvest at mid-log phase with OD600 0.6. Comparison was made between parental strains and double knockout strains.

first: Jeng-yi

last: Li

first: Chung-dar

last: Lu


title: PT2385 HIF2A inhibitor treatment of patient derived orthotopic xenograft neuroblastoma cells in the presence or absence of hypoxia

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

institute: Lund University

summary: neuroblastoma cells derived from PDOX models were treated with the HIF2A inhibitor in normoxic and hypoxic conditions.

overall_design: 3 repetitions of control (DMSO) and PT2385 treated cells +/- hypoxa were harvest and submitted for RNAseq analysis

first: Camilla

last: Persson

first: Sofie

last: Mohlin

first: Caroline

last: Wigerup

first: Daniel

last: Bexell


title: EZH2 inhibition results in genome-wide PRC2 redistribution in cancer cell models

city: Cambridge

first: Barbara

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

summary: Upon EZH2 inhibitor treatment, PRC2 components EZH2 and SUZ12 are redistributed across the genome towards a small number of genomic loci that are refractory to H3K27me3 loss. Focal PRC2 accumulation and H3K27me3 retention occur primarily at CpG islands and transcription start sites of genes, with enrichment at canonical PRC2 nucleation sites. EZH2 and SUZ12 are present at low levels at actively transcribed TSSs, and this signal is lost with EZH2 inhibition.

overall_design: ChIP-seq of PRC2 components, H3K27me3, and H3K4me3 upon treatment with EZH2 inhibitor or a control, in DLBCL and multiple myeloma cell lines.

first: Ah Jung

last: Jeon

first: Patrick

last: Trojer

first: Greg

last: Tucker-Kellogg

first: Chih-Chi

last: Yuan


city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary:
Purpose:To gain a deeper insight into how TCF20 regulates neurogenesis in mice brain, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by TCF20 deletion at E13.5.
Methods: Total RNA was extracted from E13.5 telencephalic tissue of TCF20 WT HET KO mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics.
Results: Approximately approximately one thousand transcripts showed differential expression between the WT and TCF20 KO brain cortex, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to neurogenesis, neuronal specification, neural differentiation and secretion by cells. Up-regulated genes showed a significant enrichment of terms involved in up regulation of hypersensitivity  and up regulation of inflammatory response. These results reflected the importance of TCF20 in cortical neurogenesis.
Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how TCF20 gene contribute to brain cortical development.

overall_design: Total RNA was extracted from E13.5 telencephalic tissue of  TCF20 WT HET KO mice and subjected to deep sequencing, in triplicate, using Illumina HiSeq 2500.

first: Chao

last: Feng


title: Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms of homing for neutrophils

city: Turku

first: Akira

last: Takeda

state: South-West Finland

address: Tykistökatu 6A

department: Institute of Biomedicine

institute: University of Turku

summary: Lymphatic vessels form a critical component in the regulation of human health and disease. While their functional significance is increasingly being recognized, the comprehensive heterogeneity of lymphatics remains uncharacterized. Here, we report the profiling of 33,000 lymphatic endothelial cells (LECs) in human lymph nodes (LNs) by single-cell RNA sequencing. Unbiased clustering revealed six major types of human LECs. LECs lining the sub-capsular sinus (SCS) of LNs abundantly expressed neutrophil chemoattractants, whereas LECs lining the medullary sinus (MS) expressed a C-type lectin CD209. Binding of a carbohydrate Lewis X (CD15) to CD209 mediated neutrophil binding to the MS. The neutrophil-selective homing by MS LECs may retain neutrophils in the LN medulla and allow lymph-borne pathogens to clear, preventing their spread through LNs in humans. Our study provides a comprehensive characterization of LEC heterogeneity and unveils a previously undefined role for medullary LECs in human immunity.

overall_design: Droplet-based single-cell RNA sequencing (scRNAseq) of human CD45- CD31+ PDPN+ cells from the axillary LNs (AXLNs) and head and neck LNs (HNLNs). ScRNAseq was performed using 10X Genomics Single Cell 3' solution, version 2 according to manufacture's instructions. Libraries were sequenced on HiSeq3000.

first: Sirpa

last: Jalkanen


title: TET-catalyzed 5-carboxylcytosine promotes CTCF binding to suboptimal sequences genome-wide

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

summary: The mechanisms supporting dynamic regulation of CTCF binding sites remain poorly understood. Here we describe the TET-catalyzed 5-methylcytosine derivative, 5-carboxylcytosine (5caC) as a factor driving new CTCF binding within genomic DNA. Through a combination of in vivo and in vitro approaches, we reveal that 5caC generally strengthens CTCF association with DNA and facilitates binding to suboptimal sequences. Dramatically, profiling of CTCF binding in a cellular model that accumulates genomic 5caC identified ∼13,000 new CTCF sites. The new sites were enriched for overlapping 5caC and were marked by an overall reduction in CTCF motif strength. As CTCF has multiple roles in gene expression, these findings have wide-reaching implications and point to induced 5caC as a potential mechanism to achieve differential CTCF binding in cells.

overall_design: Characterization of CTCF binding in TDG KO condition compared to wild type, and examination of 5caC

first: Kyster

last: Nanan

first: Maria

last: Prigge

first: Morgan

last: Thenoz

first: Allissa

last: Dillman

first: Mariana

last: Mandler

first: Shalini

last: Oberdoerffer


title: Gonadotropin-mediated miRNA expression at onset of puberty in rhesus monkey is posited to terminate a hypothyroid state of the testis

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5150 Center Ave

department: BioMedical Informatics

institute: University of Pittsburgh

summary:
Goal:  To identify small RNA associated with the decision of undifferentiated spermatogonia to commit to a pathway of differentiation.
Methods: testis small RNA profiles of 6 juvenile wild-type rhesus monkeys (3 vehicle-treated; 3 gonadotropin treated) were generated by deep sequencing, in triplicate, using Ion Torrent. The sequence reads that passed filters were analyzed with miRDeep2, HTSeq counts and edgeR. qRT–PCR validation was performed using SYBR Green assays
Results: We mapped about 3 million sequence reads per sample to the rhesus monkey genome (rheMac 2 and rheMac 8.0.1) and identified 932 small RNAs in the testes of wild type monkeys with Bowtie and miRDeep2 workflow.  Approximately a combined 7% of unique transcripts showed differential expression between vehicle and gonadotropin treatment for 48 and 96h, with a fold change ≥1.5 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, substantiating the RNA-seq findings.
Conclusions: The testis transcriptome of the juvenile monkey contained 932 non coding smallRNA.  Gonadotropin stimulation for 48 h resulted in the commitment of spermatogonia to differentiate and this was associated with the emergence of 51 differentially expressed genes.
Funding support: NIH R01 HD072189 to Tony Plant

overall_design: Whole testis smallRNA profiles of juvenile wild type rhesus monkeys (3 vehicle-treated; 3 gonadotropin treated) were generated by deep sequencing in triplicate, using Ion Torrent

first: Rahil

last: Sethi

first: William

last: Walker


title: RNA seq on SP specific CD8+ T cells, Ly49+ and Ly49-CD8+ T cells from MOG and MOG + SP immunized mice [RNA-Seq]

city: Stanford

first: Michael

last: Sikora

state: CA

address: 450 Serra Mall

department: Genetics

institute: Stanford University

summary: In experimental autoimmune encephalomyelitis (EAE), a model for multiple sclerosis (MS), induction generates successive waves of clonally expanded CD4+, CD8+, and gd+ T cells in the blood and central nervous system, similar to gluten challenge studies of Celiac patients. In MS patients, we also observe major expansions of CD8+ T cells. In EAE, we find that most expanded CD4+ T cells are specific for the inducing myelin peptide MOG35-55 but in contrast, peptide ligands derived from a yeast peptide-MHC display library for some of the clonally expanded CD8+ T cells inhibit disease by suppressing the proliferation of MOG-specific CD4+ T cells. These results suggest the induction of autoreactive CD4+ T cells triggers an opposing mobilization of regulatory CD8+ T cells.

overall_design: SP specific CD8 T cells were sorted from D10 immunized  B6 mice and Ly49+ and Ly49- CD8+ T cells were sorted from MOG and MOG + SP immunized mice

first: Mark

last: Davis

first: Naresha

last: Saligrama


title: Gene expression data from murine middle colons of Trim58-/- vs. Trim58+/+ mice after induction of acute DSS-colitis.

city: Essen

first: Elke

last: Cario

state: NRW

address: Virchowstr. 171

department: Division of Gastroenterology and Hepatology

institute: University of Duisburg-Essen, University Hospital of Essen

summary: The role of Trim58 in acute inflammation is so far unclear. The aim of this study was to determine the effects of Trim58 deficiency on acute DSS-colitis in mice. We used microarrays to assess gene expression profiles in middle colons of Trim58-/- vs. Trim58+/+ mice after inflammatory stress-mediated mucosal damage during the regeneration phase.

overall_design: We generated mice completely lacking the gene Trim58 (Trim58-/-). Female Trim58-/- and Trim58+/+ mice (9 weeks old, SPF) were treated with dextran sodium sulfate (DSS). In brief, colitis was induced by addition of 4.0% (wt/vol) for 7 days of DSS (molecular weight, 36,000-50,000) in drinking water and followed by normal drinking water for 5 days.  On day 12, mice were sacrificed and total RNA was extracted from middle colons (n=4 mice/group). All extracted RNA samples were analyzed independently. Microarray processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany).