title: Next Generation Sequencing Facilitates Quantitative Analysis of ISL1 Regulated Transcriptomes

city: beijing

first: guo

last: ting

address: 52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute, Beijing

summary:
The goal of this study is to analyze the transcriptome profiling (RNA-seq) after ISL1 knockdown.
The objective of this study is to elucidate the mechanisms of ISL1 in gastric carcinogenesis, RNA-Seq is performed in BGC823 cells with stable ISL1 knockdown. Comparison and identification of the candidate genes based on the intersection of RNA-seq showed that upregulated and downregulated genes had ISL1-bound regions.

overall_design: BGC823 cells were transfected by ISL1 knockdown lentivirus and scramble lentivirus as control.Total RNA was extraced by Qiagen kit and the mRNA profiles were generated by deep sequencing, in duplicate, using Illumina Hiseq 2000.

first: Jiafu

last: Ji

first: Ting

last: Guo

first: Fangxiao

last: Xing


title: BK5.ATF3-induced mammary tumors compared to normal mammary glands

status: Public on Mar 23 2021

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

country: USA

institute: The University of Texas MD Anderson Cancer Center

summary: Transcriptional profiling of mammary tumors that occur in parous, BK5.ATF3 mice, compared to normal mammary tissue

platform_organism:
Mus musculus
Murid betaherpesvirus 1
Murid gammaherpesvirus 4

overall_design: Two-condition experiment, BK5.ATF3-induced mammary tumors v. adjacent normal mammary glands. Biological replicates: 3 tumors, 3 paired normal glands. One replicate per array.

first: Jianjun

last: Shen

first: Michael

middle: C

last: MacLeod

first: Leqin

last: Yan


title: RNA sequencing  to detect the differentially expressed genes in acute Myocardial Infarction mice model after HXP treatment.

status: Public on Mar 24 2021

city: Fuzhou

first: Jun

last: Peng

state: Fujian

address: 1 Qiuyang Road, Minhou Shangjie

department: Academy of Integrative Medicine

country: China

institute: Fujian University of Traditional Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: The goals of the study are to compare differently expressed genes in heart tissues of acute Myocardial Infarction mice with control mice and idetify the targets of Traditional Chinese Medicine HXP.

overall_design: RNA sequencing was performed with heart tissue of control, MI and HXP treated mice (n = 6 for each group) to identify the differently expressed genes and related pathway.

first: Zhiqing

first: Aling

first: Xiangyan

last: Wu

first: Ying

last: Cheng

first: Xiaoping

last: Chen


title: Single-Cell Transcriptomic Analysis of mIHC Images via Antigen Mapping

city: Philadelphia

first: Kiya

middle: W

last: Govek

state: PA

address: 3700 Hamilton Walk

department: Genetics

institute: University of Pennsylvania

summary: Highly-multiplexed immunohistochemistry (mIHC) enables the staining and quantification of dozens of antigens in a tissue section with single-cell resolution. However, annotating cell populations that differ little in the profiled antigens or for which the antibody panel does not include specific markers is challenging. To overcome this obstacle, we have developed an approach for enriching mIHC images with single-cell RNA-seq data, building upon recent experimental procedures for augmenting single-cell transcriptomes with concurrent antigen measurements. Spatially-resolved Transcriptomics via Epitope Anchoring (STvEA) performs transcriptome-guided annotation of highly-multiplexed cytometry datasets. It increases the level of detail in histological analyses by enabling annotation of subtle cell populations, spatial patterns of transcription, and interactions between cell types. More generally, it enables the systematic annotation of cell populations in cytometry data. We demonstrate the utility of STvEA by uncovering the architecture of poorly characterized cell types in the murine spleen using published highly-multiplexed cytometry and mIHC data.

overall_design: Single-cell CITE-seq of two 9 month old BALBc mouse spleens

first: Emma

last: Troisi

first: Zhen

last: Miao

first: Rachael

middle: G

last: Aubin

first: Steven

last: Woodhouse

first: Pablo

last: Camara


title: ChIRC-seq  Reveals Promoter Antisense RNAs and HP1α as Key Regulators of Promoter Pause Release and of Enhancer : Architectural RNA Interactions [PRO-seq]

city: La Jolla

first: MICHAEL

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

institute: HHMI/UCSD

summary: Demonstration of a massive lncRNA RNA transcriptional program in the mammalian genome has engendered lively discussions about their biological roles, particularly the promoter antisense (PAS) transcripts of coding gene transcription units and abundant species localized to specific subnuclear structures with phase separation properties. Here, we report development of an alternative assay to quantitatively detect RNA distribution in the genome, referred to as ChIRC-seq (Chromatin Isolation by RNA-Cas13a Complex Capture by Cas13a), which has revealed that promoter antisense RNAs (PAS-RNAs) serve as a key gatekeeper of a broad transcriptional pause release program, based on decommissioning the 7SK snRNA-dependent inhibitory P-TEFb complex. Induction of PAS-RNA by liganded estrogen receptor ERα (ESR1) releases the basal recruitment of HP1α and KAP1 on target gene promoters, without the spreading characteristic of extended heterochromatic regions, based on PAS-dependent recruitment of H3K9me3 demethylases. Unexpectedly, ERα-bound MegaTrans enhancer activation with features of phase separation events proved to require recruitment of phosphorylated KAP1 to be activated, with its transfer to the cognate promoters licensing estrogen-induced pause release and target gene activation.  The ChIRC13a-seq method has proved effective for identification of the cognate promoter for activated enhancers and has revealed that the lncRNAs NEAT1/MALAT1 in phase-separated subnuclear structures interact with robust estrogen-activated MegaTrans TFF1e1 enhancer and other active enhancers, linking acute activation of a subset of enhancers to interactions with specific phase-separated subnuclear architectural structures.

overall_design: The changes in the gene expression profiles were investigated by ChIP-seq, PRO-seq, and ChIRC-seq.

first: Fan

last: Yang

first: Bogdan

last: Tanasa

first: Rudi

last: Micheletti

first: Kenneth

middle: A

last: Ohgi

last: Rosenfeld


title: Acquired deficiency of the peroxisomal bi-functional enzyme enoyl-CoA hydratase/3-hydroxyacyl CoA dehydrogenase is a metabolic vulnerability in murine hepatoblastoma

city: pittsburgh

first: Edward

middle: V.

last: Prochownik

address: 4401 Penn Avenue

department: Section of Hematology/Oncology

institute: Children’s Hospital of Pittsburgh

summary: Metabolic reprogramming provides transformed cells with proliferative and/or survival advantages. However, capitalizing on this therapeutically has been only moderately successful due to the relatively small magnitude of these differences and because cancers may re-program their metabolism to evade metabolic pathway inhibition. Mice lacking the peroxisomal bi-functional enzyme enoyl-CoA hydratase/3-hydroxyacyl CoA dehydrogenase (Ehhadh) and supplemented with the 12-carbon fatty acid lauric acid (C12) accumulate dodecanedioic acid (DDDA), a toxic C12 metabolite that causes hepatocyte necrosis and acute liver failure. In a murine model of pediatric hepatoblastoma (HB), down-regulation of Ehhadh also occurs in combination with a more general suppression of mitochondrial β- and peroxisomal ω-fatty acid oxidation (FAO) pathways. HB-bearing mice provided with C12 and/or DDDA-supplemented diets survived significantly longer than those on standard diets. The tumors also developed massive necrosis in response to short-term DDDA supplementation. Reduced Ehhadh was noted in murine hepatocellular carcinomas (HCCs) and in substantial subsets of human cancers, including HCCs. Acquired DDDA resistance was not associated with Ehhadh re-expression but was associated with 129 transcript differences ~90% of which were down-regulated in DDDA-resistant tumors and ~two-thirds of which correlated with survival in several human cancers. These transcripts often encoded components of the extracellular matrix suggesting that DDDA resistance arises from its reduced intracellular transport. Our results demonstrate the feasibility of a metabolic intervention that is non-toxic, inexpensive and likely compatible with traditional therapies. C12 and/or DDDA-containing diets could potentially be used to supplement other treatments or as alternative therapeutic choices.

overall_design: RNA purification from five representative tumors of each group was performed using Qiagen RNAeasy columns (Qiagen, Inc., Valencia, CA) followed by DNase digestion. Sample integrity was measured using an Agilent 2100 Bioanalyzer (Agilent Technologies, Foster City, CA).  All samples had RIN values of 8.5-10 prior to any further processing.  Samples for sequencing were prepared using an NEB NEBNext Ultra Directional RNA Library Prep kit according to the directions provided by the vendor (New England Biolab, Beverly, MA) and sequencing was performed on a NovaSeq 600 Instrument (Illumina, Inc., San Diego, CA) by Novagene, Inc. (Sacramento, CA).

first: Huabo

last: Wang

middle: V


title: Investigation of mechanism using highly intrahepatic metastatic cell lines of HCC

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
The prognosis of hepatocellular carcinoma (HCC) is poor due to the high incidence of intrahepatic metastasis.
The aim of this study is to investigate the mechanism of intrahepatic metastasis in HCC via extracellular vesicles (EVs).

overall_design: two samples; HuH-7-P derived exosome and HuH-7-M derived exosome

first: Yuki

last: Yokota

first: Takehiro

last: Noda


title: Bacteria-host transcriptional response during endothelial invasion by Staphylococcus aureus

city: Hoersholm

first: Christian

last: Garde

address: Dr Neergaards Vej 5F

country: Denmark

institute: Evaxion Biotech

summary: The purpose of the study was to investigate the transcriptomic responses of S. aureus and HUVEC cells before and during S. aureus invasion of HUVEC cells.

sample_organism:
Staphylococcus aureus
Homo sapiens

platform_organism:
Staphylococcus aureus
Homo sapiens

overall_design: In vitro investigation of the expression profiles of S. aureus in inoculum and uninfected HUVEC cells as well during S. aureus infection of HUVEC cells (1hpi and 16hpi).

first: Rasmus

last: Birkholm Grønnemose

first: Thomas

middle: E

last: Andersen


title: Different gene expression profiles between de novo and progressive muscle invasive bladder cancer: prognostic implications

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: INTRODUCTION: Progressive muscle-invasive bladder cancer (MIBC) has more aggressive behavior than de novo MIBC. This study aimed to ascertain the differences in gene expression profiles between both MIBC groups and to identify prognostic biomarkers to improve the treatment in these patients. MATERIAL AND METHODS: Retrospective multicentre study in which 212 MIBC patients (104 progressive and 108 de novo) who underwent radical cystectomy in the Hospital Clinic (Barcelona) and Radboud UMC (Nijmegen) were included. Total RNA from formalin-fixed paraffin-embedded tissue samples was obtained. Gene expression profiles of 27,965 coding transcripts were determined in 26 patients using Illumina microarrays. Expression levels of 94 genes selected from microarray data and literature were studied by quantitative PCR in an independent series of 186 de novo and progressive MIBC patients. Survival analysis was performed with the Kaplan-Meier method. R-software and SPSSv23 were used for all calculations.  RESULTS: A total of 480 genes were found differently expressed (FDR<0.01) between progressive and de novo MIBC samples. Differential expression of 23 out of the 94 genes selected was validated in an independent set of samples. Survival analysis showed that expression of eight genes were prognostic factors of BCR. CONCLUSION: De novo and progressive MIBC patients show different gene expression profiles. In addition, we have identified eight genes with prognostic value which may contribute to improve BC risk stratification and, consequently, to tailor treatment and surveillance strategies in these patients.

overall_design: Transcriptomic profile from 12 de novo MIBC and 14 progressive MIBC FFPE samples

first: J

middle: J

first: A

last: Alcaraz

first: L

last: Mengual


title: Gene expression profile of breast cancer cells transfected with antisense oligonucleotides (ASO) against BRCA1 pseudogene (BRCA1P1)

city: Chicago

first: Yoo-Jeong

last: Han

state: IL

address: 900E. 57th street

department: Medicine

institute: University of Chicago

summary: Analysis of genes influenced by knock-down of BRCA1P1 in breast cancer cell lines

overall_design: Total RNA obtained from breast cancer cell lines subjected to 3 days of transfection with negative control-ASO or BRCA1P1-ASO

first: Olufunmilayo

middle: I

last: Olopade


title: Ancient genomic regulatory blocks are a major source for gene deserts in vertebrates after whole genome duplications

city: Berlin

first: Rafael

middle: Domínguez

last: Acemel

state: Berlin

address: Hannoversche Str. 28

department: Berlin Institute of Medical Systems Biology (BIMSB)

country: Germany

institute: Max Delbrück Center for Molecular Medicine (MDC)

summary: 4C-seq experiments to study the evolution of the chromatin architecture of ancient gene regulatory blocks at the origin of vertebrates.

sample_organism:
Branchiostoma lanceolatum
Danio rerio
Mus musculus

overall_design: 4C-seq experiments centered at the promoters of the trans-dev genes involved in gene regulatory blocks in amphioxus plus their paralog genes in mouse and zebrafish.

first: María

last: Touceda-Suárez

first: Elizabeth

middle: M

last: Kita

middle: D

first: Panos

middle: N

last: Firbas

first: Marta

middle: S

last: Magri

first: Silvia

last: Naranjo

first: Juan

last: Tena

first: José

middle: L

last: Gómez-Skarmeta

first: Ignacio

last: Maeso

first: Manuel

last: Irimia


title: MTH1 and OGG1 maintain a low level of 8-oxoguanine in Alzheimer's brain, and prevent the progression of Alzheimer's pathogenesis

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

summary:
To investigate the role of 8-oxo-7, 8-dihydroguanine (8-oxoguanine) accumulation in DNA or nucleotide pools during the development of AD pathology, we introduced a Mth1/Ogg1-double deficiency into homozygous triple-transgenic AD model (3xTg-AD-H) mice. Mth1 encodes 8-oxo-7, 8-dihydro-2'-deoxyguanosine-5'-triphosphatase (8-oxo-dGTPase) and Ogg1 encodes 8-oxoguanine DNA glycosylase 1.
One-way eBays ANOVA of microarray data from hippocampi revealed that the gene expression profiles are most significantly altered in the hippocampi of 3xTg-AD-H with Mth1/Ogg1-double deficient (ADH/TO-DKH) mice compared to non-Tg control (NT) mice. Comparative analysis between 3xTg-AD-H (ADH/WT) and ADH/TO-DKH mice showed that the expression of genes involved in neuroprotection are significantly altered. Among them, expression of the AD-related genes including Ttr, Enpp2, Kcnj13 and Kl was significantly downregulated in ADH/TO-DKH mice.

overall_design: Non-transgenic control (NT) , homozygous 3xTg-AD mice harboring homozygous APPSwe and tauP301L transgenes with a homozygous Psen1M146V mutation (ADH/WT), and homozygous 3xTg-AD mice with MTH1/OGG1-double deficiency (ADH/TO-DKH), were used in this study (5-month-old, male, n=3 for each group). RNA samples prepared from hippocampi were subjected to microarray analysis using the Affymetrix Mouse Gene 1.0 ST platform.

first: Sugako

last: Oka


title: Amino terminus of cardiac myosin binding protein-C regulates cardiac contractility

city: Maywood

first: Michael

last: Zilliox

address: 2160 S. First Ave

department: Ophthalmology

institute: Loyola University Chicago

summary: Phosphorylation of cardiac myosin binding protein-C (cMyBP-C) regulates cardiac contraction through modulation of actomyosin interactions mediated by the protein’s amino terminal (N’)-region (C0-C2 domains, 358 amino acids). On the other hand, dephosphorylation of cMyBP-C during myocardial injury results in cleavage of the 271 amino acid C0-C1f region and subsequent contractile dysfunction. Yet, our current understanding of amino terminus region of cMyBP-C in the context of regulating thin and thick filament interactions is limited. A novel cardiac-specific transgenic mouse model expressing cMyBP-C, but lacking its C0-C1f region (cMyBP-C delta C0-C1f), displayed dilated cardiomyopathy, underscoring the importance of the N’-region in cMyBP-C. Further exploring the molecular basis for this cardiomyopathy, in vitro studies revealed increased interfilament lattice spacing and rate of tension redevelopment, as well as faster actin-filament sliding velocity within the C-zone of the transgenic sarcomere. Moreover, phosphorylation of the unablated phosphoregulatory sites was increased, likely contributing to normal sarcomere morphology and myoarchitecture. These results led us to hypothesize that restoration of the N’-region of cMyBP-C would return actomyosin interaction to its steady state. Accordingly, we administered recombinant C0-C2 (rC0-C2) to permeabilized cardiomyocytes from transgenic, cMyBP-C null, and human heart failure biopsies, and we found that normal regulation of actomyosin interaction and contractility was restored. Overall, these data provide a unique picture of selective perturbations of the cardiac sarcomere that either lead to injury or adaptation to injury in the myocardium.

overall_design: To determine the differences in mRNA regulation between non-transgenic and deletion of N’-C0-C1f region of cMyBP-C in transgenic mouse hearts

first: Sakthivel

last: Sadayappan

first: Thomas

last: Lynch IV

first: Mohit

last: Kumar


title: Effect of transgenic miR-32 expression on hiMYC-driven prostate cancer in vivo

city: Kuopio

first: Leena

last: Latonen

address: Yliopistonranta 1E

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: We compare the overall gene expression of transgenic mice expressing the MYC oncogene (hiMYC mice) to induce tumorigenesis in the mouse prostate with mice having transgenic expression of the microRNA miR-32 in hiMYC background to determine whether increased expression of miR-32 influences growth or phenotype in prostate adenocarcinoma in vivo.

overall_design: Samples of 6 month old hiMyc (n=4) and miR-32xhiMyc (n=4) mouse prostates were pooled for global gene expression analysis

first: Mauro

last: Scaravilli


title: Rice drought treatment

city: Tsukuba

first: Yoshiki

last: Habu

state: Ibaraki

address: Kannondai 2-1-2

department: Institute of Agrobiological Sciences

institute: National Agriculture and Food Research Organization

summary: Transcriptional profiling of rice shootunder drought condition. Goal was to determine the effects of drought on changes in gene expression.

overall_design: Two-condition experiment. treatments: control or drought. Shoot. Biological replicates: 4, and control replicate 4.

first: Daisuke

last: Ogawa


title: Whole genome transcriptome profiling of Thellungiella salsuginea guard cells under saline growth conditions

city: Wuerzburg

first: Sohail

middle: Mehmood

last: Karimi

state: Bavaria

address: Julius-von-Sachs-Platz 2,

department: Botany 1

institute: University of Wuerzburg

summary: The overall objective was to document transcriptomic changes in the guard cells of Thellungiella salsuginea under short (1x) - and long-term (3x) saline growth conditions. For that. microarray analysis was performed using a 60-mer oligonucleotide probe array from Agilent (44 K, design number 031554, Santa Clara, CA, USA). It was clearly observed that salt salinity alters the transcriptomic landscape of Thellungiella guard cells. However, changes in gene expression were evident under 3x saline growth conditions compared to non-saline conditions. Similarly, more GO terms were significantly enriched in differentially expressed guard cell genes of 3x salt than 1x salt treated plants.

overall_design: Salt induced gene expression studies in the guard cells of Thellungiella salsuginea was conducted. For that, guard cells enriched samples were collected from light adapted plants grown under provided saline growth conditions. Two different salt treatment protocols, a short- and long-term, were applied to 7 weeks old Thellungiella plants by soaking the soil pots in salt solutions each time for two hours. In the long-term salt stress experiment plants were treated three times : (i) On day 1 and 2 (75 mM NaCl), (ii) on day 7 and 8 (150 mM NaCl), and (iii) on day 13 and 14 (200 mM NaCl) named as 3x salt. In the short-term salt stress experiment plants were treated with 200mM NaCl on day 13 and 14 (named as 1x salt) while the control group faced tap water (named as (-) salt). All samples were collected at the end of the salt experiments on day 15 to ensure that plants have the same plant age and developmental stage. Four guard cells enriched samples were collected from each group to conduct gene expression studies.

first: Rosalia

last: Deeken

first: S


title: Microarray expression profile and functional analysis of circular RNAs in plasma for Esophageal Squamous Cell Carcinoma

city: Beijing

first: Fen

last: Liu

address: Youanmenwai Street

department: Department of Epidemiology and Health Statistics

institute: Capital Medical University

summary: The purpose of this study is to explore the circRNAs expression profiles in the plasma from esophageal squamous cell carcinoma (ESCC) patients.The purpose of this study is to explore the circRNAs expression profiles in the plasma from esophageal squamous cell carcinoma (ESCC) patients.

overall_design: We have completed the Arraystar Human circRNA Array analysis of the 10 plasma samples from preoperative ESCC patients (n=5) and healthy controls (n=5).

first: Yuanjie

last: Ding

first: Yi

last: Shen

first: Xudong

last: Guo

first: Wenqiang

last: Wei

first: Xinqing

last: Li


title: Isolation and long-term expansion of murine epidermal stem-like cells

city: Cincinanti

first: Ying

last: Xia

state: Ohio

address: 160 Panzeca Way

department: Department of Environmental and Public Health Sciences

institute: Univerisity of Cincinanti

summary: Epidermis is the most outer layer of the skin and serves as a physical barrier protecting the internal tissues from mechanical and environmental insults. Its constant renewing and regeneration capacity are sustained by the basal keratinocytes, which, through proliferation and differentiation, supply diverse cell types for homeostasis maintenance and injury repair. A major challenge in epidermal research is the difficulty to culture murine keratinocytes. Here we tested murine keratinocyte culture conditions and developed cell lines using low-Ca2+ (0.06 mM) keratinocyte serum-free medium (KSFM-Ca2+) without feeder cells. Cells derived in this condition could be subcultured for >70 passages. These cells displayed basal epithelial cell morphology and expressed keratin (KRT) 14, but lacked the epithelial-characteristic intercellular junctions. After adaptation to the Defined-KSFM (DKSFM) media containing 0.15 mM Ca2+, these cells formed tight- and adherens-junctions and exhibited increased Krt1/10 expression while retaining subculture capacity. Global gene expression studies showed that cells derived in KSFM-Ca2+ media had enriched expression of stem/proliferation markers and that cells adapted in DKSFM media had gene expression signatures of epithelial progenitors. Correspondingly, the KSFM-Ca2+-derived cells had a remarkable capacity of clonal growth, whereas DKSFM-adapted cells could differentiate to suprabasal subtypes in 3D cultures. The generation of stem-like murine keratinocyte lines and the conversion of these cells to epithelial progenitors capable of terminal differentiation provide useful in vitro tools for skin research.

overall_design: Gene exepression prolfiles of two newly established murine keratinocyte lines

first: Jingjing

last: Wang

first: Xiang

last: Zhang


title: Tissue-specific transcriptomics of the Brassica napus - Sclerotinia sclerotiorum interaction uncovers novel regulators of plant immunity

city: Winnipeg

first: Philip

last: Walker

state: Manitoba

address: 104 Dunrobin Avenue

country: Canada

institute: Agriculture and AgriFood Canada

summary: Using a combination of laser microdissection coupled with high-throughput RNA sequencing we profiled the epidermis, mesophyll and vascular leaf tissue layers in response to S. sclerotiorum. We find individual tissue layers reveal distinct defense processes, as well as processes enriched shared between all three layers

overall_design: Individual B. napus leaf tissue layers in response to S. sclerotiorum

first: Mark

middle: F

last: Belmonte


title: RNA-seq of NOTCH1 mutation in chronic lymphocytic leukemia cell BaF3.

city: Charlestown

first: Maolin

last: Ge

state: Massachusetts

address: 149 13th Street

department: MGH Cancer Center

institute: Harvard Medical School

summary: The hotspot c.7541_7542delCT NOTCH1 mutation has been proven to have a unfavorable clinical impact in chronic lymphocytic leukemia (CLL). The aim of our study was to investigate the influence of NOTCH1 mutation(c.7541_7542delCT) on NOTCH1 signaling in CLL cells using Gene Expression Profiling.

overall_design: Examination of mRNA profiles of NOTCH1 genes in BaF3 cells transfected by pmax-Clover/pmax-Clover-ICN/pmax-Clover-ICN mut plasmids.

first: Shifen

first: Han

first: Zhenshu

last: Xu


title: Myofibroblast de-differentiation proceeds via distinct transcriptomic and phenotypic transitions [RNA-Seq]

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: Myofibroblasts are the major cellular source of collagen, and their accumulation –  via differentiation from fibroblasts and resistance to apoptosis – is a hallmark of tissue fibrosis.  Clearance of myofibroblasts by de-differentiation and restoration of apoptosis sensitivity has the potential to reverse fibrosis.  Prostaglandin E2 (PGE2) and mitogens such as fibroblast growth factor-2 (FGF2) have each been shown to de-differentiate myofibroblasts, but the resultant cellular phenotypes have neither been comprehensively characterized nor compared.  Here we show that PGE2 elicited de-differentiation of human lung myofibroblasts via cAMP/PKA while FGF2 utilized MEK/ERK.   The two mediators yielded transitional cells with distinct transcriptomes, with FGF2 promoting but PGE2 inhibiting proliferation and survival.   The gene expression pattern in fibroblasts isolated from the lungs of mice undergoing resolution of experimental fibrosis resembled that of myofibroblasts treated with PGE2 in vitro. We conclude that myofibroblast de-differentiation can proceed via distinct programs exemplified by treatment with PGE2 and FGF2, with that occurring in vivo most closely resembling the former.

overall_design: CCL210 human adult lung fibroblasts were treated with PGE2 for 6 hours, FGF2 for 24 hours, or left untreated for 6 hours or 24 hours, with each condition performed in triplicate.

first: Marc

last: Peters-Golden

first: Sean

last: Fortier

first: Loka

middle: R

last: Penke

first: Dana

last: King

first: Tho

middle: X

last: Pham

first: Giovanni

last: Ligresti


title: Myofibroblast de-differentiation proceeds via distinct transcriptomic and phenotypic transitions [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing


title: Expression data from the carotid artery at 2 wks after Intimal injury

city: shanghai

first: Qi

last: yingxin

address: NO.800 Dongchuan Road, Shanghai

institute: shanghai jiao tong university

summary:
Injury of the arterial endothelial lamina, also called intimal injury, usually occurs after carotid endarterectomy, peripheral artery brachytherapy, stent placement for arterial occlusive disease and balloon dilatation surgeries.
We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up-regulated genes during this process.

overall_design: The intimal injury arteries harvested after 2 wks, and the undamaged right carotid artery served as the self-control, then performed transcriptome sequencing.

first: Ying-Xin

last: Qi

last: Bao


title: ATF3-induced mammary tumors exhibit molecular features of human basal-like breast cancer

city: Houston

first: Yue

last: Lu

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: Transcriptional profiling of mammary tumors that occurs in parous, BK5.ATF3 mice, compared to adjacent normal mammary tissue

overall_design: Two-condition experiment, BK5.ATF3-induced mammary tumors v. adjacent normal mammary glands. Biological replicates: 3 tumors, 3 paired normal glands.

first: Jianjun

last: Shen

first: Michael

middle: C

last: MacLeod

first: Leqin

last: Yan


title: A Non-Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization

city: Durham

first: David

last: Tobin

state: NC

address: 304 Research Drive, 207A Jones Building

department: Molecular Genetics and Microbiology

institute: Duke University

summary: Using the zebrafish-M. marinum model, we identify the basis of granuloma macrophage transformation. Single-cell RNA-seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis-infected macaques reveal that, even in the presence of robust type 1 immune responses, countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling, mediated via stat6, is absolutely required for epithelialization and granuloma formation.

overall_design: Wildtype zebrafish-M. marinum granuloma single-cell RNAseq profile.

first: Erika

last: Hughes

first: Mark

last: Cronan

first: Simon

middle: G

last: Gregory


title: Transcriptomics of weed stress in soybean

city: Fargo

last: Horvath

state: ND

address: 1605 Albrecht Blvd

department: Agr. Research Service

institute: US Dept. Agriculture

summary: Research conducted, including the rationale: Weeds reduce yield in soybeans through incompletely defined mechanisms. The effects of weeds on the soybean transcriptome were evaluated in field conditions during four separate gR1.fastqing seasons. Methods: RNASeq data were collected from 6 biological samples of soybeans gR1.fastqing with or without weeds. Weed species and the methods to maintain weed free controls varied between years to mitigate treatment effects and to allow detection of general soybeans weed responses.  Key results: Soybean plants were not visibly nutrient or water stressed. We identified 55 consistently down-regulated genes in weedy plots. Many of the down-regulated genes were heat shock genes. Fourteen genes were consistently up-regulated. Several transcription factors including a PHYTOCHROME INTERACTING FACTOR 3-like gene (PIF3) were included among the up-regulated genes. Gene set enrichment analysis indicated roles for increased oxidative stress and jasmonic acid signaling responses during weed stress. Main conclusion: The relationship of this weed-induced PIF3 gene to genes involved in shade avoidance responses in arabidopsis provide evidence that this gene may be important in the response of soybean to weeds. These results suggest the weed-induced PIF3 gene will be a target for manipulating weed tolerance in soybean.

overall_design: Samples were collected from two treatments ("Control" and "Weedy") with six biological replicates (2008, 2009, and twop each for 2010 and 2011) for each treatment.

first: Sharon

last: Clay


title: Down-regulation of long non-coding RNA TINCR induces cell dedifferentiation and predicts progression in oral squamous cell carcinoma

city: Guangzhou

first: Zehang

last: Zhuang

address: No. 56 Lingyuan West Road

department: Department of Oral and Maxillofacial Surgery

institute: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University

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

summary: To screen lncRNAs and mRNAs that are deregulated in oral squamous cell carcinoma (OSCC), we comparatively analyzed the lncRNAs and mRNAs profiles by using 10 OSCC patient samples and paired adjacent non-cancerous counterparts. According to the microarray data, we identified 1603 transcripts that were upregulated with more than 2-fold change in OSCC samples in contrast to non-cancerous adjacent tissues (NATs) while 989 transcripts were downregulated by more than 2-fold.

overall_design: A total of 10 fresh human HNSCC specimens and their paired adjacent non-cancerous counterparts were enrolled in this study, which were pathologically diagnosed. All patients received radical surgery and none received any form of pre-surgical adjuvant therapy.

first: Jing

last: Huang

first: Xiqiang

last: Liu


title: Implementation of CRISPR/Cas9 genome editing to generate murine lung cancer models that depict the mutational landscape of the human disease

first: Michaela

last: Reissland

address: Ihnestr. 63

department: Genome Regulation

institute: Max Planck Institut for molecular genetics

summary: Lung cancer is the most common cancer worldwide and the leading cause for cancer related death among both sexes.  Despite the development of novel therapeutic interventions, the 5-year survival rate for NSCLC patients remains low, demonstrating the necessity for novel treatments. One strategy to improve translational research is the development of surrogate models reflecting somatic mutations identified in lung cancer patients as these impact treatment responses. With the advent of CRISPR mediated genome editing, gene deletion as well as site-directed integration of point mutations enabled us to model human malignancies in more detail than ever before possible. Here, we report that, by using CRISPR/Cas9 mediated targeting of Trp53 and KRas, we recapitulated the classic murine NSCLC model, Trp53fl/fl:lsl-KRasG12D/wt. Developing tumors were indistinguishable from Trp53fl/fl:lsl-KRasG12D/wt derived tumors with regard to morphology, marker expression and transcriptional profiles. We demonstrate the applicability of CRISPR for tumor modelling in vivo and ameliorating the need to use conventional genetically engineered mouse models. Furthermore, tumor onset was not only achieved in constitutive Cas9 expressing, but also in wild type animals via infection of lung epithelial cells with two discrete AAVs encoding different parts of the CRISPR machinery.   While conventional mouse models require extensive husbandry to integrate new genetic features allowing for gene targeting, basic molecular methods suffice to inflict the desired genetic alterations in vivo. Utilizing the CRISPR toolbox, in vivo cancer research and modelling is rapidly evolving and enables researchers to swiftly develop new, clinically relevant surrogate models for translational research.

overall_design: gene expression changes of murine WT lung tissue and lung tumor derived cell lines (KPGemm and KPCrispr)

first: Oliver

last: Hartmann

first: Carina

last: Maier

first: Thomas

last: Fischer

first: Cristian

last: Prieto-Garcia

first: Apoorva

last: Baluapuri

first: Jessica

last: Schwarz

first: Werner

last: Schmidt

first: Martin

last: Garrdio

first: Nikolette

last: Pahor

first: Clare

last: Davies

first: Amir

last: Orian

first: Elmar

last: Wolf

first: Almut

last: Schulze

first: Marco

middle: A

last: Calzado

first: Mathias

middle: T

last: Rosenfeldt

first: Markus

last: Diefenbacher


title: Transcriptomic response in the intestine of gilthead sea bream (Sparus aurata) fed garlic, carvacrol and thymol essential oils (EOs) additive.

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

summary: Explore the underlying mechanisms-of-action of the essential oils diet in the intestine of gilthead seabream.

overall_design: Transcriptomic analysis was conducted in order to determine the differences on gene expression level between these two dietary strategies at mid-anterior intestine-specific level. The experimental design included two conditions: (1) fish fed basal diet with no essential oils (EOs) added (control); (2) fish fed 0.5% inclusion of a microencapsulated additive composed of a blend of garlic, carvacrol, and thymol synthetic EOs. After 65 days of feeding trial, total RNA were extracted invidually from gilthead sea bream (S. aurata) intestine fed basal diet or an experimental diet containing 0.5% inclusion. Total RNA samples were grouped into 3 pools (n= 4 fish for each condition). The transcriptomic analysis was done following a reference design using the control diet group as reference.

first: Joana

middle: P

last: Firmino

first: Eva

last: Vallejos-Vidal

middle: E

first: Enric

last: Gisbert


title: Canonical and early lineage-specific stem cell types identified in planarian SirNeoblasts

city: Hangzhou

first: Kevin

last: Niu

state: Zhejiang

address: No.18 Shilongshanjie

institute: Westlake University

summary: The pluripotent stem cells in planarians, a model for tissue and cellular regeneration, have yet to be definitively identified. We recently developed a method to enrich piwi-1+ cells in Schmidtea mediterranea, by staining cells with SiR-DNA and Cell Tracker Green, named SirNeoblasts that permits their propagation and subsequent functional study in vivo. Since traditional enrichment for planarian neoblasts by Hoechst 33342 staining, to generate X1 cells, blocks the cell cycle, inducing cytotoxicity, this method represents a substantive technological advance for functional investigation of cell fate and regeneration in basic and applied research questions. However, the similarities in heterogeneity of cell subtypes between SirNeoblasts and X1 remain unknown. In this work, we performed single cell RNA sequencing for SirNeoblasts for comparison with differential expression patterns in a publicly available X1 single cell RNA sequencing data. We found first that all of the lineage-specific progenitor cells in X1 were present in comparable proportions in SirNeoblasts. In addition, SirNeoblasts contain an early muscle progenitor unreported in X1. Analysis of new markers for putative pluripotent stem cells identified here, with subsequent sub-clustering analysis revealed earlier lineages of epidermal, muscular, intestinal, and pharyngeal progenitors than have been observed in X1. Using the ski-3 and GCM markers, we also identified a pluripotent cell population at higher resolution than that provided by tgs-1. The use of SirNeoblast will enable broad experimental advances in regeneration and cell fate specification, given the possibility for propagation and transplantation of recombinant and mutagenized pluripotent stem cells not previously afforded to this rapid and versatile model system.

overall_design: Examine gene expression profiles of sorted SirNeoblasts cells

first: Kai

last: Lei

first: Kaimeng


title: Identification of gene modulating vascular inflammation using chromosome 2 fragment substitutions and RNA sequencing [RNA-Seq]

status: Public on Mar 22 2021

city: Montreal

first: Pierre

last: Paradis

state: QC

address: 3755 ch. de la Côte-Sainte-Catherine

institute: Lady Davis Institute for medical research, Jewish General Hospital, McGill University

summary: Chromosome 2 introgression from normotensive Brown Norway (BN) rats into hypertensive Dahl salt-sensitive (SS) background (consomic S2B) reduced blood pressure (BP) and vascular inflammation under normal salt diet (NSD). We hypothesized that BN chromosome 2 contains anti-inflammatory genes that could reduce BP elevation and vascular inflammation in rats fed NSD and high salt diet (HSD). We used chromosome 2 fragment substitutions to map chromosome 2 portion associated with vascular inflammation changes and next generation sequencing (NGS) to profile messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) in thoracic descending aorta of SS and congenic rats fed NSD or HSD.

overall_design: Four- to 6-week-old male SS and congenic rats containing the Brown Norway (BN) chromosome (Chr) 2 distal portion (identified as SBA or S2Ba) and middle segment (identified as SBB or S2Bb) were fed NSD or HSD (4% NaCl) up to 12-to-13 weeks old. At the end of the treatment period, total RNA was extracted from a segment of the thoracic descending aorta and mRNAs and ncRNAs were profiled by total RNA sequencing using Illumina HiSeq 2500.

first: Olga

last: Berillo

first: Sofiane

last: Ouerd

first: Asia

last: Rehman

first: Chantal

last: Richer

first: Daniel

last: Sinnett

first: Anne

last: Kwitek

first: Ernesto

last: Schiffrin


title: Profiling of Alu cDNA in the cytoplasmic fraction of human RPE cells

city: Charlottesville

first: Akhil

last: Varshney

state: Virginia

address: 415 Lane Rd

department: Ophthalmology and Center for Advanced Vision Science

institute: University of Virginia

summary: We performed next-generation sequencing of cytoplasmic fractions of primary human RPE cells. Cytoplasmic sample were size-fractionated on a Blue Pippin device (Sage Science) for size restriction to 200–800-nt long species to eliminate genomic DNA contamination and embedded Alu elements. We found that Alu S predominated (61% of Alu reads), with lower levels of Alu J (31%) and Alu Y (8%). No significant difference in the overall distribution of these Alu sequences that mapped to RPE-specific 47 and non-RPE-specific genes was observed. However, we did identify a cluster of Alu sequences within 2,000 bp of 7 single-nucleotide variant loci statistically associated with AMD48.

overall_design: Examination of cytoplasmic DNA in human RPE cells

first: Shinichi

last: Fukuda

first: Benjamin

last: Folower

first: Jayakrishna

last: Ambati


title: The Genetic Architecture of CCl4-induced Liver Fibrosis in Mice

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

summary: Liver fibrosis is a multifactorial trait that develops in response to chronic liver injury. Our aim was to characterize the genetic architecture of carbon tetrachloride (CCl4)-induced liver fibrosis using the Hybrid Mouse Diversity Panel (HMDP), a panel of over 100 genetically distinct mouse strains optimized for genome wide association studies and systems genetics. Chronic liver injury was induced by CCl4 injections twice weekly for six weeks. 437 mice received CCl4 and 256 received vehicle, after which animals were sacrificed for liver histology and gene expression. Using automated digital image analysis, we quantified fibrosis as the collagen proportionate area % (CPA%) of the whole section, excluding normal collagen. We discovered broad variation in fibrosis among the HMDP strains, demonstrating a significant genetic influence on this trait, with an estimated heritability (H2) of 44%. Genome-wide association analyses revealed significant and suggestive loci underlying susceptibility to fibrosis, some of which overlapped with loci identified in mouse crosses and human population studies. Liver global gene expression was assessed by RNA sequencing, and gene set enrichment analyses identified the underlying pathways, of which stellate cell involvement was prominent. We also performed expression quantitative trait locus analyses to identify strong causal candidate genes. Our results provide a rich resource for the design of experiments to understand mechanisms underlying fibrosis and for rational strain selection when testing anti-fibrotic drugs.

overall_design: Mice from 99 mouse strains were injected with either olive oil or CCl4 to induce liver fibrosis; the livers were harvested and RNA extracted from the tissue was used to prepare sequencing libraries. Paired-end sequencing (2x75) was performed.

first: Simon

middle: W

last: Beaven

first: Aldons

middle: J

last: Lusis

first: Brie

last: Fuqua


title: Clever-1 on lymphatics regulates dendritic cell trafficking and modifies adaptive immune responses

city: Turku

first: Sina

last: Tadayon

address: Tykistökatu 6A, 4 floor

institute: Turku University

summary: The goal of this study is to compare gene expression differences between  WT and Stab1-/-  lymphnode's lymphatic endothelial cells  for the identification of biological processes regulated by Stab1 expression.

overall_design: Transcriptome profiles of lymph node's lymphatic endothelial cells of wild type (WT) and stab1-/-  mice were generated by NGS, in triplicate, using Illumina Hiseq3000

first: Akira

last: Takeda

first: Sirpa

last: Jalkanen


title: Identification of gene modulating vascular inflammation using chromosome 2 fragment substitutions and RNA sequencing

first: Pierre

last: Paradis

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

overall_design: Refer to individual Series


title: Cecr2 promotes somatic cell reprogramming as a downstream target of SALL4 [ChIP-seq]

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Sall4 is among one of the most important reprogramming factors. However, the underline molecular mechanisms for such importance remains unclear. In this report, we first described the gene expression and chromatin accessibility dynamics in OKS-Sall4 induced somatic cell reprogramming, and screened a group of downstream targets of Sall4, among which, cecr2, regulated by Sall4 directly, can significantly promote OKS induced reprogramming. Moreover, Cecr2 and Sall4 shared several downstream targets, such as Esrrb, Nanog, T etc., at transcription level when overexpress in the context of OKS induced reprogramming. We further showed that the DTT domain of cecr2 was responding to the reprogramming activity. Our findings provide a new important reprogramming factors and suggesting the cecr2-associted protein network may contributes to overcoming the epigenetic barriers in reprogramming.

overall_design: Examination of SALL4 binding in mouse embryonic stem cells.

first: Linlin

last: Wu


title: Cecr2 promotes somatic cell reprogramming as a downstream target of SALL4 [RNA-seq]

overall_design: In total, we collected 10  cell samples in reprogramming D0, D1, D3,D5 and D7 from 2 independent expriments. mRNA Library sequencing done with NextSeq500.


title: Cecr2 promotes somatic cell reprogramming as a downstream target of SALL4


title: Cecr2 promotes somatic cell reprogramming as a downstream target of SALL4 [ATAC-seq]

overall_design: In total, we collected 10  cell samples in reprogramming D0, D1, D3,D5 and D7 from 2 treatments and perform ATACseq analysis on them.


title: Identification of genes regulated by DUSP4

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

institute: Oita University

summary: In this study, we compared expression profiles between colorectal cancer cell line HCT116 with and without DUSP4 knockdown.

overall_design: Colorectal cancer cell line HCT116 with DUSP4 knockdown (n = 2) vs those without knockdown (n = 2)


title: Paxbp1 is indispensable for cell cycle re-entry of  adult muscle stem cells

city: Hong Kong

first: Shaopu

last: Zhou

address: Room 6202D, Academic Building, HKUST, Clear Water Bay

department: Life Science

institute: HKUST

summary: Adult muscle stem cells (MuSCs) transit from a quiescent state to a highly proliferative state to support muscle repair. Paxbp1 deletion in MuSCs blocked their cell cycle re-entry and caused  subsequent muscle regeneration failures. To understand the underlying molecular mechanisms, we compared the transcriptomes of  control and Paxbp1 mutant MuSCs by RNA-seq. Our data confirmed a marked repression of cell cycle machineries in Paxbp1 mutant MuSCs. We also uncovered down-regulation of mutliple metabolic pathways in mutant MuSCs. In summary, our study highlights an essential role of Paxbp1 in MuSCs growth and cell cycle re-entry.

overall_design: 3 pairs of control (Pax7creER:Paxbp1flox/+:R26R-YFP) and Paxbp1-iKO (Pax7creER:Paxbp1flox/flox:R26R-YFP) mice were subjected to lower hindlimb muscle injury by cardiotoxin (CTX). 24 hours post injury, satellite cells were sorted using FACS based on their YFP fluorescence. Total RNAs were then extracted and used for RNA-seq experiments.

first: Zhenguo


title: Targeting KDM4A epigenetically activates tumor cell-intrinsic immunity and overcomes resistance to PD1 blockade in squamous cell carcinoma by inducing DNA replication stress

city: Shanghai

first: WUCHANG

last: ZHANG

state: Shanghai

address: 115 Jinzun Road

department: School of stomatology

institute: Shanghai Jiao Tong University

summary: To investigate the mechanisms by which KDM4A knockout ameliorates the invasive growth and metastasis of primary mouse squamous cell carcinoma (SCC),  we isolated fresh SCCs from tumor cell-specific KDM4A knockout and control mice,  and then did the whole transcriptome analysis using RNA-Seq. Results showed that KDM4A knockout stimulated anti-tumor immunity.

overall_design: Analysis of the whole transcriptome of primary mouse SCCs.

first: Wuchang

last: Zhang

first: Cun-Yu

last: Wang


title: Expression data for the siCtrl and siHPIP treated BeWo cells

status: Public on Mar 21 2021

city: Hyderabad

first: Bramanandam

last: Manavathi

state: Telangana

address: Dept. of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad

department: Department of Biochemistry

country: India

institute: University of Hyderabad

summary: HPIP is an oncogenic protein and plays a major role in cancer progression, while its role in trophoblast differentiation is largly unknown. Therefore we analysed the effect of HPIP knockdown on gene expression signature in BeWO cells.

overall_design: We knockdown HPIP in BeWo cells using gene specific siRNA or control siRNA and subsequently total RNA was isolated and then was analysised for global RNA profiling using microarray.

first: Vasudevarao

last: Penugurti


title: Rice acetate treatment

city: Tsukuba

first: Yoshiki

last: Habu

address: Kannondai 2-1-2

institute: National Agriculture and Food Research Organization

summary: Transcriptional profiling of rice shoot or root treated with acetate. Goal was to determine the effects of acetate on changes in gene expression.

overall_design: Three-condition experiment. Treatments: control, acetic acid or potassium acetate. Root or shoot. Biological replicates: 3, and control replicate 3.

first: Daisuke

last: Ogawa


title: The Androgen Receptor Directly Regulates CD44 Expression in Androgen Sensitive Bladder Cancer

first: Dan

last: Theodorescu

state: CA

address: 8700 Beverly Blvd., Davis Building, Rm 3057

institute: Cedars Sinai Medical Center


title: Transcriptomic analysis of  fungus Penicillium oxalicum and its laeA, clrB and rcoA deletion strains

city: jinan

first: Zhang

last: Xiujun

state: shandong province

address: south road of shanda

institute: shandong university

summary: The goals of this study are to compare differential gene expressions for Penicillium oxalicum wild type strain (WT), laeA knockout strain (ΔlaeA), rcoA knockout strain (ΔrcoA), and  clrB knockout strain (ΔclrB). The deletion of laeA downregulated genes involved in oxidation- reduction process, alkaloid metabolic process, and transmembrane transport. We find the expression levels of seven secondary metabolism gene clusters (totally 28 clusters) were silenced inΔlaeA. The deletion of clrB downregulated genes involved in hydrolase activity, acting on glycosyl bonds. Many genes involved in conidiation were drastically regulated in ΔrcoA. This study provides the information that combined laeA, clrB and rcoA function are required in conidiation and hydrolase activity of P. oxalicum.

overall_design: Examination of differential gene expressions by digital gene expression tag profiling in Penicillium oxalicum wild type strain and three mutant strains (laeA knockout strain, rcoA knockout strain and clrB knockout strain). qRT–PCR validation was performed using SYBR Green assays.

first: Yuqi

last: Qin

first: Xiujun

first: Yinbo

last: Qu


title: The Androgen Receptor Directly Regulates CD44 Expression in Androgen Sensitive Bladder Cancer [ChIP-seq]

summary:
To study androgen receptor transcriptomic activation in the presence of androgen in bladder cancer cell lines.  A uniquely derived AR expressing clone of the bladder cancer cell line UMUC3 was derived and validated prior to ChIP-seq experiments.
Androgen receptor chromatin immunoprecipitation (AR ChIP-seq) was used to determine the overall expression changes in repsonse to treatment with synthetic androgen.  Evaluation of genes associated with androgen receptor stimulation were used for focused analysis when combined with microarray data.

overall_design: Cell were treated with vehicle control (ethanol) or synthetic androgen (R1881) with 5 biological replicates per condition

first: Joseph

last: Sottnik

first: Lauren

last: Vanderlinden


title: Identification of gene modulating vascular inflammation using chromosome 2 fragment substitutions and RNA sequencing [miRNA-Seq]

first: Pierre

last: Paradis

summary: Chromosome 2 introgression from normotensive Brown Norway (BN) rats into hypertensive Dahl salt-sensitive (SS) background (consomic S2B) reduced blood pressure (BP) and vascular inflammation under normal salt diet (NSD). We hypothesized that BN chromosome 2 contains anti-inflammatory genes that could reduce BP elevation and vascular inflammation in rats fed NSD and high salt diet (HSD). We used chromosome 2 fragment substitutions to map chromosome 2 portion associated with vascular inflammation changes and next generation sequencing (NGS) to profile microRNAs in thoracic descending aorta of SS and congenic rats fed NSD or HSD.

overall_design: Four- to 6-week-old male SS and congenic rats containing the Brown Norway (BN) chromosome (Chr) 2 distal portion (identified as SBA or S2Ba) and middle segment (identified as SBB or S2Bb) were fed NSD or HSD (4% NaCl) up to 12-to-13 weeks old. At the end of the treatment period, total RNA was extracted from a segment of the thoracic descending aorta and microRNAs were profiled by small RNA sequencing using Illumina HiSeq 2500.

first: Olga

last: Berillo

first: Sofiane

last: Ouerd

first: Noureddine

last: Idris-Khodja

first: Asia

last: Rehman

first: Chantal

last: Richer

first: Daniel

last: Sinnett

first: Anne

last: Kwitek

first: Ernesto

last: Schiffrin


title: The Androgen Receptor Directly Regulates CD44 Expression in Androgen Sensitive Bladder Cancer [gene expression]

summary:
To study androgen receptor transcriptomic activation in the presence of androgen in bladder cancer cell lines.  A uniquely derived AR expressing clone of the bladder cancer cell line UMUC3 was derived and validated prior to microarray experiments.
Microarrays were used to determine the overall expression changes in repsonse to treatment with synthetic androgen.  Evaluation of genes associated with androgen receptor stimulation were used for focused analysis when combined with ChIP-seq data.

overall_design: Cell were treated with vehicle control (ethanol) or synthetic androgen (R1881) with 3 biological replicates per condition


title: Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify differences in DNA methylation [RRBS]

status: Public on Mar 20 2021

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

type: Methylation profiling by high throughput sequencing

summary:
Background The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology.
Results We used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group.
Conclusions Our data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.

overall_design:
DNA was collected from mouse entorhinal cortex samples and methylation levels quantified using both array and RRBS technology. For the RRBS data, library pools were distributed across thirty-two HiSeq2500 (Illumina) lanes and subjected to 50 bp single-end sequencing.
Randomly assigned groups 1 and 2 are used for power calculations and are not meaningful biological groups in the paper that this data is associated with.

first: Dorothea

last: Seiler Vellame

first: Isabel

last: Castanho


title: RNA-seq analysis of diploid and tetraploid neonatal rat cardiomyocytes

city: Chongqing

first: Yun-Han

last: Jiang

address: No. 183 Xinqiao Street

institute: Xinqiao Hospital

summary: In response to pathological stress such as congenital heart disease and heart valvular disease, cardiomyocytes (CMs) generally increased the content of DNA and the number of nuclear. This process named CM polyploidization and multi-nucleation, result in the presence of multi-nucleated polyploid CM. However, the significance of multi-nucleated polyploid CM (M*Pc CM) for heart disease remains enigmatic. We speculated that the process of CM polyploidization and multinucleation may be an adaptative response, which may help CM function recovery and survive the stress condition. We sought to determine the mechanism of enhanced mitophagy in M*Pc CMs during hypoxia adaptation.

overall_design: After hypoxia (1% oxygen) for 48h, neonatal rat cardiomyocytes (NRCMs) were stained with Hoechst 33342 and sorted into two subpopulation including diploid (2n) and tetraploid (4n). Four biological replicates of each condition (hypoxia) and flow cytometry sorting were used from independent experiments.


title: Gene Expression Profile of Central Centrifugal Cicatricial Alopecia

city: Baltimore

first: Crystal

last: Aguh

state: Maryland

address: 1500 Orleans St, CRB II Suite 200

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: Background: Central Centrifugal Cicatricial Alopecia (CCCA) is a primary cicatricial alopecia that most commonly affects women of African descent. Like CCCA, fibroproliferative disorders (FPDs) such as keloids, atherosclerosis and fibroids, are characterized by low-grade inflammation and irritation resulting in end stage fibrosis.   Objective: We sought to determine if fibroproliferative genes were upregulated in patients with CCCA  Methods: Five patients with biopsy proven CCCA were recruited for this study. Two scalp biopsies were obtained from each patient; one from CCCA affected vertex scalp and one from the unaffected occipital scalp. Microarray analysis was performed to determine the differential gene expression patterns  Results: Several pathways responsible for excess collagen deposition and aberrant wound healing were up-regulated in CCCA affected scalp when compared to unaffected scalp with patterns similar to other FPDs. Genes downregulated in CCCA affected tissue included those with roles in lipid metabolism and fatty acid biosynthesis.  Limitations: Small sample size and the use of whole skin tissue for analysis.  Conclusion: We have identified the up-regulation of critical genes implicated in fibroproliferative disorders in the gene expression profile of patients with CCCA. These findings may help identify future therapeutic targets for this otherwise difficult to treat condition.

overall_design: We performed gene expression microarrays on paired samples of affected and unaffected scalp tissue to assess markers of fibroblast activation in five patients with CCCA.

first: Yemisi

last: Dina

first: C.

last: Conover Talbot Jr

first: Luis

last: Garza


title: LncRNA microarray analysis of coronary heart disease (CHD)

city: Fuzhou

first: Yi

last: Sun

state: Fujian Province

address: Minhou County, Fuzhou, 350122, China Minhou County, Fuzhou, 350122, China

institute: Fujian Medical University

summary: The present study aims to explore the expression profiles and biological functions of long-chain noncoding RNA (lncRNA) in coronary heart disease (CHD)

overall_design: Ten human blood samples (five each from the CHD and control groups) were included. The differentially expressed lncRNAs were evaluated using microarray.


title: Whole-genome microRNA microarray for CD44 positive and negative pediatric posterior fossa ependymoma

city: tianjin

first: chang

last: shu

address: 94 weijin road

institute: Tianjin HuanHu hospital,School of medicine,Nankai university

summary: we used whole-genome microRNA microarray expression profiling as a discovery platform to identify a subset of miRNAs that were differently expressed in CD44-positive pediatric posterior fossa ependymoma compared with CD44-negative ones.

overall_design: we used six CD44 positive and negative pediatric posterior fossa ependymoma respectively from the same hospital during the same period to do the microarray.

first: Chang

last: Shu

first: Jinhuan

last: Wang


title: The effect of Repeated Social defeat stress (RSD) on transcriptomic profiles of rat heart

status: Public on Mar 19 2021

city: Rome

first: Luisa

last: Lo Iacono

address: via del fosso di Fiorano 64

department: behavioral neuroscience

country: Italy

institute: Fondazione Santa Lucia IRCCS

summary: This study investigated risk factors that may contribute to stress-related cardiac disease susceptibility and progression in a rodent model. The experiment was designed to evaluate the transcriptomic changes in in the heart of male adult rats after repeated episodes of social defeat stress.

overall_design: We performed comparison between the Heart left ventricle mRNA profiles of adult RSD (n=6) and control (CTR) (n=6) male rats - two experimental groups.

first: Luca

last: Carnevali

first: Diego

last: Andolina

first: Andrea

last: Sgoifo


title: Single-cell RNA-seq reveals landscape of cell-type-specific lincRNAs in somatosensory neuron and lincRNA CLAP in itch sensation

city: Zhuhai

first: Bin

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

institute: Guangdong institute of intelligence and science technoloty

summary: The expression of differential genes after knockdown of CLAP in L4/5 DRGs of mice

overall_design: RNA-seq of CLAP knockdown in L4/5 DRGs of mice

first: Lan

last: Bao

first: Li

last: Yang

first: Guowei

last: Li


title: Human Placental Exosomes in Gestational Diabetes Mellitus Carry a Specific Set of miRNAs Associated with Skeletal Muscle Insulin Sensitivity

city: Brisbane

first: Dominic

last: Guanzon

state: Queensland

address: Building 71/918 RBWH Herston

department: UQCCR

country: Australia

institute: University of Queensland

summary: The objective of this study was to investigate whether placental exosomes in gestational diabetes mellitus (GDM) carries a specific set of miRNAs associated with skeletal muscle insulin sensitivity. Exosomes were isolated from chorionic villi-conditioned media and plasma from normal and GDM pregnancies. A specific set of miRNAs was identified to be selectively enriched within exosomes when compared to their cells of origin indicating specific packaging of miRNAs into exosomes. In addition, miRNA expression varies in a consistent pattern in placenta, placental-derived exosomes, circulating exosomes and skeletal muscle in GDM.

overall_design: miRNAs were profiled from exosomes and tissues using next generation seqeuencing (Illumina NextSeq 500 platform).

first: Soumyalekshmi

last: Nair

first: Carlos

last: Salomon


title: Procaspase3-Cyclin D1 assembly rewires cancer cells from apoptosis to proliferation

city: Montpellier

first: Frederic

middle: Emile

last: Bienvenu

address: 141 rue de la Cardonille

department: Cancer Biology

country: France

institute: CNRS-Institute of Functinal Genomics

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

overall_design: Refer to individual Series


title: Procaspase3-Cyclin D1 assembly rewires cancer cells from apoptosis to proliferation [in vivo]

summary:
Purpose: To gain insights into the activity of Cyclin D1 in tumor maintenance, we developed a specific RNAi strategy to knock down its expression and analyze the outcome on gene expression profile of the entire tumor.
Method: MMTV-ErbB2 or RAS/DNP53-driven tumor mRNA profiles were generated by RNA-Sequencing.
Results: Cyclin D1 knock down in RAS-G12V or MMTV-ErbB2-driven tumors leads to expression change of genes involved in developmental processes, but no change in FAS or FASL levels.

first: Benjamin

last: Maurel

first: Laetitia

last: Linares

first: Emeric

last: Dubois


title: CDK7 Inhibition by THZ1 Suppresses Cancer Stemness in both Chemonaïve and Chemoresistant Urothelial Carcinoma via the Hedgehog Signaling Pathway

city: Taipei

first: Po-Ming

last: Chow

address: No. 7, Zhongshan S. Rd., Zhongzheng Dist.

department: Department of Urology

country: Taiwan

institute: National Taiwan University Hospital

summary: THZ1 inhibits cancer stemness via Hedgehog pathway.

overall_design: T24/R cells were treated with 1600 nM THZ1 for 6 hours.

first: Yu-Wei

last: Chang


title: RNA Helicase DDX5 Acts as a Critical Regulator for Gonocyte Survival in Neonatal Mouse

city: Guangzhou

first: Cui

last: Guizhong

state: Guangdong

address: 188 KaiYuan Road, Huangpu District

department: Center of Cell Lineage and Atlas

institute: Guangzhou Laboratory

summary: Mammalian spermatogenesis is a dynamic and highly coordinated biological process. The production of spermatozoa relies on a pool of spermatogonial stem cells (SSCs), formed in infancy from their precursor cells, the gonocytes. In this study, we found that Ddx5 is highly expressed in male germ cells from embryonic period. We generated germ-cell-specific Ddx5 knockout mice (Ddx5 cKO) by using Mvh-Cre transgenic mice. Ddx5 homozygous knockout mice resulted in significant smaller size and light weight of testes, but Ddx5 heterzygous knockout mice have no effect on reproduction. Furthermore, Ddx5 homozygous knockout resulted in gradual loss of germ cells in neonate’s testes and a complete loss of germ cells within 6 days after birth, leading to azoospermia and infertility in male adults. Single cell RNA sequencing (scRNA-seq) experiments showed that the expression of genes that are involved in cell cycle and GDNF pathway were significantly decreased in gonocytes after Ddx5 knockout. Together, these results reveal critical functions of Ddx5 in the survival and cell fate determination of gonocytes.

overall_design: Single cell gene expression profiling of whole testes from wild type (WT) and germ-cell-specific Ddx5 knockout mice (Ddx5 cKO) at postnatal day 2.

first: Qing

last: Xia

first: Guizhong

last: Cui


title: The Protective Role of the Epitranscriptome against Acetaminophen Toxicity

city: Albany

first: Thomas

last: Begley

address: 1400 Washington Ave

institute: SUNY Albany

summary: We report differential mRNA sequencing data on C57BL/6 background of both Wildtype and Alkbh8Def in saline and acetaminophen exposure conditions in acute (6 hour) and chronic (4 day) conditions.

overall_design: Total RNA was isolated from murine liver tissue and treated with DNAse.  Samples were prepped and processed at the University at Albany Center for Functional Genomics with Poly-A selection and ran on Illumina Nextseq500 (Illumina, Inc., San Diego, CA) at 75 million single-end reads per run.

first: Sara

last: Evke

first: Marcy

last: Kuentzel

first: Sridar

last: Chittur


title: MiRNAs sequence  of macrophages derived exosoms in WT group and Roquin-1 san:san group.

first: Lei

last: Zheng

address: 639 Zhizaoju Road

institute: Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medi-cine

summary: We reported the function of Roquin-1 in the miRNA-sorting of macrophages derived exosomes. At first, we used the supernatant of 929 cells to culture the bone marrow derived macrophages (BMDM) from bone marrow cells of WT and Roquin-1 san:san mice. Then, we isolated the macrophages derived exosomes by ultracentrifugation. At last, we performed Next-generation sequencing to detect the differences of miRNA-sorting between WT and Roquin-1 macrophages derived exosomes.

overall_design:
miRNA profiles of macrophages derived exosomes in WT and Roquin-1 san:san mice
[contributor]  Nanjing Medical University


title: Association of sputum microbiome with exacerbations, patient subgroups and host response in chronic obstructive pulmonary disease

city: Collegeville

first: Zhang

last: Wang

state: PA

address: 1250 S Collegeville Rd

institute: GlaxoSmithKline R&D

summary:
Little is known about the lung microbiome dynamics and host-microbiome interactions in relation to chronic obstructive pulmonary disease (COPD) exacerbations and in patient subgroups based on smoking status and disease severity.
Here we performed a 16S ribosomal RNA survey on sputum microbiome from 16 healthy and 43 COPD subjects. For COPD subjects, a longitudinal sampling was performed from stable state to exacerbations, at two and six weeks post-exacerbations and at six months from first stable visit. Host sputum transcriptome were characterized for a subset of COPD patient samples.

overall_design: We used microarrays to profile host transcriptomes at stable and exacerbtions of COPD patients.

first: Barbara

last: Maschera

first: Mark

last: Lennon

first: Dave

last: Singh


title: DNA damage-induced genes in KMS12PE cells

city: Maebashi

first: Tsukasa

last: Oda

state: Gunma

address: Showa-machi, 3-39-15

department: IMCR

institute: Gunma University

summary: The major histocompatibility complex class II (MHC II) is important for the adaptive immune response because it presents processed antigens to CD4-positive T-cells. Conventional chemotherapeutic agents (e.g., melphalan, adriamycin, hydroxyurea) induce tumor cell death by causing DNA double strand breaks (DSBs), which are crucial for anti-tumor effects. However, the cellular response induced at low doses of these agents that do not cause immediate cell death is unclear. We have employed microarray expression profiling to identify genes which are induced by low dose of chemotherapeutic agents. Multiple myeloma cell line KMS12PE was treated with vehicle, 2 μM melphalan, or 50 nM adriamycin. These agents transcriptionally induced the major histocompatibility complex class II (MHC II) genes. They also increased the expressions of MHC class II transactivator (CIITA), the master regulator of MHC II genes and interferon regulatory factor 1 (IRF1), a transcription factor for CIITA.

overall_design: We treated multiple myeloma cell line KMS12PE with vehicle, 2 μM melphalan or 50 nM adriamycin for 5 days


title: Global gene expression and Stromal contents improve prognostic power in PMP patients treated by CRS+HIPEC

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

institute: Candiolo Cancer Institute, University of Torino

summary: In recent years, cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC) have substantially improved the clinical outcome of pseudomyxoma peritonei (PMP) originating from mucinous appendiceal cancer. However, current histopathological grading of appendiceal PMP frequently fails in predicting disease outcome. We recently observed that the integration of cancer cell transcriptional traits with those of cancer-associated fibroblasts (CAFs) improves prognostic prediction for tumors of the large intestine. We therefore generated global expression profiles on a consecutive series of 24 PMP patients treated with CRS plus HIPEC. Multiple lesions were profiled for nine patients. We then used expression data to stratify the samples by a previously published "high-risk appendiceal cancer" (HRAC) signature and by a CAF signature that we previously developed for colorectal cancer, or by a combination of both. The prognostic value of the HRAC signature was confirmed in our cohort and further improved by integration of the CAF signature. Classification of cases profiled for multiple lesions revealed the existence of outlier samples and highlighted the need of profiling multiple PMP lesions to select representative samples for optimal performances. The integrated predictor was subsequently validated in an independent PMP cohort. These results provide new insights into PMP biology, revealing a previously unrecognized prognostic role of the stromal component and supporting integration of standard pathological grade with the HRAC and CAF transcriptional signatures to better predict disease outcome.

overall_design: Global expression profiling with DNA microarrays of frozen samples of pseudomixoma peritonei from mucinous appendiceal cancer.

first: Claudio

last: Isella

first: Marco

last: Vaira


title: Whole genome transcriptome profiling of Arabidopsis thaliana guard cells under saline growth conditions

city: Wuerzburg

first: Sohail

last: Karimi

state: Bavaria

address: Julius-von-Sachs-Platz 2,

department: Botany 1

institute: University of Wuerzburg

summary: The overall objective was to document transcriptomic changes in the guard cells of Arabidopsis thaliana under short (1x) - and long-term (3x) saline growth conditions. Guard cells of Arabidopsis responded also to the intensity of the salt management by the microarray datasets clearly clustering in (-) salt, 1x salt and 3x salt. Similarly, more GO terms were significantly enriched in differentially expressed guard cell genes of 1 x salt than 3x salt treated plants.

overall_design: Salt induced gene expression studies in the guard cells of glycophyte Arabidopsis thaliana was conducted. For that, guard cells enriched samples were collected from light adapted plants grown under provided saline growth conditions. Two different salt treatment protocols, a short- and long-term, were applied to 4 to 5 weeks old Arabidopsis plants by soaking the soil pots in salt solutions each time for two hours. In the long-term salt stress experiment plants were treated three times : (i) On day 1 and 2 (75 mM NaCl), (ii) on day 7 and 8 (150 mM NaCl), and (iii) on day 13 and 14 (200 mM NaCl) named as 3x salt. In the short-term salt stress experiment plants were treated with 200mM NaCl on day 13 and 14 (named as 1x salt) while the control group faced tap water (named as (-) salt). All samples were collected at the end of the salt experiments on day 15 to ensure that plants have the same plant age and developmental stage. Four samples were collected from each group except for 1x salt where 3 samples were analyzed for gene expression studies.

first: Rosalia

last: Deeken


title: Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify differences in DNA methylation

first: Emma

last: Walker

address: RILD Barrack Rd

institute: University of Exeter

type: Methylation profiling by genome tiling array

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus


title: Secreted milk transcriptome from early lactation dairy cows

city: WEST LAFAYETTE

first: Shaojun

last: Xie

state: Indiana

address: 3135 Decatur Street

institute: Purdue University

summary: Our objective was to characterize the protein coding portion of the bovine mammary gland transcriptome by magnitude of RNA-seq read counts. EBseq analysis determined no differentially expressed genes due to postruminal lysine infusion, therefore, read counts were averaged across treatment and block. DAVID functional annotation analysis was utilized to determine specific gene ontologies and KEGG pathways to describe the data by magnitude of reads.

overall_design: Six Holstein cows' milk RNA sequenced to determine effects of postruminal lysine treatment on mammary transcriptome profile.

first: Linda

last: Beckett

first: Shawn

last: Donkin

first: Theresa

last: Casey

first: Jyothi

last: Thimmapuram


title: Transcriptome analysis using Arabidopsis leaves after exogenous FAD treatment

status: Public on Mar 18 2021

city: Matsue-shi

first: Takahisa

last: Ogawa

state: Shimane

address: Nishikawatsu-cho 1060

institute: Shimane University

summary:
Riboflavin (RF) and its cofactors (FMN and FAD) are essential molecules for vital metabolic processes in all organisms. Thus, the flavin metabolism must be tightly regulated in the cells. We previously demonstrated that the intracellular levels of flavins were tightly maintained by the enzymes involved in their synthesis and degradation, inducing a plastidic FAD hydrolase (AtNUDX23), in Arabidopsis. However, information of regulatory factors involved in the flavin homeostasis and transporters in each organelle are mostly limited.
Terefore, we tried to identify novel factors involved in the flavin metabolism, such as transcription factors and transporters by a transcriptome analysis after exogenous FAD treatment.

overall_design: Wild-type Arabidopsis plants were grown on soil in a growth chamber kept at 23°C during 16 h of light (100 µmol/m2/s) and 8 h of darkness for 3 weeks. At 4 h after the illumination, detached rosette leaves were floated on water (mock) or 0.1 mM FAD solution for 1h. After 1h, collected leaves were washed and used for microarray analysis. Two biological replicates were analyzed.

first: Kazuya

last: Yoshimura

first: Shigeru

last: Shigeoka


title: Identification of age-related changes in gene expression and chromatin accessibility in T cells from thymus to periphery (44K)

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

summary: Aging of immune system is characterized by progressive decline of physiological and cellular function of T cells. Recent studies of naïve T cells from young and old mice have identified age-related altered gene expressions but the mechanisms underlying age associated changes of naïve T cells remain poorly understood. Here we compared the transcriptome and chromatin accessibility in mature CD4 and CD8 thymocytes and in naïve CD4 and CD8 T cells of spleen between young (6-8 weeks) and old (79-121 weeks) C57Bl/6 mice. We used Agilent microarray method and identified the age-related altering gene expressions 1) only in mature CD4 and CD8 T cell from thymus, 2) shared by both thymus and spleen naïve T cells, and 3) only in naïve T cells from spleen. The shared changes include increased chemokine and chemokine receptor expressions and decreased cell cycle regulator expression. We further analyzed the chromatin basis of altered gene expression using Assaying Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) between young and old mice. We have identified age-related changes of chromatin accessibility in T cells from thymus and spleen, and some correlated changes between gene expression and chromatin accessibility. Overall, we observedmore age-related alterations of gene expression and chromatin accessibility inthymus than in spleen, suggesting some age-related changes of T cells in thymus did not retain in periphery. Together, our findings have identified tissue specific altered gene expressions and chromatin status in T cells during aging and further study of these altered genes will shed new insights into the mechanisms underlying these age-related changes.

first: Guobing

last: Chen

first: Nan-ping

last: Weng


title: Does early treatment of PKU patients with sapropterin dihydrochloride affect brain development?

city: Lausanne

first: Sandra

last: Calderon

address: Génopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary:
Background: Phenylketonuria (PKU) is an inborn error of metabolism caused by phenylalanine hydroxylase (PAH) deficiency. Patients with mild or moderate PKU can be successfully treated with sapropterin dihydrochloride (SD) which since recently is registered for usage from the age of 4 months. SD is a pharmaceutical version of tetrahydrobiopterin (BH4), a cofactor of PAH. Similar BH4 concentrations to those observed in plasma have been found in CSF of patients after a single oral administration thus proving that SD crosses the BBB. Hyperactivity has recently been reported as a post-marketing observation in some PKU patients treated with SD.
Methods: 60 or 120 ng/ml sepiapterin, a stable precursor of BH4, were applied to study the effects of BH4 on developing brain cells in 3D organotypic rat brain cell cultures at two developmental stages. Immunohistochemistry, western blotting, metabolomics and RNA sequencing were performed.
Findings: BH4 and BH2 measurements confirmed a successful conversion of sepiapterin to the active form BH4. In the earlier developmental stage, brain cell specific markers showed swollen astrocytes and diminished astrocytic fibres, delayed differentiation of oligodendrocytes and perturbation of axonal elongation. Immunofluorescence for activated caspase-3 revealed an increased apoptosis rate. We also found signs of perturbated GABAergic neurotransmission. RNAseq analyses revealed a number of significantly affected genes. GO enrichment allowed to identify key biological processes. Interestingly, none of these effects was observed in the later developmental stage.
We show deleterious effects of SD on developing brain cells in a rat in vitro model. This observation raises the question whether the use of SD can be recommended in very young PKU patients as currently licensed.

overall_design: Examination of 3 replicates of 3D brain cell agreggates treated with 120 ng/ml sepiapterin or aggregates control (treated with PBS) at 3 different time points

first: Noémie

last: Remacle

first: Mary

last: Gonzalez-Melo

first: Hong-Phuc

last: Cudré-Cung

first: Claire

middle: M

last: Dubois

first: Hugues

last: Henry

first: Ashley

middle: B

last: Hale

first: Keith

last: Channon

last: Copete

first: Johann

last: Weber

first: Sylvain

last: Pradervand

first: Olivier

last: Braissant

first: Diana

last: Ballhausen


title: Procaspase3-Cyclin D1 assembly rewires cancer cells from apoptosis to proliferation [in vitro]

first: Frederic

last: Bienvenu

summary:
Purpose: To gain insights into the activity of Cyclin D1 in tumor maintenance, we developed a specific RNAi strategy to knock down its expression and analyze the outcome on gene expression profile of RAS/DNP53-driven cancer cells (transformed MEFs). Cells were treated by RNAi or with Leptomycin B over night.
Method: RAS/DNP53-transformed MEFs mRNA profiles were generated by RNA-Sequencing.
Results: Cyclin D1 knock down in RAS-G12V-driven cancer cells leads to expression change of genes involved in developmental processes, but no change in FAS or FASL levels.

first: Julien

last: Champagne

first: Emeric


title: Multi-omic analyses reveal minimal impact of the CRISPR-Cas9 nuclease on the host

city: Shanghai

first: Zaijun

last: Ma

address: Qiuyue Road 26

institute: Chinese Academy Science

summary: Transcriptomics strategies were applied to explore the cellular feedback after incorporating the Cas9. HEK293T cell lysates  were collected after 24h transfected with PX330-GFP-cas9-6T, PX330-GFP-cas9-luciferase, PX330-GFP-noCas9-6T, PX330-GFP-noCas9-luciferase. RNA-seq data were generated from deep sequence. We found the impact caused by Cas9 is very minor

overall_design: mRNA profiles of HEK293T transfected with Cas9 or transfected without Cas9 were generated by deep sequencing using Illumina.

first: Jiali

last: Qiang


title: Exosomal-miRNA sequencing of optineurin gene knockdown BV2 cells and wild type BV2 cells

first: Ye

last: He

address: No.1023, South Shatai Road, Baiyun District

institute: Southern Medical University Nanfang Hospital

summary: To compare the miRNA profiles in exosomes derived from optineurin gene knockdown (Optn-KD)BV2s cells and wild type (WT) BV2 cells, BV2 cells were divided into two groups, Optn-KD group or WT group. We treated the Optn-KD group with Optn siRNA for 24 hours. Then, MiRNA profiles for each group were examined by Illumina HiSeq4000. We found differentiated miRNA profiles in the two groups. Compared with WT BV2 cell-derived exosomes, 4 miRNAs (miR-125b-5p, miR-351-5p, miR-505-5p, miR-novel-chr8_37700) were up-regulated and 2 miRNAs (miR-574-5p, miR-99b-5p) were down-regulated in Optn-KD BV2 cell-derived exosomes. This study provides a framework for characterizing the exosomal-miRNAs in Optn-KD BV2 cells.

overall_design: Exosomal-miRNA sequences of Optn knockdown BV2 cells and wild type BV2 cells were examined by Illumina HiSeq4000

first: Haishan

last: Jiang

first: Weiyi

last: Yu


title: Transcript profiling of WT and SIRPα KO BMDMs post-M1 activation in the presence of mCD47.ex

city: Atlanta

first: Lei

last: Shi

state: GA

address: 100 Piedmont Avenue SE

department: Department of Biology

institute: Center for Diagnostics & Therapeutics

summary: To compare the inflammatory responses of WT and SIRPα KO macrophage, we performed a complete transcript profiling of WT and SIRPα-KO M1 macrophage using transcriptome sequencing as a discovery platform. SIRPα-KO mice and WT mice were kept under the same condition. BMDMs were produced from WT and SIRPα-KO mice followed by M1 polarization. RNA was then isolated from the same number of BMDMs.

overall_design: In each group, 5 mice were used. The bone marrow-derived macrophages (BMDM) produced from WT and SIRPα-KO mice were treated with IFNγ(20ng/ml) plus LPS (100ng/ml) in the presence of mCD47.ex for 6h. The M1 BMDM from 5 SIRPα-KO or 5 WT mice were mixed before RNA extraction.

first: Yuan

last: Liu


title: Gene expression analysis of single and co-cultured HER2 L755S mutants in MCF-10A background

city: Baltimore

first: Swathi

last: Karthikeyan

address: 733 N Broadway

institute: Johns Hopkins University School of Medicine

summary:
PIK3CA E545K mutants induce epidermal growth-factor independent proliferation of HER2 L755S mutants through a contact-mediated mechanism.
We used RT2 Profiler PCR Arrays to study changes in gene expression in the HER2 L755S mutants when co-cultured with the PIK3CA E545K mutants and compared it to the HER2 L755S mutants grown in isolation.

overall_design:
There are two groups. HER2 L755S mutants were co-cultured with PIK3CA E545K mutants. The co-culture was then flow-sorted to separate the HER2 L755S mutants. The flow-sorted HER2 L755S mutants were the test group. HER2 L755S mutants grown in isolation were used as the control group.
Each group (test and control) had two biological replicates and each biological replicate had two technical replicates (quadrapilcates for each group in total).


title: Analysis of Wild Type and MFN2-/- Macrophage Transcriptomes

city: Seoul

first: June-young

last: Lee

department: Dept. of Biology

country: South Korea

institute: KyungHee University

summary: Macrophage mRNA profiles of WT and MFN2 -/- macrophage upon Mtb treatment

overall_design: Macrophage mRNA profiles of Mtb or untreated wild type (WT) and MFN2-/- macrophage

first: Jin

middle: K

last: Kim

first: Prashanta

last: Silwal

first: Jin-Woo

last: Bae

first: Eun-Kyeong

last: Jo


title: Apoptotic cells induce proliferation of peritoneal macrophages

city: Frankfurt am Main

first: Anne-Kathrin

last: Knuth

address: Komturstraße 3a

institute: Institut of experimental cancer research in pediatrics

summary: The interaction of macrophages with apoptotic cells is required for efficient resolution of inflammation. While apoptotic cell removal prevents inflammation due to secondary necrosis, it also alters the macrophage phenotype to hinder further inflammatory reactions. The interaction between apoptotic cells and macrophages is often studied by chemical or biological induction of apoptosis, which may introduce artifacts by affecting the macrophages as well and/or triggering unrelated signaling pathways. Here, we set up a pure cell death system in which NIH 3T3 cells expressing dimerizable Caspase-8 were co-cultured with peritoneal macrophages in a transwell system. Phenotype changes in macrophages induced by apoptotic cells were evaluated by RNA sequencing, which revealed an unexpectedly dominant impact on macrophage proliferation. This was confirmed in functional assays with primary peritoneal macrophages and IC-21 macrophages. Moreover, inhibition of apoptosis during Zymosan-induced peritonitis in mice decreased mRNA levels of cell cycle mediators in peritoneal macrophages. Proliferation of macrophages in response to apoptotic cells may be important to increase macrophage numbers to allow efficient clearance and resolution of inflammation.

overall_design: mRNA profiles of peritoneal macrophages after co-culture with apoptotic cells

first: Peter

last: Rappl

first: Rebekka

last: Bauer

first: Ana

last: Mota

first: Tobias

last: Schmid

first: Simone

last: Fulda

first: Andreas

last: Weigert


title: Unravelling the Biological Functions of Type 1 Diabetes Associated Noncoding Single-Nucleotide Polymorphism in Human Pancreatic β Cells

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

country: USA

institute: Weill Cornell Medical College

summary: Over 90% of disease associated single nucleotide polymorphisms (SNPs) identified by genome wide association studies (GWAS) are noncoding variants. Platform to efficiently validate the biological function of variants thus discovered remain distinctly lacking. Here, we used β-like cells derived from isogenic human pluripotent stem cells (hPSCs), carrying the type 1 diabetes (T1D)-associated noncoding SNP rs2542151T>G or the knockout of the SNP-associated gene PTPN2−/−, to systematically examine the role of the T1D associated noncoding variant in β cell function and survival. PTPN2−/− and rs2542151T>G both decrease insulin production and elevate cell apoptosis in vitro as well as in vivo. A high content chemical screen identified sodium butyrate, a short-chain fatty acid, to rescue the defects of PTPN2−/−and rs2542151G/G β-like cells in vitro and a humanized mouse model. The combined phosphoproteomics, proteomics and RNA-seq analyses discovered a LAMIN A/HDAC/ERK/complex 1 axis as the downstream pathway of PTPN2 to control β cell survival. Together, this study proved the principle to apply hPSC-derived β cells to study diabetes associated noncoding SNP, and identified a drug candidate for the precision therapy of T1D.

overall_design: WT or PTPN2-/- hESC derived beta cells were purified based on INS-GFP expression.

first: Zeping

last: Zhao

first: Tuo

last: Zhang


title: Dysregulated gene expression in human osteoarthritis cartilage

city: NEW YORK

first: MUKUNDAN

last: ATTUR

address: 301E, 17TH STREET FL16, RM1609

department: MEDICINE

institute: NYU GROSSMAN SCHOOL OF MEDICINE

summary: Osteoarthritis causes pain and functional disability for over 500 million people worldwide and characterized by progressive loss of cartilage from the articulating surfaces of diarthrodial joints. Although the etiology of the disease is unknown, it is widely accepted that these degenerative changes arise from an imbalance of synthetic and degradative pathways that control cartilage extracellular matrix metabolism. Genome-wide U133A Affymetrix oligonucleotide array set was used to comprehensively investigate the expression pattern in non-osteoarthritis (normal) and cartilage obtained from OA patients undergoing knee replacement surgery. This study was undertaken to better understand the molecular basis of the disease and to provide relevant insight into phenotypical alterations and mechanisms involved in OA pathogenesis.

overall_design: Analyzed 5 normal and 6 OA pool samples. Each pool has 5 individual RNA samples pooled for target preparation.

first: Mukundan

last: Attur

first: Steven

last: Abramson


title: RNAseq_nalm6 and Sem_Asparaginase_Ibrutinib

city: Utrecht

first: Frank

last: van Leeuwen

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

summary: To determine how inhibition of BTK synergizes with ASNase, we performed RNA sequencing investigating which genes are affected in response to ASNase, ibrutinib or the combination

overall_design: Nalm6 and Sem cells were either left untreated or treated for 24h 10um Ibrutinib, 1 IU/ml Asparaginase or a combination of both drugs.

first: Miriam

last: Butler

first: Laurens

last: van der Meer

middle: N


title: Novel indirect co-culture of immortalized hepatocytes with monocyte derived macrophages is supported by pro-inflammatory cytokine networks

city: Berlin

first: Florian

last: Padberg

address: Max-Dohrn-Strasse 8-10

department: Chemicals and Product Safety

institute: German Federal Institute for Risk Assessment (BfR)

summary: The  liver  is  composed  of  different  cell  populations. Interactions of  different  cell  populations can  be investigated bya newly established  indirect  co-culture system consisting  of  immortalised  primary human hepatocytes and human monocyte derived macrophages(MDMs). Using the time-dependent cytokine secretion of the co-cultures and singlecultures, correlation networks(includingthe cytokinesG-CSF, CCL3, MCP-1, CCL20, FGF, TGF-β1, GM-CSF, IL-8 IL-6, IL-1β, and IL-18)were generated and the correlationswere validatedbyapplication of IL-8and TNF-α-neutralising antibodies. Thedata reveal that  IL-8  is  crucial  for  the  interaction  between  hepatocytes  and  macrophages in  vitro.In  addition, transcriptome analyses showedthat a change in the ratio between macrophages and hepatocytes may triggerpro-inflammatory signalling pathways of the acute phase responseand the complement system(release of, e.g., certaincyto-and chemokines).Using diclofenac and LPS showed that the release of cytokines is increasingwith higher ratios of MDMs. Altogether we coulddemonstratethat the current co-culture  system is better  suited  to  mirror  thein  vivosituation  when compared  to previously established co-culturesystems composed of HepG2and differentiated THP-1cells.Further, our data reveal  that  the cytokine  IL-8  is  crucial  for the  interaction  between  hepatocytes and  macrophages in vitro.

overall_design: Characterization of Fa2N-4 cells under influence of monocyte derived macrophages using the Affymetrix Human Clariom S. Array data was processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany). Three biological replicates were performed for each condition.

first: Tessa

last: Höper

first: Sebastian

last: Henkel

first: Dominik

last: Driesch

last: Luch

last: Zellmer