title: Anti-lipopolysaccharide antibody ruminal administration mitigates the ruminal lipopolysaccharide release without acute phase inflammatory and hepatic transcriptomic responses during the subacute ruminal acidosis challenge in Holstein bull cattle

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

summary: The effects of anti-lipopolysaccharide (LPS) antibody on ruminal fermentation, LPS activity, and liver transcriptomes were investigated during the subacute ruminal acidosis (SARA) challenge.

overall_design: Eleven fistulated Holstein bull cattle (164 ± 14 kg; 5–6 months of age) were used in a replicated 3×3 Latin square design. Cattle were fed a roughage (orchard and timothy mixed hay) diet during the first 11 days (days -11 to -1; pre-challenge), a high-grain (50% concentrate and 50% soybean flakes) diet for 2 days (days 0 and 1; SARA-challenge), and then a roughage diet for 1 day (day 2; post-challenge) (Table 1). The cattle were administered with 0 (control group), 2, or 4 g immunoglobulin yolk containing anti-LPS antibody per head once daily through the rumen fistula for 14 consecutive days.

first: Yo-Han

last: Kim


title: Gestational diabetes and human amniocytes

status: Public on May 15 2020

city: Philadelphia

first: Paul

middle: Zhiping

last: Wang

state: pa

address: 3440 Market St

country: USA

institute: Bioinformatics Core, IBI, UPen

type: Expression profiling by high throughput sequencing

summary:
Context: Context: Gestational diabetes (GDM) has profound effects on the intrauterine metabolic milieu and is linked to obesity and diabetes in offspring, but the mechanisms driving these effects remain largely unknown.  Alterations gene expression in amniocytes exposed to GDM in utero may identify potential mechanisms leading to metabolic dysfunction later in life.
Objective: Objective: To profile changes in the transcriptome in human amniocytes exposed to GDM
Methods: A nested case-control study was performed in second trimeseter amniocytes matched for offspring sex, maternal race/ethnicity, maternal age, gestational age at amniocentesis, gestational age at birth and gestational diabetes status. Sex-specific RNA-sequencing was completed and gene expression changes were identified.
Results: Expression of interferon-stimulated genes was increased in GDM amniocytes accounting for 6 of the top 10 altered genes (q<0.05). Enriched biological pathways in GDM anmiocytes included pathways involving inflammation, the interferon response, fatty liver disease, monogenic diabetes and atherosclerosis.
Conclusion: In a unique repository of human amniocytes exposed to GDM in utero, trancriptome analysis identified enrichment of inflammation and interferon-related pathways.

first: Sara

middle: E

last: Pinney

first: Apoorva

last: Joshi

first: Victoria

last: Yin

first: Sowon

last: Min

first: Cetewayo

last: Rashid

first: David

last: Condon

middle: Z


title: Transcriptomics profiling of CD141+ dendritic cells isolated from peripheral blood or synovial fluid of arthritis patients

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

summary: Total RNA sequencing was performed on CD141+ DC isloated from peripheral blood of healthy individuals (n=5) or synovial fluid of patients with inflammatory arthritis (n=6)

overall_design: One RNA sample per subject was analysed without replicates

middle: M

first: Mary

last: Canavan


title: Human bone marrow-derived mesenchymal stromal/stem cells retain their trophic repair and immunoregulatory properties but lose their multipotent differentiation capacity after extensive ageing in vitro

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

country: United Kingdom

institute: University of Liverpool

summary: To assess the hierarchical importance of multipotent differentiation compared with trophic/immunoregulatory functions of MSCs, we have undertaken a detailed analysis of how these properties change with in vitro ageing of the cells.  Using in vitro differentiation and repair models and integrating transcriptomics and proteomics data, we show that the multipotent differentiation capacity of MSCs falls with increasing passage, whereas trophic repair and immunoregulatory potency are maintained.

overall_design: In total four cell lines were profiled using Illumina whole genome RNA-seq. Cell lines were isolated from four individuals. RNA was extracted from each cell line at passage 1, 5, 10 and 15 for a total of 16 samples. Two samples (PN251_p15, PN241_p10) were sequenced twice to improve sequencing depth.

first: Anna

last: Salerno

first: Anthony

middle: P

last: Hollander


title: The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

type: Methylation profiling by high throughput sequencing

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Comparative evaluation of metabolic, electrophilic, and immunologic effects of itaconate and its ester derivatives on macrophage activation

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Itaconate is a metabolite naturally produced in large amounts in macrophages after exposure to immune stimulation. Following the discovery of itaconate’s immunoregulatory properties, several ester derivatives of this dicarboxylic acid were designed to further examine its role. We evaluated the metabolic, electrophilic, and immunologic profiles of macrophages treated with unmodified itaconate and a panel of itaconate derivatives. We found that only unmodified itaconate strongly enhances LPS-induced IFNb secretion after 12h pre-treatment. Thus, we compared the transcriptional profile of wild type and Irg1-/- cells, which are unable to produce itaconate, after 24h LPS stimulation. We find that cells lacking itaconate have impaired downstream type I interferon signaling, and that addition of itaconate Irg1-/- BMDMs restores this signaling back to levels comparable to wild type. This data highlights the role of itaconate as an immunoregulatory metabolite, and highlights the importance of using unmodified itaconate or genetic knockout models in future mechanistic studies.

overall_design: BMDMs were prepared from 6 to 16-week-old mice as described and seeded at 100,000 cells 100 mL in 96 well tissue-culture plates in RMPI-1640 medium supplemented with 10% FBS, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin. Cells were stimulated with LPS (100 ng/mL; Sigma, E. coli 0111:B4) for 24 hours. For the Irg1 KO + ITA condition, 1 mM itaconate was added to the cells 4 hours after addition of LPS to mimic the natural production of itaconate in wild type cells, which increases from 4 – 24 hours after LPS stimulation. After stimulation, cells were washed with PBS, and directly resuspended in Lysis/Binding Buffer (Dynabeads mRNA DIRECT Kit, Invitrogen).

first: Amanda

last: Swain

first: Monika

last: Bambouskova

first: Hyeryun

first: Prabhakar

middle: S

last: Andhey

first: Dustin

last: Duncan

first: Karine

last: Auclair

first: Victor

last: Chubukov

first: Donald

last: Simons

first: Thomas

last: Roddy

first: Kelly

last: Stewart

middle: N


title: TIMP3, a CLOCK-controlled gene, determines cell susceptibility to UV-induced expression of inflammatory factors in human keratinocytes.

city: Yongin-si

first: Sunyoung

last: Park

state: Gyeonggi-do

address: 1920, Yonggu-daero

country: South Korea

institute: Amorepacific corporation

summary: To search for CLOCK-controlled genes in human keratinocytes, we introduced siRNAs against CLOCK and harvested the cells at two time points, ZT 32 and 44. We speculated that those genes that were downregulated at both ZT time points may be selectively regulated by CLOCK

overall_design: mRNA profiles of scrambled or CLOCK siRNAs treated NHEK at 2 different time points

first: Kyuhan

last: Kim


title: Local adaptation of Avicennia schaueriana to freshwater availability and solar radiation suggested by genomic and ecophysiological approaches

city: Campinas

first: Mariana

middle: Vargas

last: Cruz

state: Sao Paulo

address: 400 Avenida Candido Rondon

department: Department of Plant Biology

country: Brazil

institute: UNICAMP

summary: Local adaptation is often a product of environmental variations in geographical space and has implications for biodiversity conservation. We investigated the role of latitudinal heterogeneity in climate on the organization of genetic and phenotypic variation in the dominant coastal tree Avicennia schaueriana. In a common garden experiment, samples from an equatorial region, with pronounced seasonality in precipitation, accumulated less biomass, and showed lower stomatal conductance and transpiration, narrower xylem vessels, smaller leaves and higher reflectance of long wavelengths by the stem epidermis than samples from a subtropical region, with seasonality in temperature and no dry season. Transcriptomic differences identified between trees sampled under field conditions at equatorial and subtropical sites, were enriched in functional categories such as responses to temperature, solar radiation, water deficit, photosynthesis and cell wall biosynthesis. Remarkably, the diversity based on genome-wide SNPs revealed a north-south genetic structure and signatures of selection were identified for loci associated with photosynthesis, anthocyanin accumulation and the responses to osmotic and hypoxia stresses. Our results suggest the existence of divergence in key resource-use characteristics, likely driven by seasonality in water deficit and solar radiation. These findings provide a basis for conservation plans and for predicting coastal plants responses to climate change.

overall_design: mRNA profiles of leaves, stems and flowers from six adult trees under field conditions: three from an equatorial mangrove forest and three from a subtropical mangrove forest in the Atlantic coast of South America. Sequencing platform: Illumina GA Iix

middle: V

first: Gustavo

last: Mori

first: Caroline

last: Müller

first: Carla

middle: C

last: Silva

first: Dong-Ha

last: Oh

first: Maheshi

last: Dassanayake

first: Maria

middle: I

last: Zucchi

first: Rafael

last: Oliveira

first: Anete

last: Souza


title: Androgen Receptor Signaling Regulates the Transcriptome of Prostate Cancer Cells by Modulating Global Alternative Splicing

status: Public on May 14 2020

city: Gaithersburg

first: Kalpit

last: Shah

state: MD

address: 8717 Grovemont Cir

institute: DCEG

summary: HTA2.0 affy array was used to study the effect of androgen inhibitors on alternative splicing in LNCaP cells

overall_design:
To study the effect of pharmacological manipulation of AR signaling in prostate cancer cells, we performed expression profiling of LNCaP cells that were cultured for 72 hours in charcoal-stripped fetal bovine serum and stimulated with 10nM AR agonist dihydrotestosterone (DHT) or 10uM of the AR antagonist casodex for 24 hours.
3 biological replicates for each group.


title: Coagulopathy signature precedes and predicts severity of end-organ heat stroke pathology in a mouse model

city: Hershey

first: Elizabeth

middle: Anne

last: Proctor

address: 500 University Dr

department: Neurosurgery

institute: Pennsylvania State University

summary: Heat stroke is a life-threatening condition characterized by loss of thermoregulation and severe elevation of core body temperature, which can cause organ failure and damage to the central nervous system. While no definitive test exists to measure heat stroke severity, immune challenge is known to increase heat stroke risk, although the mechanism of this increased risk is unclear. In this study, we used a mouse model of classic heat stroke to test the effect of immune challenge on pathology. Employing multivariate supervised machine learning to identify patterns of molecular and cellular markers associated with heat stroke, we found that prior viral infection simulated with poly I:C injection resulted in heat stroke presenting with high levels of factors indicating coagulopathy. Despite a decreased number of platelets in the blood, platelets are large and non-uniform in size, suggesting younger, more active platelets. Levels of D-dimer and soluble thrombomodulin were increased in more severe heat stroke, and in cases presenting with the highest level of organ damage markers D-dimer levels dropped, indicating potential fibrinolysis-resistant thrombosis. Genes corresponding to immune response, coagulation, hypoxia, and vessel repair were up-regulated in kidneys of heat-challenged animals, and these increases correlated with both viral treatment and distal organ damage while appearing before discernible tissue damage to the kidney itself. We conclude that heat stroke-induced coagulopathy may be a driving mechanistic force in heat stroke pathology, especially when exacerbated by prior infection, and that coagulation markers may serve as an accessible biomarker for heat stroke severity and therapeutic strategies.

overall_design: 48 kidney samples from mice that were heat-stressed or unheated, poly I:C- or saline-injected, at time point of Tcmax or 1 day following (8 groups total, N=6 per group) were subjected to RNAseq for total mRNA

middle: A

first: Douglas

last: Lauffenburger

first: Lisa

middle: R

last: Leon


title: Gene expression signatures in IL27RA- and IL27RA+ hematopoietic stem cell

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

summary: Analysis of IL27RA- and IL27RA+ hematopoietic stem cell (lineage-, c-kit+ Sca-1+ CD150+, CD34-). The two population of hematopoietic stem cell (HSC) purified from the bone marrow of young (2 months) and old (28 months) mice. Results provide insight into the role of IL27RA in HSC.

overall_design: IL27RA- and IL27RA+ HSC are sorted from young and old bone marrow, then subjected into deep sequencing, in triplicate, using Illumina HiSeq platform.


title: Tumor-derived prostaglandin E2 promotes p50 NF-κB-dependent differentiation of monocytic MDSC.

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Myeloid-derived suppressor cells (MDSC) include immature monocytic (M-MDSC) and granulocytic (PMN-MDSC) cells that share the ability to suppress adaptive immunity and hinder the effectiveness of anti-cancer treatments. Of note, in response to interferon-γ (IFNγ) M-MDSC release the tumor-promoting and immunosuppressive molecule nitric oxide (NO), whereas macrophages largely express anti-tumor properties. Investigating these opposing activities, we found that tumor-derived prostaglandin E2 (PGE2) induces nuclear accumulation of p50 NF-κB in M-MDSC, diverting their response to IFNγ towards NO-mediated immunosuppression and reducing TNFα expression. At the genome level, p50 NF-κB promoted binding of STAT1 to regulatory regions of selected IFNγ-dependent genes, including inducible nitric oxide synthase (Nos2). In agreement, ablation of p50 as well as pharmacological inhibition of either the PGE2 receptor EP2 or NO production reprogrammed M-MDSC towards a NOS2low/TNFαhigh phenotype, restoring the in vivo antitumor activity of IFNγ. Our results indicate that inhibition of the PGE2/p50/NO axis prevents MDSC suppressive functions and restores the efficacy of anticancer immunotherapy.

overall_design:
Poly(A) RNA capture followed by multiparallel sequencing performed in Monocytic Myeloid Derived Suppressor Cells (M-MDSC) or Peritoneal Exudate Macrophages (PEC) from wild-type and p50ko mice

Chromatin immuno-precipitations of  the transcription factor Stat1 in PECs followed by multiparallel sequencing

first: Chiara

last: Porta

first: Francesca

last: Consonni

first: Renato

last: Ostuni

first: Giulia

last: Soldà

first: Gioacchino

last: Natoli

first: Antonio

last: Sica


title: HIV-1 SortSeq identifies HIV-1-infected cells from HIV-1-infected individuals

city: New Haven

first: Ya-Chi

last: Ho

state: CT

address: BCMM 349, 295 Congress Ave, BCMM 349

department: Microbial Pathogenesis

institute: Yale University School of Medicine

summary: Using HIV-1 SortSeq, we identified HIV-1-infected cells containing inducible HIV-1 for RNAseq from resting CD4+ T cells treated with PMA/ionomycin for 16 hours from HIV-1-infected, antiretroviral therapy treated, virally suppressed individuals. Using custom bioinformatic pipeline, we identified HIV-1 genomic RNA, host RNA and HIV-1-host chimeric RNA junctions.

overall_design: We examined the gene transcription level of the infected cells.


title: p53 amyloid formation induced cellular transformation and tumor formation in xenograft model

city: Mumbai

first: Samir

last: Maji

address: Indian Institute of Technology Bombay, Powai

department: Biosciences and Bioengineering

country: India

institute: Indian Institute of Technology Bombay

summary: p53 mutation and its subsequent loss of function along with gain of oncogenic functions is associated with cancer. However, the exact mechanism of how altered p53 acts as an oncogene is not clear yet. Recently, it was suggested that p53 aggregation and amyloid formation leads to both loss of tumor suppressive function and gain of oncogenic functions in cells. In this study, we directly demonstrate that wild-type p53 amyloid formation imparts oncogenic properties to normal cells. Cells with p53 amyloid aggregates show enhanced survival, apoptotic resistance with increased proliferation and migration rate. We further establish the tumorigenic potential of p53 amyloid containing cells in a mice xenograft model. Furthermore, these tumors tested positive for p53 amyloid aggregates. Comprehensive gene-expression analysis suggests that p53 amyloid formation triggers aberrant expression of pro-oncogenes while downregulating the tumor suppressor associated genes. Interestingly, disaggregating p53 rescues the cellular transformation and also inhibits tumor development in mice. We propose that wild-type p53 amyloid formation can potentially contribute to initiation of tumor development.

overall_design: MCF10A cells were cultured in DMEM growth medium under appropriate conditions, treated with 30 µM of p53 core fibrils  and were incubated for 48 hours at 37 °C in a 5 % CO2 incubator.

first: Ambuja

last: Navalkar

first: Satyaprakash

last: Pandey

first: Namrata

last: Singh

first: Amit

last: Kumar Dey

first: Sandhini

last: Saha

first: Komal

last: Patel

first: Bhabani

last: Mohanty

first: Sachin

last: Jadhav

first: Pradip

last: Chaudhari

first: Tushar

middle: K

last: Maiti


title: Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy [miR146aKO_LSK_WGBS]

city: Vancouver

first: Aly

last: Karsan

state: British Columbia

address: 675 W 10th Ave

country: Canada

institute: BC Genome Science Centre

summary: Aging is associated with significant changes in the hematopoietic system, including increased inflammation, impaired hematopoietic stem cell (HSC) function, and increased incidence of myeloid malignancy. Inflammation of aging (“inflammaging”) has been proposed as a driver of age-related changes in HSC function and myeloid malignancy, but mechanisms linking these phenomena remain poorly defined. Here, we identify loss of miR-146a as driving aging-associated inflammation in AML patients. miR-146a expression declined in old wild-type mice, and loss of miR-146a promoted premature HSC aging and inflammation in young miR-146a-null mice, preceding development of aging-associated myeloid malignancy. Using single-cell assays of HSC quiescence, stemness, differentiation potential, and epigenetic state to probe HSC function and population structure, we found that loss of miR-146a depleted a subpopulation of primitive, quiescent HSCs. DNA methylation and transcriptome profiling implicated NF-κB, IL6, and TNF as potential drivers of HSC dysfunction, activating an inflammatory signaling relay promoting IL6 and TNF secretion from mature miR-146a-/- myeloid and lymphoid cells. Reducing inflammation by targeting Il6 or Tnf was sufficient to restore single-cell measures of miR-146a-/- HSC function and subpopulation structure, and reduced the incidence of hematological malignancy in miR 146a-/- mice. miR-146a-/- HSCs exhibited enhanced sensitivity to IL6 stimulation, indicating that loss of miR-146a affects HSC function via both cell-extrinsic inflammatory signals and increased cell-intrinsic sensitivity to inflammation. Thus, loss of miR 146a regulates cell-extrinsic and -intrinsic mechanisms linking HSC inflammaging to the development of myeloid malignancy.

overall_design: 2 genotypes, 1 cell type: WT LSK (see GSE95697), miR-146a-/- LSK (this series)

first: Jennifer

last: Grants


title: Dietary lipids accumulate in macrophages and stromal cells and change the microarchitecture of the mesenteric lymph node II

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

country: Germany

institute: Medical School Hannover

summary: Obesity has emerged as a worldwide problem in human health. Dietary lipids are taken up and transported via lymphatics into the circulatory system. During this process, lipids pass the mesenteric lymph node (mLN). These organs filter the lymph fluid for foreign antigens to induce and control immune responses. Alteration of that function during obesity has only slightly been studied. Here, we characterize changes within the microarchitecture of the mLN during high levels of lipid transport and highlight the role of stromal cells. Microarray experiments detected gene probes expressed by mLN stromal cells. Transmission electron microscopy enabled us to identify lipid droplets in different stromal cells, and in macrophages. Sizes, numbers and intercellular distances increased after 10 weeks of a high-fat diet. Thus, we propose that changes in the microarchitecture and increased accumulation of lipid droplets in stromal cells and macrophages have an influence on the immunological function of the mLN.

overall_design: Different stromal cell populations (FRC, LEC, BEC) from mesenteric lymph node (mLN) were sorted. Total RNA was prepared and subjected to single color microarray analysis (3 hybridizations in total).

first: Katharina

last: Streich

first: Manuela

last: Buettner


title: Integrin α3β1-dependent mRNA expression profile of hair bulge keratinocytes and their progeny during DMBA/TPA-mediated skin tumorigenesis

city: Amsterdam

first: Veronika

last: Ramovs

address: Plesmanlaan 121

department: Cell Biology

country: Netherlands

institute: Netherlands Cancer Institute

summary: Integrin α3β1 in hair bulge population affects the tumor formation following DMBA/TPA carcinogenesis protocol, however linage tracing showed that hair bulge cells do not largely contributre to tumor mass. To investigate whether α3β1 might affect tumor promoting environment and to better understand its role in hair bulge population during skin tumorigenesis, we determined the expresison profile of hair bulge-originating keratinocytes isolted from α3β1KO and WT mice during initiation of tumorigenesis.

overall_design: CRE-induced GFP-positive keratinoctes from K19(Cre-ERT); mTmG; Itga3 fl/fl and K19(Cre-ERT); mTmG mice, submitted to short-term DMBA/TPA treatment, were isolated using FACS and their expression profile was determined using next generation RNA sequencing

first: Arnoud

last: Sonnenberg

first: Iris

last: de Rink


title: Human iPSC-derived microglia are genetically relevant to Alzheimer’s disease

city: Stanford

first: Robert

middle: Raymond

last: Butler

state: CA

address: 3172 Porter Dr., MC 5475

department: Neurology & Neurological Sciences

institute: Stanford University School of Medicine

summary: Microglia is a primary brain immune cell type that has been implicated in the pathogenesis of neurodegenerative disorders such as Alzheimer’s disease (AD) and neurodevelopmental disorders such as schizophrenia. Generating microglia from human induced pluripotent stem cells (hiPSC) has become an attractive approach to study the microglia-mediated causal mechanism of AD. Among other methods, Brownjohn et al. recently developed a particularly efficient and simple hiPSC-derived microglia (iMG) protocol. However, the transferability of this method to other labs, the transcriptomic similarity of these iMG to primary adult microglia, and their genetic relevance to AD remain unclear. With two hiPSC lines, we demonstrated that the Brownjohn method can efficiently give rise to iMG that were morphologically and functionally like microglia. Our pure iMG were also transcriptionally similar to previously reported iMG lines, as well as fetal and adult microglia. More importantly, we further showed the genetic relevance of iMG to AD using cell type-specific gene expression to partition disease heritability. Contrasting with neuronal and immune cell types, our iMG and several primary microglia and microglia-like cell types were all significantly enriched for AD relevant GWAS loci. These results supported  the use of iMG as a valid human cellular model for understanding AD disease progression and a feasible mechanism for generation of AD patient-specific cell types for more precise in vitro analyses, and potentially more effective clinical care.

overall_design: Two hiPSC cell lines were used for generation of samples, with collections of induced microglia and PMPs at various timepoints after plating cells. Three replicates that featured contamination of a fibroblast-like cell type are also included.

last: Butler III

first: Alena

last: Kozlova

first: Hanwen

last: Zhang

first: Siwei

first: Michael

last: Streit

first: Alan

last: Sanders

first: Zhiping

last: Pang

first: Pablo

last: Gejman

first: Jubao

last: Duan


title: Podocyte-released migrasomes in urine serve as an indicator for early podocyte injury

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

institute: Nanjing University

summary: miRNA microarray was performed for migrasomes and exosomes derived from urine

overall_design: one migrasome and one exosome  was analyzed.

first: Ke

last: Zen


title: Episodic vestibular syndrome with hyperventilation-induced downbeat nystagmus

city: Yangsan

first: Jae-Hwan

last: Choi

address: Kumo-ro 20, Beomo-ri, Mulgum-eup

department: Neurology

institute: Pusan National University Yangsan Hospital

summary: The aim of this study was to investigate the clinical characteristics and underlying pathogenesis of episodic vestibular syndrome (EVS) with hyperventilation-induced downbeat nystagmus (HV-DBN).

overall_design: Total RNAs were extracted from peripheral blood mononuclear cells of 7 EVS with HV-DBN patients and 7 normal controls. Using the Affymetrix Human Clariom S Assay, the differentially expressed genes (DEGs) between AUV and normal control samples were screened by the cut-off criteria (|fold changes| > 1.5 and p-value < 0.05). Functional enrichment analysis for DEGs was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and the protein-protein interaction (PPI) network was constructed using the STRING database.

first: Eun-Hye

last: Oh


title: A commensal Clostridium bacteria restricts alphavirus dissemination through a bile acid-type I IFN signaling axis

status: Public on May 13 2020

first: Maxim

last: Artyomov

summary: The emerging alphavirus chikungunya virus (CHIKV) has infected millions of people. However, the factors modulating disease outcome remain poorly understood. We show that depletion of the gut microbiota in oral antibiotic-treated or germ-free mice leads to greater CHIKV infection and spread within one day of virus inoculation. Perturbation of the gut microbiota alters TLR7-MyD88 signaling in plasmacytoid dendritic cells (pDCs) and blunts systemic production of type I interferon (IFN). Consequently, circulating monocytes express fewer IFN-stimulated genes and become permissive for CHIKV infection. Reconstitution with a single commensal bacterial species, Clostridium scindens, or its derived metabolite, the bile acid deoxycholic acid, can restore pDC- and MyD88-dependent type I IFN responses to restrict systemic CHIKV infection and transmission back to vector mosquitoes. Thus, commensal gut bacteria modulate antiviral immunity and levels of circulating alphaviruses within hours of infection through a bile acid-pDC-IFN signaling axis, which affects virus dissemination and potentially, epidemic spread

overall_design:
Droplet-based 3′ end massively parallel single-cell RNA sequencing was performed by isolating leukocytes of the peripheral blood following a magnetic bead-based CD4/CD8/CD19 depletion step. 3'GEX enrichment libraries were prepared using Chromium Single Cell 5′ Reagent Kits according to manufacturer’s protocol (10x Genomics). The generated scRNAseq libraries were sequenced using NovaSeq S4 sequencers.
3 biologically independent mice per age were pooled, procesed and sequenced.

first: Emma

last: Winkler

first: Swathi

last: Shrihari

first: Barry

middle: L

last: Hykes

first: Scott

last: Handley

first: Prabhakar

last: Andhey

first: Yan-Jang

last: Huang

first: Amanda

last: Swain

first: Lindsay

last: Droit

first: Kranthi

last: Chebrolu

first: Matthias

last: Mack

first: Dana

last: Vanlandingham

first: Larissa

middle: B

last: Thackray

first: Marina

last: Cella

first: Marco

last: Colonna

first: Thaddeus

last: Stappenbeck

last: Diamond


title: Arabidopsis thaliana KO1 and KO3 deletion lines of the selective autophagy receptor AtNBR1

city: Warsaw

first: Agnieszka

last: Sirko

address: Pawinskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics

summary:
We used the CRISPR/Cas9 technique to construct nbr1-KO lines (KO1 and KO3) in order to test the effects of AtNBR1 depletion. Reduced expression of several ABA-up regulated genes were observed in shoots of the two KO lines.
Grant number: 2014/15/B/NZ3/04854
Grant funding source: National Science Centre (Poland)
Grantee Name: Agnieszka Sirko
Grant title: Upstream regulators and cellular targets of the selective autophagy cargo receptor AtNBR1 in different phases of sulfur deficiency in plants.

overall_design: Plant material for transcript profiling was grown in Araponic boxes (16 plants/box) kept in short day conditions (22 °C 8h day/18 °C 16h night) for about 4 weeks, with weekly changes of the 0.5 x Hoagland medium. Individual plants were divided into shoot and root tissue and frozen in liquid nitrogen. Portions of plant material, drawn from at least 3 plants, were homogenised in TRI Reagent (Molecular Research Centre), and genomic DNA was removed with a RapidOut DNA removal kit (ThermoScientific) and total RNAs were separately isolated from shoots and roots. We looked for effects of the NBR1 gene deletion in the KO1 and KO3 lines compared to the the wild type plants (Col-0). These effects were investigated in roots and shoots separately. Totally, 18 samples of RNA were prepared.

first: Leszek

middle: J

last: Tarnowski

last: Gromadka

first: Jerzy

last: Brzywczy


title: Expression profiles of long noncoding RNAs and mRNAs in A549 cells infected by Influenza virus

city: hangzhou

first: Hu

last: boli

state: zhejiang

address: Yuhangtang Road No.866

institute: Zijingang Campus of Zhejiang University

summary: Long noncoding RNAs (lncRNAs) participate in regulating many biological processes. However, their roles in influenza A virus (IAV) pathogenicity are largely unknown. Here, we analyzed the expression profile of lncRNAs and mRNAs in the H3N2-infected cells and H7N9-infected cells by high-throughput sequencing

overall_design: Expression profiles of long noncoding RNAs and mRNAs in A549 cells infected by H3N2 or H7N9 were generated by deep sequencing, in duplicates, using Illumina Hiseq 3000.

first: Yina

last: Zhang

first: Tianqi

last: Yu

first: Boli

last: Hu

first: Jiyong

last: Zhou


title: Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy

first: Aly

last: Karsan

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

overall_design: Refer to individual Series


title: A novel model of pulmonary KPC infection reveals critical roles of NK cell and group 3 ILC cytokines in host resistance

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: Both NK cells and group 3 ILCs play key roles and that effector cytokines made by these cells can provide immunoprophylaxis against Carbapenem resistant K. pneumoniae infection.

overall_design: Our data had indicated that 12 hours post pulmonary infection of ST258 at 10e6 CFU reveals similar bacterial clearance between C57BL/6 and Rag2-/- mice, and therefore we harvested lung tissues to obtain single cell suspension for single cell RNAseq at this time point because any differences in gene expression would not be due to differences in lung bacterial burdens. Similarly, about the experiment for comparison between PBS and FK506 treated C57BL/6 mice, we decided to analyze at 24 hours after infection based on the same bacterial burden between the groups.


title: Gene expression patterns of tumor-infiltrating CD8 T cells according to the CD137 expression in human metastatic ovarian cancer

status: Public on May 12 2020

city: Daejeon

first: Galam

last: Leem

address: 291 Daehakro Yusunggu

institute: KAIST

summary: We report the differences of gene expression pattern of tumor-infiltrating CD8 T cells between CD137 expressing cells and CD137 non-expressing cells in human metastatic ovarian cancer. Samples are obtained from 3 ovarian cancer patients, and we sorted CD137 expressing cells and CD137 non-expressing cells in CD39 expressing CD8 T cells for RNA sequencing. We found that even though the CD39 expression and PD-1 expression levels are similar, CD137 expressing cells showed more activated and less exhausted phenotypes than CD137 non-expressing cells.

overall_design: Compare gene expression patterns between CD137 expressing CD39+ CD8 T cells and CD137 non-expressing CD39+ CD8 T cells. Control cells were CD39- CD8 T cells.

first: Su-Hyung

last: Park


title: Differential gene expression in miR-146a-/- vs. WT hematopoietic stem and progenitor cells [miR146aKO_vs_WT_RNA-seq_bulk]

summary: To identify pathways and processes driving the observed hematopoietic stem cell (HSC) aging-like phenotypes in miR-146a-/- vs. WT, we performed RNA-seq gene expression profiling of Lin- Sca-1+ c-Kit+ (LSK) cells isolated from miR-146a-/- or WT mouse bone marrow (BM). Differential expression analysis and EnrichmentMap network analysis identified cytokine signalling and immune pathways as potential drivers of aging-like alterations in miR-146a-/- HSC proliferation and differentiation.

overall_design: RNA sequencing of miR-146a-/- vs. WT (C57BL/6J) Lin- Sca-1+ c-Kit+ cells from young mice.

first: Jennifer

middle: M

last: Grants


title: Changes of gene expression patterns of human cancer cell lines responding to Interferon-gamma

summary: We report the differences of gene expression pattern of 4 different human cancer cell lines responding to Interferon-gamma. 4 different human cancer cell lines were treated with 20ng/ml of Interferon-gamma for 72 hours and gathered for RNA seq. We found that in response to Interferon-gamma, cancer cell lines expressed increased amounts of RNA related to immune responses.

overall_design: Compare gene expression patterns between Interferon-gamma treated human cancer cell lines and untreated human cancer cell lines

first: Eui-Cheol

last: Shin


title: Transcriptome response of lung in response to A. baumannii infection

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

summary: We apply RNAseq of lung tissues to study the innate immune response to pulmonary Acinetobacter baumannii infection.

overall_design: Rag1-/- mice were infected with a lethal dose of A. baumannii. Lung samples were collected from control mice, A. baumannii-infected mice at 24 hours post infection.

first: Xi

last: Zeng


title: Altered microRNA expression links IL6 and TNF-induced inflammaging with myeloid malignancy [miR146aKO_ESLAM_SCBS]

overall_design: 2 cell types, 2 genotypes, single-cell analysis: 64 WT LSK cells (see GSE89545), 83 WT ESLAM cells (see GSE89545), & 69 miR-146a-/- ESLAM cells, 43 passing QC (this series)


title: Genes regulated by SDC1 in Caco-2 cells

city: Singapore

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

country: Singapore

institute: National University of Singapore

summary: We used Affymetrix HG U133 Plus 2.0 GeneChips to compare the transcriptome of Caco-2 cells transfected with SDC1-siRNA against negative control siRNA-transfected cells.

overall_design: Caco-2 cells were transfected with SDC1-siRNA or negative control siRNA. Subsequently, total RNA was collected and processed for analysis using Affymetrix microarrays. Three independent replicates were prepared for each comparison group.

first: G

first: M

last: Götte


title: Human alveolar and splenic macrophage populations display a disctinct transcriptomic response to infection with Mycobacterium tuberculosis

city: Medellín

first: LELIA

last: LAVALETT

state: Antioquia

department: Antioquia

country: Colombia

institute: Universidad de antioquia

summary: Mycobacterium tuberculosis (Mtb) infects alveolar macrophages (AMs) causing pulmonary tuberculosis (PTB), the more frequent form of the disease. Less frequently, Mtb disseminates to many other organs and tissues resulting in different extrapulmonary forms of TB. Nevertheless, very few studies have addressed the global mRNA response of human AMs, in particular from humans with the active form of the disease. Strikingly, almost no studies have addressed the response to infection with Mtb by human extrapulmonary macrophages.

overall_design: Total RNA obtained from alveolar macrophages from TB patientients infected with clinical isolates of Mtb to compared to alveolar macrophages from control subjects.  Total RNA from splenic macrophages  obtained from spleen slices from deceased donor and infected in vitro with clinical isolates of Mtb to compared splenic macrophages noninfected.

first: Lelia

last: Lavalett

first: Hector

last: Ortega

first: Luis

last: Barrera


title: Dietary lipids accumulate in macrophages and stromal cells and change the microarchitecture of the mesenteric lymph node I

first: Oliver

last: Dittrich-Breiholz

overall_design: In two independent approaches, CD45- stem cells from pLN or mLN were sorted, total RNA was prepared and subjected to single color microarray analysis (4 hybridizations in total).

first: Katharina

last: Streich

first: Manuela

last: Buettner


title: Macrophage-Tumor Cell Interaction Promotes ATRT Progression and Chemoresistance

city: Münster

first: Kornelius

last: Kerl

address: Albert-Schweitzer-Campus 1

department: Department of Pediatric Hematology and Oncology

institute: University Children's Hospital Münster


title: Toxicity of LCDD monoclonal Ig free light chains

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS


title: Intrinsic toxicity of LCDD monoclonal Ig free light chain on plasma cells (PC)

summary:
We analyzed the transcriptome (RNA-seq) of mouse plasma cells (PC) expressing a human Ig light chain from a patient suffering light chain deposition disease (LCDD) as compared to control plasma cells (WT and DH-LMP2A, the latter producing no complete immunoglobulins, only free Ig light chains).
Ig light chains causing LCDD present structural peculiarities leading to their aggregation and deposition into tissues and organs, mainly the kidney. We sought to determine if plasma cells producing these abnormal Ig could present specific phenotypes.
The aim of the present study is to analyse the transcriptomic signature of plasma cells producing abnormal Ig free light chains.

overall_design: Spleen plasma cells from non-immunized mice were magnetically-purified using CD138 beads (purity > 80%). Each sample corresponds to the total CD138+ plasma cells from one spleen. Cells are from 3-month-old mice.

first: A

last: Paquet

first: V

last: Magnone

first: C

last: Sirac


title: Toxicity of LCDD monoclonal Ig free light chains on renal glomeruli

summary:
We analyzed the transcriptome (RNA-seq) of glomeruli in a mouse model of light chain deposition disease (LCDD) as compared to control mice (WT and DH-LMP2A, the latter producing no complete immunoglobulins, only free Ig light chains).
Kidney lesions in LCDD are due to the deposition of an abnormal monoclonal free Ig light chain and comprise progressive thickening of basement membranes (tubular and glomerular) and nodular glomerulosclerosis resembling the lesions observed in diabetic nephropathy.
The aim of the present study is to analyse the transcriptomic changes at early steps of glomerulosclerosis.

overall_design: Glomeruli were purified using magnetic beads as described in Takemoto et al. (2002). Each sample is the pool of 3 different mice except for WT1, WT2 and WT3, which are only one mouse each. Glomeruli are from 6-month-old mice, corresponding to the early steps of glomerulosclerosis.


title: Asxl1 and Cebpa cooperation in AML revealed by a novel Asxl1 mutant mouse model

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

summary: Asxl1 is one of the most commonly mutated genes in malignancies including myelodysplastic syndromes (MDS) and Acute Myeloid Leukemia (AML). We generated a mouse model that harbors the most common mutation on ASXL1 gene detected in MDS patients: c.1934dupG, p.G646WfsX12 at the endogenous murine Asxl1 locus: the G643WfsX12 mutant, from here on referred as Asxl1G643W. Mutations on Asxl1 co-occur with mutations on CEBPA in AML patients, therefore, in order to understand how Asxl1 and Cebpa co-operate, we set up to cross our Cebpa-p30 mutant mouse model with our newly generated Asxl1 G643Wfs12 mutant. In this study we provided mechanistic information about the cooperation between these two factors. Furthermore, our mouse model proved able to recapitulate the chemotherapy response of human patients with Asxl1 mutations, thus representing a potent tool for future preclinical studies focusing on Asxl1 mutant AML.

overall_design: RNA sequencing of Cebpa-/p30; Asxl1WT and Cebpa-/p30; Asxl1G643W/G643W blast cells from transplanted mice

first: Teresa

last: D'Altri

first: Anne

last: Wenzel

middle: T


title: The role of the core PRC1 members Ring1 and Rnf2 in expression regulation during oocyte growth

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: Comparative expression analysis between germinal vesicle (GV) stage mouse oocytes of Ring1-deficient oocytes ("control") versus oocytes deficient for Ring1 and Rnf2 ("mutant").

overall_design: Two genotypes, 3 replicates per genotype.

first: Nathalie

last: Véron

first: Evgeniy

last: Ozonov

middle: H


title: CBX2.1/PRC1 regulates the targeting of the Histone H3.3 chaperone DAXX to the genome (ChIP-Seq)

summary: We report the genome-wide occupancy of exogenous DAXX (Myc-tagged), exogenous full length CBX2.1 (tagged with GAL4 DNA binding domain) and exogenous splice variant CBX2.2 (tagged with GAL4 DNA binding domain) in transiently transfected HEK293 cells. We observe that CBX2.1 but not CBX2.2 can efficiently target DAXX to chromatin.

overall_design: Examination of genome-wide occupancy of DAXX, CBX2.1 and CBX2.2.

first: Mathieu

last: Tardat

first: Helene

last: Royo

first: Zichuan

last: Liu

first: E


title: The phosphatase regulator NIPP1 controls epidermal homeostasis

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary: To delineate the in vivo function of NIPP1 in epidermal homeostasis, we generated skin-specific NIPP1 knockout (SKO) mice where NIPP1 is conditionally removed from keratinocytes. To gain unbiased insight into the molecular mechanism that underlies the hyperproliferation phenotype, we performed RNA-seq of the isolated epidermis of control (CTR) and SKO mice.

overall_design: We extracted RNA from tail epidermis of 4 CTR and 4 SKO mice and performed RNA-seq on each sample.

first: Iris

last: Verbinnen

first: Aleyde

last: Van Eynde

last: Bollen


title: PRMT5 regulates T cell interferon response and is a target for acute graft-versus-host disease

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

country: USA

institute: Ohio State University

summary: Acute Graft-Versus-Host Disease (aGVHD) is a T cell mediated immunological disorder and the leading cause of non-relapse mortality in patients who receive allogeneic hematopoietic cell transplants. Based on recent observations that PRMT5 and arginine methylation is upregulated in activated memory T cells, we hypothesized that PRMT5 is involved in the pathogenesis of aGVHD.  Here, we show that PRMT5 expression and enzymatic activity is upregulated in activated T cells in vitro and in T cells from mice developing aGVHD after allogeneic transplant. PRMT5 inhibition using a selective small-molecule inhibitor (C220) significantly reduces mouse and human allogeneic T cell proliferation and inflammatory IFN-g and IL-17 cytokine production. Administration of PRMT5 small-molecule inhibitors significantly improves survival, reducing disease incidence and clinical severity in mouse models of aGVHD without adversely affecting engraftment. Importantly, we show that PRMT5 inhibition retains the beneficial GVL effect by maintaining cytotoxic CD8 T cell responses. PRMT5 inhibition potently reduces transcription of pro-inflammatory genes including Interferon Stimulated Genes (ISG) and IL-17. PRMT5 inhibition deregulates cell-cycle in activated T cells and disrupts signaling by impacting ERK1/2 phosphorylation. Thus, we have identified PRMT5 as a regulator of T cell responses and as a novel therapeutic target in aGVHD.

overall_design: RNA sequencing profiles of CD3/CD28 stimulated T cells stimulated  in the presence or absence of the PRMT5 inhibitor, C220.

first: Parvathi

last: Ranganathan

first: Katiri

last: Snyder


title: Long noncoding RNA (lncRNA) expression profiles in colorectal cancer tissues and paired adjacent normal tissues

city: Jinan

first: Xin

last: Zhang

state: Shandong

address: 107 Wenhua Xi Road

institute: Qilu Hospital, Shandong University

summary: Long noncoding RNAs (lncRNAs) play important roles in the tumorigenesis and metastasis of colorectal cancer (CRC). This study used a lncRNA microarray to analyze the aberrant lncRNA expression profiles in CRC tissues compared with paired adjacent normal tissues as well as CRC with regional lymph nodes metastasis compared with CRC without regional lymph nodes metastasis.

overall_design: Six primary colorectal cancer tissues and paired adjacent normal tissues were obtained from 6 patients with colorectal cancer (three cases with regional lymph nodes metastasis and three cases without regional lymph nodes metastasis). LncRNA expression profiles were evaluated by Arraystar Human LncRNA MicroArray v3.0.


title: In planta and in vitro RNA sequencing of Parastagonospora nodorum SN15 and a knockout mutant lacking the transcription factor Pf-2.

city: Bentley

first: Darcy

middle: Adam Bain

last: Jones

state: Western Australia

address: Kent Street

department: Centre for Crop and Disease Management

country: Australia

institute: Curtin University

summary: The fungus Parastagonospora nodorum infects wheat through the use of necrotrophic effector (NE) proteins that cause host-specific tissue necrosis. The Zn2Cys6 transcription factor PnPf2 positively regulates NE gene expression and is required for virulence on wheat. Little is known about other downstream targets of PnPf2. We compared the transcriptomes of the P. nodorum wildtype and a strain deleted in PnPf2 (pf2-69) during in vitro growth and host infection to further elucidate targets of PnPf2 signalling. Gene ontology enrichment analysis of the differentially expressed (DE) genes revealed that genes associated with plant cell wall degradation and proteolysis were enriched in down-regulated DE gene sets in pf2-69 compared to SN15. In contrast, genes associated with redox control, nutrient and ion transport were up-regulated in the mutant. Further analysis of the DE gene set revealed that PnPf2 positively regulates twelve genes that encode effector-like proteins. Two of these genes encode proteins with homology to previously characterised effectors in other fungal phytopathogens. In addition to modulating effector gene expression, PnPf2 may play a broader role in the establishment of a necrotrophic lifestyle by orchestrating the expression of genes associated with plant cell wall degradation and nutrient assimilation.

sample_organism:
Triticum aestivum
Parastagonospora nodorum

overall_design:
Two P. nodorum isolates SN15 and pf2-69 (a mutant lacking the PnPf2 transcription factor), were grown in vitro, and on wheat cultivar "Halberd" (in planta).
The four treatments each had four biological replicates for a total of 16 samples. The treatments were: “in planta – SN15”, “in vitro – SN15”, “in planta – pf2-69”, and “in vitro – pf2-69”.

first: Evan

last: John

first: Kasia

last: Rybak

first: Huyen

last: Phan

first: Karam

last: Singh

first: Shao-Yu

last: Lin

first: Peter

middle: S

last: Solomon

first: Richard

middle: P

last: Oliver

first: Kar-Chun

last: Tan


title: Transcriptional profile of human macrophages stimulated by cartilage fragments

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

summary: Accumulating evidence suggests that synovitis is associated with osteoarthritic process. Macrophages are predominant cell type in synovium and play principal role in development of synovitis. Our earlier study suggests that the interaction between cartilage fragments and macrophages exacerbates osteoarthritic process. However, molecular mechanisms by which cartilage fragments trigger cellular responses remain to be investigated. Therefore, the current study aims at analyzing molecular response of macrophages to cartilage fragments by RNA-seq

overall_design: RNA-seq for macrophages exposed to cartilage fragments

first: Mohamad

first: Masanari

last: Hamasaki

first: Tomohiro

last: Onodera

first: Norimasa

last: Iwasaki


title: Transcriptome analyses reveal epigenetic and radiation related genes in NSCLC cell

city: Seoul

first: Tae-Gul

last: Lee

address: 75 Nowon-Ro, Nowon-Gu

country: South Korea

institute: Korea Cancer Center Hospital

summary:
Purpose: Radiotherapy is useful for non-small cell lung cancer (NSCLC) patients who cannot be treated surgically. Modification of histone proteins occurs during radiotherapy, and affects gene expression.In this study, we assessed the effects of radiotherapy on histone modification via 3-deazaneplanocin A (DZNep) in NSCLC cells.

Methods: NCI-H460 NSCLC cell line were subjected to gamma irradiation. To reveal histone modification reagent DZNep targeted genes, we conducted mRNA-sequencing.

Results: We evaluated the epigenetic regulation of autophagy-related genes by DZNep through mRNA-sequencing, and we identified genes that are differentially expressed upon irradiation, including a candidate histone modification target gene.

overall_design: We subjected DZNep- or DMSO-treated NCI-H460 cells exposed to 0 or 4 Gy of radiation to mRNA-seq and searched for differently differentially expressed genes.

first: Cheol

last: Kim


title: qPCR array analysis of brain tissue from postnatal germ free mice and mice colonized with bifidobacteria

city: Houston

first: Melinda

last: Engevik

state: TX

address: 1 Baylor Plaza

department: Pathology & Immunology

institute: Baylor College of Medicine

summary: Germ-free mice were colonized as neonates with either a simplified human infant microbiota consortium consisting of four Bifidobacterium species, or with a complex, conventional murine microbiota. Cultures were combined in equal ratios based on OD600 readings (volume equal to approximately OD600 1.0 for each of the species), pelleted, then re-suspended in 3 mL sterile PBS. Colonization of males and females with bifidobacteria was achieved by administering 0.2 mL of this treatment directly to the stomach of each dam via oral gavage on alternating days post-partum. The treatment was also administered with the drinking water. Pups were administered 0.02 mL of the treatment mixture starting at P1, and on alternating days until P20. Dilution plating of the treatment mixture on MRS plates at several timepoints during the experiment confirmed that the dams received approximately 1.1x1010 total CFUs (viable bacterial cells) per gavage. The pups received a smaller volume of the gavage mixture, approximate to 1.1x109 total CFUs per treatment. Conventionalized (colonization of germ-free mice with normal complex murine microbiota) males and females were derived by administering fecal slurries from specific pathogen free mice, which harbor a complex microbial community, via oral gavage to the dams on P1, and by adding used bedding (containing fecal pellets) to the cages on P1 and P3. Germ-free control mice received gavages of sterile 0.1 M phosphate buffered saline (PBS; Gibco) in the same manner as the experimental mice. We examined the cerebellum, cortex, and hippocampus of both groups of colonized mice in addition to germ-free control mice at P4, P10, and P20. For preparation of RNA for gene expression analysis, the mice were individually anesthetized using isoflurane until no reflex was observed. The mice were rapidly decapitated, and the brains were dissected to isolate the cerebellum, hippocampus, and cortex. The tissues were flash frozen and stored separately at -80°C until RNA isolation. RNA was isolated from the cerebellum, cortex, and hippocampus of male mice from each developmental timepoint via Trizol. The 260/280 ratio was measured for each sample using a Nanodrop spectrophotometer, and after this step ranged between 1.8 and 2.0. RNA samples were stored at −80°C until use. Two µg of RNA from 5 samples (male mice only) were pooled into one representative sample per treatment, time point, and brain region (27 pooled samples total, n=5 mice per pooled sample). Pooled RNA was purified with the Zymo RNA clean and concentrate kit according to the manufacture’s protocol with one modification. Zymo-Spin IIICG columns were used instead of Zymo-Spin IC Columns in order to purify larger quantities of RNA (~100 µg of RNA). A Bioanalyzer (Agilent) was used to verify that the purity and concentration of pooled and cleaned RNA was of sufficient quality and quantity prior to use with the synaptic plasticity qPCR array. Using the “Mouse Synaptic Plasticity RT² Profiler PCR Array” (PAMM-126Z; Qiagen), 96 genes were profiled on the 27 samples (1 pooled sample as described above for each of the 3 brain regions, at each of the 3 time points, in each of the 3 treatment groups). The manufacturer’s protocol was followed for sample preparation. Briefly, 500 ng of each pooled sample was treated with DNase to eliminate genomic DNA contamination, followed by conversion to cDNA using the RT2 First Strand Kit. The cDNA was added to the kit mastermix on ice, and distributed to the 384-well plate containing 4 replicate primer assays for the 84 pathway-specific genes. Reactions using SYBR Green chemistry (Qiagen SYBR Green qPCR Mastermix, Cat. no. 330529) were performed in a 384 well block ViiATM 7 Real-Time PCR system (Applied Biosystems, Foster City, USA). The threshold values were set consistently across all runs in the same analysis (threshold manually set to 0.5 and lower limit of detection set to 35).

overall_design: qPCR gene expression profiling.  Brain tissue (cerebellum, hippocampus, cortex) from germ-free, conventionalized, and bifidobacterium-treated mice was collected at 3 timepoints after birth (P4, P10, and P20). RNA from each brain region was isolated independently in each mouse, and RNA from 5 male mice was pooled into one sample representing each brain region, in each group, at each of the 3 time points (n=27 samples total) 96 genes were profiled on the 27 samples.

first: Berkley

last: Luck

first: James

last: Versalovic


title: Transcriptome analysis of postharvest de-astringency treatments in persimmon fruit

city: hangzhou

first: Wei

last: Wu

address: yuhangtang road 866

country: China

institute: zhejiang university

summary: High CO2 treatment achieved significant acceleration of deastringency of ‘Jingmianshi’ persimmon fruit and subsequent softening, which could be retarded by adding 1-MCP. Comparison of the differentially expressed genes in the different treatments narrowed down the potential candidate genes for persimmon post-deastringency or softening.

overall_design: Samples of three treatments (CO2, CO2+1-MCP, control) at 0, 1, 4 days in storage were selected to perform the RNA-seq, and each had three replicates. The SRA Study accession are SRR10020142-SRR10020162 and BioProject accession is PRJNA562104.

first: Qinggang

last: Zhu

first: Xueren

last: Yin


title: Characterization of T cells from the larval zebrafish tail via single-cell RNAseq

city: Chicago

first: Elizabeth

last: Jerison

state: IL

address: 529 E 57th St

department: Physics

institute: University of Chicago

summary: We report single-cell RNA sequencing of cells from the Tg(lck:GFP) larval zebrafish tail, to identify cell types expressing the marker and to identify gene candidates related to T cell migration behaviors. We identified 330 putative T cells and 131 putative epithelial cells. Differential expression analysis between the two groups revealed genes related to actin cytoskeleton remodeling associated with the T cells, in addition to canonical T and ubiquitous immune cell markers.

overall_design: Single cells (n=461) isolated from FACS of Tg(lck:GFP) Danio rerio (FITC+) were analyzed.


title: Gene expression signatures between lean and diabetes resistant B6 and 129/Ola, diabetes susceptible DBA and C3H mice and obese and diabetes susceptible NZO mice

status: Public on May 11 2020

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Whole genome microarray expression was measured in liver of 6 week old mice to detect changes in gene expression related to early onset of non-alcoholic fatty liver disease.

overall_design: Male NZO, B6, C3H, 129/Ola and DBA mice were kept on a high fat diet (HFD) until week 6. Then samples of liver were aliquoted for RNA extraction

first: Kristin

last: Schwerbel

first: Wenke

last: Jonas

first: Annette

last: Schürmann


title: Comparative gene expression profiling of telomerase-reverse transcriptase (TERT)-immortalised BJ fibroblasts and those with overexpression of myristoylated AKT1 (myrAKT1)

city: Melbourne

first: Keefe

last: Chan

state: VIC

address: 305 Grattan St

department: Division of Cancer Research

institute: Peter MacCallum Cancer Centre

summary: We use RNA-seq to characterise the transcriptional programs of proliferating BJ-TERT fibroblasts versus those undergoing myrAKT1-induced senescence (6 days).

overall_design: BJ-TERT fibroblasts were either non-transduced or transduced with pBabe-puro-myrAKT1 to induce senescence and at 6 days post-transduction, total RNA was extracted for RNA-seq.

first: Richard

last: Pearson


title: RNA-seq analysis for mRNA expression change in oxygen/glucose deprivation-treated cultured oligodendrocyte precursor cells

city: Kobe

first: Yuichi

last: Ono

state: Hyogo

address: 6-8-2 Minatojima-minamimachi, Chuo-ku

department: Developmental Neurobiology

institute: KAN Research Institute Inc.

summary: Oligodendrocyte precursor cells (OPCs) regulate neuronal, glial and vascular systems in diverse ways and display phenotypic heterogeneity beyond their well-known role as a reservoir for mature oligodendrocytes. Here we demonstrated that perivascular OPCs in cerebral cortex were increased coupling with post-stroke angiogenesis in a mouse model of stroke induced by middle cerebral artery occlusion (MCAO). RNA-seq analysis revealed that primary cultured OPCs notably increased the gene expressions of numerous pro-angiogenic factors, while decreased those related to OPC maturation after oxygen glucose deprivation. The data showed that cerebral ischemia shifts the phenotype of OPCs to perivascular subtypes which can promote angiogenesis.

overall_design: mRNA profiles of primary cultured rat oligodendrocyte precursor cells incubated under normal or oxygen glucose deprivation conditions for 6 hours were generated by deep sequencing, in quadruplicate, using Illumina MiSeq.

first: Natsue

last: Kishida

first: Takakuni

last: Maki

first: Yusuke

last: Kinoshita

first: Ryosuke

last: Takahashi


title: Development of a new macrophage-specific TRAP mouse (MacTRAP) and the definition of the renal macrophage translational signature

city: Marburg

first: Andreas

last: Hofmeister

state: Hessen

address: Baldingerstrasse 1

department: Zentrum für Innere Medizin

institute: Philipps-Universität Marburg

summary: We generated a new macrophage-specific mouse line for the application of Translating Ribosome Affinity Purification (MacTRAP). MacTRAP mice express an eGFP-tagged ribosomal protein (L10a) under the control of the macrophage-specific c-fms promoter (driver of Csf1r). The TRAP line was characterized and expression of the transgene confirmed in kidney and other tissues. Validation included testing the responsiveness of the transgene under pro-inflammatory challenge in the kidney. Using TRAP, we successfully extracted macrophage-specific polysomal RNA from MacTRAP kidneys and conducted RNA-Seq following bioinformatic analyses to establish a comprehensive in vivo gene expression and pathway signature of resident renal macrophages, which may be of use to investigators studying the gene expression profile of these cells. Overall, this new in vivo tool may be of great value for the study of macrophage biology in different organs and various models of injury and disease.

overall_design: Unbound and bound (immunopreciptated) fractions of three nine week old male MacTRAP mice were analyzed.

first: Ivica

last: Grgic


title: Persistence of inflammatory phenotype in residual psoriasic plaques in patients on effective biologic therapy

city: Cambridge

first: Kathleen

middle: Marie

last: Smith

state: MA

address: 200 Sidney Street

department: Systems Computational Biology

institute: AbbVie

summary: The goal of our study is to elucidate mechanisms of plaque persistence despite overall good drug response.

overall_design: RNA-seq of cross sectional cohort of psoriasic patients and healthy controls


title: Hippocampal Subfield Transcriptome Analysis in Schizophrenia Psychosis

city: Dallas

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

summary: We have previously demonstrated functional and molecular changes in hippocampal subfields in individuals with schizophrenia (SZ) psychosis associated with hippocampal excitability. In this study, we use RNA-seq and assess global transcriptome changes in the hippocampal subfields, DG, CA3, and CA1 from individuals with SZ psychosis and controls to elucidate subfield-relevant molecular changes. We also examine changes in gene expression due to antipsychotic medication in the hippocampal subfields from our SZ ON- and OFF-antipsychotic medication cohort. We identify unique subfield-specific molecular profiles in schizophrenia postmortem samples compared to controls, implicating astrocytes in DG, immune mechanisms in CA3, and synaptic scaling in CA1. We show a unique pattern of subfield-specific effects by antipsychotic medication on gene expression levels with scant overlap of genes differentially expressed by SZ disease effect versus medication effect. These hippocampal subfield changes could provide the basis for previously observed hippocampal SZ pathology and explain the lack of full efficacy of conventional antipsychotic medication on SZ symptomatology. With further characterization, the identified distinct molecular profiles of the DG, CA3, and CA1 in SZ psychosis may serve to identify potential hippocampal-based therapeutic targets.

overall_design: We compared hippocampal subfield-specific transcriptome profiling from individuals with schizophrenia and healty controls. We analyzed genome-wide expression levels in adult dentate gyrus (DG), cornu Ammonis 1 (CA1) and cornu Ammonis 3 (CA3) from 13 individuals with schizophrenia and 13 healthy controls. Gene expression was balanced for technical, biological, and surrogate covariates.

first: Stefano

last: Berto

first: Jessica

last: Perez

first: Kelly

last: Gleason

first: Carol

last: Tamminga


title: Dual Histone Methyl Reader ZCWPW1 Facilitates Repair of PRDM9-Induced Meiotic Double Strand Breaks

city: Bethesda

first: Mohamed

last: Mahgoub

state: MD

address: 6 Center Dr

department: Division of Developmental Biology

institute: NICHD

summary: Meiotic crossovers result from homology-directed repair of double strand breaks (DSBs). Unlike yeast and plants, where DSBs are generated near gene promoters, in many vertebrates, DSBs are enriched at hotspots determined by the DNA binding activity of the rapidly evolving zinc finger array of PRDM9 (PR domain zinc finger protein 9), which subsequently catalyzes trimethylation of lysine 4 and lysine 36 of Histone H3 in nearby nucleosomes. Here, we identify the dual histone methylation reader ZCWPW1, which is tightly co-expressed during spermatogenesis with Prdm9 and co-evolved with Prdm9 in vertebrates, as an essential meiotic recombination factor required for efficient synapsis and repair of PRDM9-dependent DSBs. In sum, our results indicate that the evolution of dual histone methylation reader/writer system involving Prdm9 and Zcwpw1 facilitated a shift in genetic recombination away from a static pattern near genes towards a flexible pattern controlled by the rapidly evolving DNA binding activity of PRDM9

overall_design: (1) CUT&RUN experiment for mapping chromatin binding of ZCWPW1 and H3K4me3 were performed on testis from adult C57BL/6N (B6/B6) mouse and F1 B6/CAST hybrid mouse from mating male CAST (CAST/EiJ ) and female B6 (C57BL/6J). (2) END-seq experiments were performed on testes from juvenile/adult Zcwpw1WT/WT and Zcwpw1WT/KO to map meiotic hotspots for DNA double strand breaks (DSBs)


title: Transcriptome and epigenome analyses reveal epigenetic and radiation related genes in NSCLC cell

first: Tae-Gul

last: Lee

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

overall_design: Refer to individual Series


title: Epigenome analyses reveal histone H4K20me3 and radiation related genes in NSCLC cell

summary:
Purpose: Radiotherapy is useful for non-small cell lung cancer (NSCLC) patients who cannot be treated surgically. Modification of histone proteins also occurs during radiotherapy, and affects gene expression. In this study, we assessed the effects of radiotherapy on histone H4K20me3 in NSCLC cells.

Methods: NCI-H460 NSCLC cell line were subjected to gamma irradiation. To reveal H4K20me3-related genes, we conducted chromatin immunoprecipitation(ChIP) and ChIP-sequencing.

Results: We evaluated the H4K20me3-related genes through ChIP-sequencing.

overall_design: We subjected NCI-H460 cells exposed to 0 or 4 Gy of radiation to ChIP using H4K20me3 antibody (Cell signaling technology,Tri-Methyl-Histone H4 (Lys20) (D84D2) Rabbit mAb #5737) and sequencing.

first: Cheol

last: Kim


title: The role of the Death Domain Associated Protein DAXX in expression regulation during oocyte growth and 2-cell pre-implantation embryos of the mouse

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

summary: Comparative expression analysis between meiosis II (MII) stage mouse oocytes of wildtype ("WT") or deficient ("KO") for Daxx expression as well as for 2-cell embryos maternally wildtype of Daxx deficient.

overall_design: Two genotypes, 3 (or 2) replicates per genotype, two cell types (oocytes, 2-cell embryos).

first: Zichuan

last: Liu

first: Evgeniy

last: Ozonov


title: Comparative gene expression profiling of telomerase-reverse transcriptase (TERT)-immortalised BJ fibroblasts transduced with pBabe empty vector control or HRASG12V

first: Keefe

last: Chan

summary: We use RNA-seq to characterise the transcriptional programs of proliferating BJ-TERT fibroblasts versus those undergoing HRASV12-induced senescence (14 days)

overall_design: BJ-TERT fibroblasts were transduced with pBabe-puro empty vector or pBabe-puro-HRASG12V to induce senescence and at 14 days post-transduction, total RNA was extracted for RNA-seq.

first: Richard

last: Pearson


title: Effects of Korean red ginseng against the influence of bisphenol A on ovariectomized mouse liver and uterus

city: seoul

first: Jeonggeun

address: Kwangjin-gu, Seoul

institute: sejong univ

summary: Bisphenol A (BPA), known as an endocrine disruptor, is widely used in the world. BPA is reported to cause inflammation-related diseases. Although efforts to identify the effects of BPA are ongoing, the impact of BPA on postmenopausal women is not well known. Korean red ginseng (KRG) has been used safely in human for a long time for the treatment of diverse diseases. KRG has been reported of its mitigating effect on menopausal symptoms and suppress adipose inflammation. Here, we investigate the protective effect of orally administered KRG on the impacts of BPA in the liver and uterus of menopausal mouse model.

overall_design: Six-weeks-old female CD-1 mice were ovariectomized and had 1 week of purification period. Gene expression of liver was measured after exposed for 7 days to bisphenol A at dose 200 mg/kg/day with or without Korean red ginseng at dose 1.2g/kg/day via oral administration.

first: Yonyook

first: YoungJoo


title: Niche-Specific Re-Programming of Epigenetic Landscapes Drives Myeloid Cell Diversity in NASH [RNA-seq]

status: Public on May 10 2020

city: La Jolla

first: Christopher

last: Glass

state: CA

address: 9500 Gilman Drive

department: School of Medicine

institute: University of California, San Diego

summary: Tissue resident macrophages and recruited monocyte-derived macrophages contribute to host defense but also play pathological roles in a diverse range of human diseases. Multiple macrophage phenotypes are often represented in a diseased tissue, but we lack a deep understanding of the mechanisms that control diversification. Here we use a combination of genetic, genomic, and imaging approaches to investigate the origins and epigenetic trajectories of hepatic myeloid cells during a diet-induced model of nonalcoholic steatohepatitis (NASH). We provide evidence that distinct microenvironments within the NASH liver induce strikingly divergent transcriptomes of resident and infiltrating cells. Myeloid cell diversification results from both remodeling open chromatin landscapes of recruited monocytes and altering activities of preexisting enhancers of resident Kupffer cells. These findings provide evidence that niche-specific combinations of disease-associated environmental signals instruct resident and recruited macrophages to acquire distinct programs of gene expression and corresponding phenotypes.

overall_design: RNA-seq, ATAC-seq, H3K27ac ChIP-seq and LXR alpha + beta ChIP-seq on liver and peripheral myeloid cells in healthy and NASH model diet mice


title: Heterochromatin-driven nuclear softening protects the genome against mechanical stress-induced damage

city: Münster

first: Sara

last: Wickström

address: Röntgenstraße 20

department: Cell & Tissue Dynamics

institute: Max Planck Institute for Molecular Biomedicine

summary: RNA and H3K9me3 ChIP sequencing data of normal human neonatal keratinocytes subjected to 40% uniaxial cyclic stretch

overall_design: Total RNA from 3 biological replicates of control cells and cells stretched for 30 and 360 minutes. Paired-end sequencing 100bp reads HiSeq2000. H3K9me3 chromatin immunoprecipitation paired-end 100 bp reads NovaSeq6000


title: ZBED2 is an antagonist of Interferon Regulatory Factor 1 and modifies cell identity in pancreatic cancer

status: Public on May 09 2020

city: Cold Spring Harbor

first: Tim

middle: D D

last: Somerville

state: NY

address: 1 Bungtown Road

department: CSHL

institute: Cold Spring Harbor Laboratory


title: Nano gold simulated autophagy prevents cell death

city: Wuhan

first: Miusi

last: Shi

state: Hubei

address: No.237 in Luoyu Road

department: School of Stomatology

institute: The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei MOST)

summary: We showed a kind of rectangular shaped gold-based nanoparticles (gold nanocages, GNC) could enhance the survival of cells from hydroxyurea induced cell apoptosis and significantly reduced the reactive oxygen species (ROS) levels.The nanoparticles could initiate single layer isolation membrane elongation after been phagocytosed, followed by autophagosome and autolysosome formation, then specifically integrated into the autophagosome inner membrane and bind to p62. Through recycling ribosome proteins and activate Nrf2 mediated activation of GATA3 signaling, rescue the cell death and enhanced cell and life survival.

overall_design: We used hydroxyurea to induce the cell damage condition and performed cell apoptosis assay and western blot to verify the rescue ability of gold nanoparticles. To gain deeper insights into the molecular functions GNC, we performed RNAseq analysis. RAW 264.7 cells were treated with 0.5mM hydroxyurea (HU, H8627, Sigma Aldrich) and gold nanoparticles at same time. After 12hrs, total RNA of each sample was extracted using RNAiso Plus (TaKaRa Bio Inc., Japan)  following the manufacturer’s protocol. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop 2000 (Thermo Fisher Scientific Inc.). 1 μg total RNA with RIN value above 7 was used for following library preparation. RNA sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacturer’s protocol (NEB, Ipswich, MA, USA). Sequencing was carried out using a 2x150bp paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS)+OLB+ GAPipeline-1.6 (Illumina) on the HiSeq instrument. GO-TermFinder was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05. The sequencing reactions were conducted at GENEWIZ, LLC (South Plainfield, NJ, USA).

first: Bing

last: Hu

first: Yufeng

last: Zhang


title: Voltage-gated Sodium Channel SCN5A Promotes Tumor Progression and Enhances Chemosensitivity to 5-Fluorouracil in Colorectal Cancer

city: Guangzhou

first: Qiaoqi

last: Sui

address: Dongfeng East Road 651

institute: Sun Yat-sen University Cancer Center

summary: SCN5A was reported to promote proliferation and invasiveness potential in colorectal cancer, yet the mechanism was not clarified, and little was known about its association with chemosensitivity to 5-fluorouracil. In the current study, elevated SCN5A expression were associated with poor prognosis and metastasis in colorectal cancers, whereas stage II-III patients with up-regulated SCN5A expression were more likely to benefit from 5-fluorouracil-based adjuvant chemotherapy. SCN5A could promote proliferation and invasiveness potential through regulating cell cycle and epithelial-mesenchymal transition in colorectal cancer cells. Furthermore, SCN5A regulated Ras signaling by stabilizing KRas-calmodulin complex through Ca2+ influx. Apart from that, under 5-fluorouracil treatment, SCN5A promoted calmodulin-dependent apoptosis in colorectal cancers.

overall_design: This study was carried out in Sun Yat-Sen University Cancer Center. CRC cases receiving surgical treatment were investigated, and IHC scores of SCN5A were determined.We also obtained Online data on SCN5A expression and clinical data from The Cancer Genome Atlas (TCGA) as well as the GEO data sets. SCN5A knockdown SW480 and DLD1 cells were constructed to investigate the regulatory role of SCN5A in cellular phenotypes. RNA sequencing was applied to explore the underlying mechanism. To demonstrate the association between SCN5A and chemosensitivity to 5-FU, cell apoptosis assay was conducted following 5-fluorouracil treatment.

first: Jianhong

last: Peng

first: Kai

last: Han

first: Junzhong

last: Lin

first: Rongxin

first: Qingjian

last: Ou

first: Yuxiang

last: Deng

first: Wenhao

last: Zhou

first: Lingheng

last: Kong

first: Jinghua

last: Tang

first: Binyi

last: Xiao

first: Yuan

last: Li

first: Long

last: Yu

first: Yujing

last: Fang

first: Peirong

last: Ding

first: Zhizhong

last: Pan


title: ChIP-seq BHT-101 cells and BHT-101 ASH1L KO cell lines

city: Ann Arbor

first: Ronald

last: Koenig

state: MI

address: 1150 West Medical Center Dr

department: Metabolism, Endocrinology & Diabetes

institute: University of Michigan

summary: The goal of this study is to assess the role of ASH1 like histone lysine methyltransferase (ASH1L) in the biology of anaplastic thyroid cancer. CRISPR-Cas9 was used to create cell lines derived from BHT-101 anaplastic thyroid cancer cells with premature stop codons prior to the catalytic domain within both alleles of ASH1L. ChIP-seq for H3K36me2, the histone mark catalyzed by ASH1L, was performed on two KO cell lines, and compared to wild type BHT-101 cells.

overall_design: H3K36me2 ChIP-seq was performed on wild type BHT-101 cells and 2 BHT-101 ASH1L KO cell lines. Three biological replicates were performed and analyzed.

first: Bin

last: Xu

first: Tingting

last: Qin

first: Jingcheng

first: Thomas

last: Giordano

first: Maureen

last: Sartor


title: Expression data from patient-derived primary glioblastoma cell lines

city: Durham

first: Landon

last: Hansen

state: NC

address: 203 Research Drive, MSRB1 Rm 171

institute: Duke University School of Medicine

summary:
Genetic alterations that give rise to tumorigenesis result in altered epigenetic and gene expression profiles. We sought to identify and better understand potential consequences of MTAP deletion in glioblastoma by examining gene expression profiles of MTAP deleted and MTAP WT GBM cell lines.
MTAP deletion results in accumulation of the abberant metabolite, MTA, with potential consequences to epigenetic regulation and signal transduction. We also examined the cellular response (gene expression) to purine deprivation with L-Alanosine treamment

overall_design: We used 5 patient-derived GBM cell lines. Three cell lines (12-0160, 12-0106, and 13-0302) were MTAP-null and two cell lines (12-0358 and 12-0008) were MTAP WT. Each cell line was treated with the vehicle control NaOH (1:1000 dilution)

first: Lee

last: Chen

first: Rui

last: Yang

first: Yiping

last: He

first: Simranjit

last: Singh

first: Wenzhe

last: Wang


title: Brd4, H3K27Ac, and H3K36me3 binding profiles with or without Dinaciclib in human neuroblastoma CLB-GA cells

city: Stanford

first: Min

last: Huang

address: 265 Campus Drive

department: Internal Medicine

institute: Stanford Cancer Institute

summary: Promoter rearrangement of the telomerase reverse transcriptase (TERT) gene juxtaposes the coding sequence to strong enhancer elements, leading to TERT overexpression and poor prognosis. TERT associated oncogenic signaling in neuroblastoma remains unclear. Gene set enrichment analysis of RNA-seq data from 498 neuroblastoma patients revealed a coordinated activation of oncogenic signaling pathways and differentially overexpressed gene signature in a subgroup of MycN non-amplified neuroblastomas with TERT overexpression. ChIP-seq analysis of human neuroblastoma cell line CLB-GA harboring TERT rearrangement uncovered genome-wide chromatin co-occupancy of Brd4 and H3K27Ac and robust enrichment of H3K36me3 in TERT and multiple TERT-associated genes. We demonstrated a critical regulatory role of Brd4 and cyclin-dependent kinases in the expression and chromatin activation.  Inhibition of both with AZD5153 and dinaciclib proved most effective in tumor growth suppression of neuroblastoma cell lines, primary cells, and xenograft. Our study provides a therapeutic strategy utilizing epigenetic targeting of neuroblastoma with TERT overexpression.

overall_design: Chromatin immunoprecipitation of Brd4, H3K27Ac, and H3K36me3 followed by high-throughput sequencing (ChIP-seq) in human neuroblastoma CLB-GA cells in the presence or absence of Dinaciclib.

first: Bill

last: Chiu


title: Experience recruits MSK1 to expand the dynamic range of synapses and enhance cognition

city: Coventry

first: Bruno

middle: G.

last: Frenguelli

state: Coventry

address: Gibbet Hill Road

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

summary: Experience powerfully influences neuronal function and cognitive performance, but the cellular and molecular events underlying the experience-dependent enhancement of mental ability have remained elusive. In particular, the mechanisms that couple the external environment to the genomic changes underpinning this improvement are unknown. To address this we have used male mice harbouring an inactivating mutation of mitogen- and stress-activated protein kinase 1 (MSK1), a BDNF-activated enzyme downstream of the MAPK pathway. We show that MSK1 is required for the full extent of experience-induced improvement of spatial memory, for the expansion of the dynamic range of synapses, exemplified by the enhancement of hippocampal LTP and LTD, and for the regulation of the majority of genes influenced by enrichment. In addition, and unexpectedly, we show that experience is associated with an MSK1-dependent downregulation of key MAPK and plasticity-related genes, notably of EGR1/Zif268 and Arc/Arg3.1, suggesting the establishment of a novel genomic landscape adapted to experience. By coupling experience to homeostatic changes in gene expression MSK1, represents a prime mechanism through which the external environment has an enduring influence on gene expression, synaptic function and cognition.

overall_design: Hippocampal mRNA profiles were generated from 24 samples taken from 3 month old mice on a C57-Bl/6 background homozygous for either the WT or kinase-dead MSK1 allele.

first: Lucia

last: Privitera

first: Lorenzo

last: Morè

first: Daniel

middle: D

last: Cooper

first: Philippa

last: Richardson

first: Marianthi

last: Tsogka

last: Hebenstreit

first: Simon

middle: C

last: Arthur

middle: G


title: Gene expression signature between recombinant congenic mice on genetic background of NZO mice differing in 5.3 Mbp on chromosome 18 (Ltg/NZO.5.3N/N and Ltg/NZO.5.3N/B)

city: Nuthetal

first: Heike

last: Vogel

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

summary: Whole genome microarray expression was measured in livers of 5 weeks old mice to detect changes in gene expression related to early onset of non-alcholic fatty liver.

overall_design: Male Ltg/NZO.5.3N/N and Ltg/NZO.5.3N/B mice were kept on a high fat diet (HFD) until week 5. Than samples of liver were aliquoted for RNA extraction.

first: Kristin

last: Schwerbel

first: Wenke

last: Jonas

first: Annette

last: Schürmann


title: Genome wide analysis of thoracic spinal cord at 5 days after T9 hemisection injury.

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: The goal of this study is to elucidate the influence of hemisection injury at thoracic spinal cord (T9) and epidural electrical spinal stimulation (L2-S1) on transcriptome of injured thoracic spinal cord. mRNA profiles of spinal cord at 5 days-post injury with or without epidural electrical spinal stimulation (L2-S1) and before injury were generated. Our study represents the detailed analysis of transcriptomes of injured spinal cord with biologic replicates, generated by RNA-seq technology.

overall_design: The effect of epidural electrical spinal stimulation (L2-S1) after spinal cord injury on the transcriptom of injured spinal cord (T9) was investigated.

first: Kazu

last: Kobayakawa

first: Masamitsu

last: Hara

first: V

middle: R

last: Edgerton

first: Akihito

last: Harada

first: Jumpei

last: Nogami


title: RNA-Sequencing reveals mechanisms by which human glial progenitor cells (hGPCs) initiate remyelination

city: Rochester

first: John

last: Mariani

address: 601 Elmwood Avenue

department: Neurology

institute: University of Rochester

summary: To investigate transcriptomic drivers of human myelination, immunodeficient mice were chimerized with fetal derived hGPCs at P1, sacrified at 36 weeks, and hGPCs were extracted for RNA-Sequencing via FACS.  Mice were either fed a control diet for the entireity of their lives or a demyelinating diet beginning at 12 weeks of age until 24 weeks, when they were transitioned to a control diet to allow for remyelination to begin.

overall_design: RNA-Sequencing of FACS isolated hGPCs from the corpora callosa of 36 week old mice fed a control diet (n=6) or following 12 weeks of a demyelinating cuprizone diet beginning at 12 weeks, for 12 weeks, before being allowed to recover on a control diet for 12 weeks (n=6).

middle: N

first: Steven

middle: A

last: Goldman


title: Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

institute: University of Wuerzburg

summary: A major challenge for RNA-seq analysis of gene expression is to achieve sufficient coverage of informative non-ribosomal transcripts. In eukaryotic samples, this is typically achieved by selective oligo(dT)-priming of messenger RNAs to exclude ribosomal RNA (rRNA) during cDNA synthesis. However, this strategy is not compatible with prokaryotes in which functional transcripts are generally not polyadenylated. To overcome this, we adopted DASH (Depletion of Abundant Sequences by Hybridization), initially developed for eukaryotic cells, to improve both the sensitivity and depth of bacterial RNA-seq. DASH employs the Cas9 nuclease to remove unwanted cDNA sequences prior to library amplification. We report the design, evaluation, and optimization of DASH experiments for standard bacterial short-read sequencing approaches, including software for automated guide RNA (gRNA) design for Cas9-mediated cleavage in bacterial rDNA sequences. Using these gRNA pools, we effectively removed rRNA reads (56-86%) in RNA-seq libraries from two different model bacteria, the Gram-negative pathogen Salmonella enterica and the anaerobic gut commensal Bacteroides thetaiotaomicron. DASH works robustly, even with sub-nanogram amounts of input cDNA. Its efficiency, high sensitivity, ease of implementation, and low cost (~$5 per sample) render DASH an attractive alternative to rRNA removal protocols, in particular for material-constrained studies where conventional ribodepletion techniques fail.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: rRNA-derived cDNA molecules were depleted in Salmonella Typhimurium or Bacteroides thetaiotaomicron libraries through DASH, with varying Cas9:sgRNA ratios, sgRNA pools and reaction conditions.

first: Gianluca

last: Prezza

first: Tobias

last: Heckel

first: Sascha

last: Dietrich

first: Christina

last: Homberger

first: Alexander

middle: J

last: Westermann

first: Jörg


title: Hippo pathway induces PIEZO1 expression to promote oral squamous cell carcinoma cell proliferation

status: Public on May 08 2020

first: Kana

last: Hasegawa

state: Fukuoka

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

department: Faculty of Dental Science

institute: Kyushu University

summary: Most cancer cells are exposed to extracellular environments, such as extracellular matrix, which commonly becomes stiffer along with transformation. It is conceivable that tumorous extracellular environments would be changing to affect tumor cell behavior. It has been reported that Hippo pathway responds to the extracellular environments and induces the nuclear localization of transcription activator, yes-associated protein (YAP), resulting in stimulating cell proliferation. Its pathway also regulates gene expression, but the precise molecule to meditate cell proliferating effect of Hippo pathway in oral squamous cell carcinoma (OSCC) is not well understood. Here, we examined the effects of YAP-mediated Hippo pathway in OSCC tumorigenesis. Loss-of-function experiments using siRNA or an inhibitor, and immunohistochemical analyses of tissue specimens obtained from OSCC specimens demonstrated that YAP-mediated Hippo pathway was involved in OSCC cell proliferation. We identified Piezo-type mechanosensitive ion channel component 1 (PIEZO1), a Ca2+ channel, as a downstream molecule of Hippo pathway and showed that elevated PIEZO1 expression was required for PIEZO1 agonist-dependent Ca2+ entry and cell proliferation in OSCC cells. Furthermore, the experiments using three-dimensional culture and suspension culture revealed that PIEZO1, of which expression was regulated by YAP-mediated Hippo pathway, was involved in OSCC cellular growth. Immunohistochemically, YAP overexpression with nucleus and/or cytoplasm was detected with both PIEZO1 and Ki-67 expression at high frequencies in tumor lesion, but not in non-tumor region, of OSCC specimens. These results suggest that the YAP-mediated Hippo/PIEZO1 axis, which might be activated by the tumorous extracellular environments, promotes OSCC tumor cell growth.

overall_design: Microarray analyses were performed using HSC-4 cells cultured in 2D culture, and transfected without or with LATS2 siRNA in suspension culture. Compare1: HSC-4 cells cultured in 2D culture were compared with  HSC-4 cells cultured in suspension culture. Compare2: HSC-4 cells transfected with siLATS2 were compared with  HSC-4 cells transfected with control siRNA in suspension culture

first: Shinsuke

last: Fujii

first: Yudai

last: Tajiri

first: Tamotsu

last: Kiyoshima


title: Exploration of wound signaling pathway in Calotropis procera

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

summary: To explore the wound response in C.procera seedlings, a customized microarray chip (8x60K) was developed using the annotated transcripts obtained from de novo transcriptome data of C.procera. 3-month-old seedlings were subjected to mechanical wounding for 1h, 3h and 6 hours and RNA was isolated for the microarray hybridization and analysis.  Expression analysis of transcripts involved in defense, primary metabolism, secondary metabolism, TFs were studied in comparison of control seedlings.

overall_design: Agilent Custom Calotropis Gene Expression 8x60K Array (AMADID: 085482) designed by Dr. Vineeta Tripathi with the help of Genotypic Technology Private Limited, Bangalore

first: Vineeta

last: Tripathi

first: Akansha

last: Pandey

first: Tushar


title: Initial ERF ChIP in VCaP, no biologic replicates

city: New York

first: Rohit

last: Bose

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Given ERFs known role in competing with ERG-dependent tumor formation, we sought to examine ERF ChIP in the presence or absence of doxycycline-induced shERG knockdown.

overall_design: VCaP cells were infected with Tet-inducible shERG lentivirus and selected with antibiotics.  Subsequently, cells were treated with 100ng/mL doxycycline vs vehicle.  Samples were then sonicated and genomic DNA extracted for ChIP-seq.

first: Ping

last: Wang

first: Anna

last: Patruno

first: Deyou

last: Zheng

first: Charles

middle: L

last: Sawyers


title: Stromal beta-catenin activation impacts nephron progenitor differentiation in the developing kidney and may contribute to Wilms tumor

city: Dallas

first: Thomas

last: Carroll

address: 6000 Harry Hines Blvd.

institute: UT Southwestern

summary: Wilms tumor (WT) morphologically resembles the embryonic kidney, consisting of blastema, epithelial, and stromal components, suggesting tumors arise from the dysregulation of normal development. Activation of beta-catenin is observed in a significant proportion of human WTs; however, much remains to be understood about how it contributes to tumorigenesis. While activating beta-catenin mutations are observed in both blastema and stromal components of human WT, current models assume that activation in the blastemal lineage is causal. Paradoxically, studies performed in mice suggest that activation of b-catenin in this lineage results in loss of nephron progenitor cell (NPC) renewal, a phenotype opposite to WT. Here, we show that activation of beta-catenin in the stromal lineage acts non-autonomously, resulting in expansion of NPCs and an inhibition of differentiation. Comparisons of the transcriptomes of kidneys expressing an activated allele of beta-catenin in the stromal or nephron progenitor cells reveals that human WT more closely resembles the stromal-lineage mutants. These findings suggest that stromal beta-catenin activation results in histological and molecular features of human WT, providing insights into how stroma signaling may play an active role in tumorigenesis.

overall_design: Mouse models with activated beta-catenin specifically in the nephron progenitor or stromal lineages were generated by crossing mice carrying an inducibly activated allele of beta-catenin (CTNNB1 ex3/+) to mice expressing Cre in nephron progenitor (Six2Cre) or the stroma (Foxd1Cre) cell lineages.

first: Keri

last: Drake


title: RNA-seq BHT-101 cells and BHT-101 ASH1L KO cell lines

first: Ronald

last: Koenig

summary: The goal of this study is to assess the role of ASH1 like histone lysine methyltransferase (ASH1L) in the biology of anaplastic thyroid cancer. CRISPR-Cas9 was used to create 4 independent cell lines derived from BHT-101 anaplastic thyroid cancer cells with premature stop codons prior to the catalytic domain within both alleles of ASH1L. RNA-seq was performed on these 4 KO cell lines, and compared to 3 biological replicates of wild type BHT-101 cells.

overall_design: 3 biological replicates of wild type BHT-101 cells were compared to singlicates of the 4 ASH1L KO cell lines

first: Bin

last: Xu

first: Tingting

last: Qin

first: Jingcheng

last: Yu

last: Giordano

first: Maureen

last: Sartor


title: RNA-seq analysis of Men1-/- versus Men1wt MN1-driven AML

city: Philadelphia

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

summary:
Purpose: To characterize transcriptional changes associated with homozygous inactivation of Men1 in MN1 driven AML
Methods: In vivo MN1 transformed cells  were transduced with Cre-vector to inactivate Men1 and injected into sublethially irradiated syngeneic recipients. Men1-/- and Men1wt MN1-driven leukemic cells were isolated from moribund recipients and plated in methylcellulose for 7 days before RNA was extracted.
Results: Men1-/- MN1-driven leukemic cells failed to propagate leukemia in most secondary recipients, in comparison with Men1wt MN1-driven. In vitro, cells had lost their colony forming activity. Gene expression analysis revealed a downregulation of the MN1 leukemic expression program.
Conclusions: Men1 regulates long term maintenance of MN1-driven leukemia.

overall_design:
Men1-/- and Men1wt MN1-driven leukemic cells were isolated from moribund mice and plated in methylcellulose for 7 days.
mRNA from murine Men1-/- and Men1wt MN1-driven AML was submitted for RNAseq

first: Clara

last: Libbrecht

first: Hongbo

middle: M

last: Xie

first: Molly

last: Kingsley

first: Jessica

last: Haladyna

first: Simone

last: Riedel

first: Gerald

last: McGeehan

first: Patricia

last: Ernst


title: Inflammatory Type 2 cDCs Acquire Features of cDC1s and Macrophages to Orchestrate Immunity to Respiratory Virus Infection

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

institute: VIB-University of Ghent

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

overall_design: Refer to individual Series