title: FCN3 functions as a tumor suppressor of lung adenocarcinoma through induction of endoplasmic reticulum stress

first: Yukyung

last: Jun

address: 245 Daehak-ro, Yuseong-gu

department: Center for Supercomputing Applications

institute: Korea Institute of Science and Technology Information

summary: In this study, we report a novel function of FCN3 (Ficolin 3), a secreted lectin capable of activating the complement pathway, as a tumor suppressor of lung adenocarcinoma (LUAD). First, the expression of FCN3 was strongly down-regulated in cancer tissues compared to matched normal lung tissues, and down-regulation of FCN3 was shown to be significantly correlated with increased mortality among LUAD patients. Interestingly, while ectopic expression of FCN3 led to cell cycle arrest and apoptosis in A549 and H23 cells derived from LUAD, the secreted form of the protein had no effect on the cells. Rather, we found evidence indicating that activation of the unfolded protein response is induced from ectopic expression of FCN3 which lead to endoplasmic reticulum (ER) stress. Consistently, inhibition of ER stress response led enhanced survival of the LUAD cells. Collectively, our data indicate that FCN3 is a tumor suppressor gene functioning through induction of ER stress.

overall_design: Examination of transcriptome on control and FCN3 overexpressed lung cancer cell lines by deep sequencing

first: Haeyeon

last: Jang

first: Suyeon

last: Kim

first: Eunjeong

first: Yeonjoo

last: Jung

first: Byung

last: Park

first: Jinseon

last: Lee

first: Jhingook

first: Sanghyuk

first: Jaesang


title: Reprogramming the spleen into a functioning “liver” in vivo III

status: Public on Apr 17 2021

city: Nanjing

first: Chunyan

last: Liu

address: 163 Xianlin Avenue

country: China

institute: Nanjing University

summary: We restored liver function in the spleen by direct reprogramming splenic fibroblasts in situ and thereby transformed the spleen into a “liver” with sufficient physiological functions within a living animal.

overall_design: The Gene Expression profiling of PBS-treated spleens (PBS) vs SiO2-remodelled spleens (SiO2), PBS as control; primary mouse SiO2-remodelled spleen fibroblasts (MF) vs hepatocyte-like cells (iHep) vs primary hepatocytes (PH), MF as control; SiO2-treated spleens (SiO2) vs SiO2-3TF-3C-treated spleen (hepatized spleens) vs normal liver tissues, SiO2 as control.Five cell/spleen samples were pooled according to individual groups.

first: Lei

last: Dong

first: Chunming

last: Wang

first: Junfeng

last: Zhang


title: miRNA array to determine changes in sEV miRNA cargo composition in endothelial cells during inflammatory response

city: Ulm

first: Tim

last: Eiseler

address: Albert-Einstein Allee 23

department: Internal Medicine 1

country: Germany

institute: Ulm University

summary: We performed miRNA micro array to asses the miRNA profile differences in sEVs during inflammation vs. homeostatic conditions in endothelial cells. Therefore HUVEC cells were treated with a polytrauma cocktail comprised of IL1ß, IL6, CXCL8, C3a and C5a-des-Arg (PTC) at concentrations measured in patient serum 24hrs after polytrauma

overall_design: Confluent HUVEC cells were treated with PTC in serum-free medium for 24hrs before supernatant was harvested and sEVs purified. Total RNA was then extracted from corresponding sEVs and used for miRNA microarray to analyze miRNA composition

first: Thomas

last: Seufferlein

first: Tanja

last: Seibold


title: RNAseq in BRD4 reporter KBM7 cells (REDS1 and REDS15) with SLC nucleoside transporter knockout 23 days post sgRNA transduction

city: Vienna

first: Kai-Chun

last: Li

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM

type: Expression profiling by high throughput sequencing

summary: To investigate the transcriptional profile in two BRD4 reporter clones (REDS1 and REDS15) after knocking out SLC35F5/29A4/28A3 for 23 days

overall_design: 3'mRNA sequencing in REDS1 and RED15 clones with sgRen or SLC35F5/29A4/28A3 knockout for 23 days

first: Vitaly

last: Sedlyarov

first: Giulio

last: Superti-Furga


title: Total and subcellular small RNA profiles in human THP-1 cells

status: Public on Apr 18 2021

city: Palo Alto

first: Kevin

last: Van Bortle

state: CA

address: 3165 Porter Dr

department: Genetics

country: USA

institute: Stanford University

type: Non-coding RNA profiling by high throughput sequencing

summary: We isolated and sequenced small RNA profiles in THP-1 cells, including total, nuclear, cytoplasmic, and exosomal repertoires, as well as monitored small RNA dynamics during THP-1 differentiation and in response to Pol III inhibitor ML-60218

overall_design: Pol III-transcribed genes were profiled by small RNA-seq and integrated with Pol III ChIP-seq occupancy profiles. Here, small RNA was enriched using the mirVana small RNA isolation kit under standard procedures; sequencing libraries were prepared using the NEBNext Small RNA library prep reagents

first: Michael

last: Snyder


title: RNA-seq analyses of PDAC cells

city: Shanghai

first: Shenglin

last: Huang

address: 270 Dongan

institute: Fudan University

summary: Total RNAs were subjected to RNA isolation and RNA-seq analyses were generated by deep sequencing using Illumina Hiseq.

overall_design: RNA-seq analyses of PDAC cells by deep sequencing using Illumina Hiseq.

first: Haidi

last: Chen


title: NF-kB Perturbation Reveals Unique Immunomodulatory Functions in Prx1+ Fibroblasts that Promote Atopic Dermatitis

city: Philadelphia

first: Kang

last: Ko

state: PA

address: 240 S 40th St

department: Periodontics

institute: University of Pennsylvania

summary: Skin is composed of diverse cell populations that cooperatively maintain homeostasis. Upregulation of the NF-kB pathway may lead to the development of chronic inflammatory disorders of the skin, but the early events in situ are not well understood. Through analysis of single cell RNA sequencing (scRNA-seq) data via iterative Random Forest Leave One Out Prediction (iRF-LOOP), an explainable artificial intelligence (X-AI) method, we identified an immunoregulatory role for a unique Prx1+ fibroblast subpopulation. Disruption of Ikkb/NFkB under homeostatic conditions in these fibroblasts paradoxically induced skin inflammation due to the over-expression of CCL11 (eotaxin-1) characterized by eosinophil infiltration and a subsequent Th2 immune response. Because the inflammatory phenotype resembled that seen in human atopic dermatitis (AD), we examined validated human AD skin samples and found that human AD fibroblasts also over-expressed CCL11 compared to control skin. Importantly, we demonstrate that monoclonal antibody treatment against CCL11 was therapeutically effective in reducing the eosinophilia and Th2 inflammation in vivo. Taken together, the murine model and human AD specimens point to dysregulated Prx1+ fibroblasts as a previously unrecognized etiologic factor that may contribute to the pathogenesis of AD-like lesions and suggest targeting CCL11 as a novel way to treat AD-like lesions.

overall_design: Ventral skin single-cell mRNA profiles of 4 week old wild type (WT) and Prx1Cre+Ikkbf/f (Ikkb-deleted) mice.

middle: I

first: Jean

middle: J

last: Merlet

first: Brett

middle: P

last: DerGarabedian

first: Huang

last: Zhen

first: Yoko

last: Horiuchi

first: Eileen

last: Hu

first: Anh

middle: T

last: Nguyen

first: Stephen

last: Prouty

first: Faizan

last: Alawi

first: Matthew

middle: C

last: Walsh

first: Yongwon

last: Choi

first: Sarah

middle: E

last: Millar

first: Ashley

last: Cliff

first: Jonathon

last: Romero

middle: R

last: Garvin

first: John

last: Seykora

first: Daniel

last: Jacobson

first: Dana

last: Graves


title: Gene Expression profile for the characterization of PD-L1 blockade in melanoma model

city: Frederick

first: RAJAA

last: EL MESKINI

state: MD

address: 1050, Boyles Street

department: Center for Advanced Preclinical Research

institute: Leidos Biomedical Research, Inc

summary: Only a subset of patients responds to immune checkpoint blockade in melanoma. A preclinical model recapitulating the clinical activity of ICB would provide a valuable platform for mechanistic studies. We used melanoma tumors arising from an Hgftg;Cdk4R24C/R24C genetically engineered mouse (GEM) model to evaluate the efficacy of an anti-mouse PD-L1 antibody similar to the anti-human PD-L1 antibodies durvalumab and atezolizumab. Consistent with clinical observations for ICB in melanoma, anti-PD-L1 treatment elicited complete and durable response in a subset of melanoma-bearing mice. We also observed tumor growth delay or regression followed by recurrence.  For early treatment assessment, we analyzed gene expression profiles, T cell infiltration, and T cell receptor (TCR) signatures in regressing tumors compared to tumors exhibiting no response to anti-PD-L1 treatment. We found that CD8+ T cell tumor infiltration corresponded to response to treatment, and that anti-PD-L1 gene signature response indicated an increase in antigen processing and presentation, cytokine-cytokine receptor interaction, and natural killer cell-mediated cytotoxicity. TCR sequence data suggest that an anti-PD-L1-mediated melanoma regression response requires not only an expansion of the TCR repertoire that is unique to individual mice, but also tumor access to the appropriate TCRs. Thus, this melanoma model recapitulated the variable response to ICB observed in patients and exhibited biomarkers that differentiate between early response and resistance to treatment, providing a valuable platform for prediction of successful immunotherapy.

overall_design: Mice were treated with anti-mouse PD-L1 mIgG1 D265A (clone 80; AstraZeneca Cat# AB740080, Batch# SP15-221) in PBS at 10mg/kg or 20mg/kg intraperitoneally twice weekly for a maximum of 6 doses over 3 weeks in the initial efficacy study, or over a longer period to assess tumor response as indicated in the text. For each study the vehicle control group received PBS (10ml/kg) and an additional antibody control group received mouse IgG1 D265A (AstraZeneca clone: Cat# NIP228, Batch# SP16-017) in PBS at 10 or 20mg/kg. Tumor growth was monitored by caliper measurement. Tumors were harvested from treated mice at several different endpoints (delayed growth, stabilization, regression) or when they reached a maximum tumor volume of 2000 mm3. At necropsy, tumors were divided into sections for fixation or flash-freezing. Blood samples were taken from each mouse prior to treatment and at the time of tumor harvest.     To evaluate response in biomarker studies (Study 2 or 3), tumors from mice treated with anti-PD-L1 were harvested after 2-12 doses based on regression in tumor volume after two consecutive measurements (Responders). Anti-PD-L1-treated tumors that exhibited growth progression were harvested at matching timepoints (Non-responders). Tumors that regressed to below measurable volumes after initial treatment but regrew after 4-10 doses of anti-PD-L1 were also harvested (Relapse). PBS- and control IgG-treated tumors were also harvested at multiple time points for comparison. Additionally, any mice that did not experience initial tumor growth, but developed tumors after anti-PD-L1 treatment were designated as Growth Delay. Any tumor that decreased in volume by 5% or more was designated as a Responder. Within the Responder group, tumors with no volume change between 2 consecutive measurements were designated as growth stabilization.

first: Rajaa

last: El Meskini

first: Devon

last: Atkinson

first: Alan

last: Kulaga

first: Abdalla

last: Abdelmaksoud

first: Susana

last: Hayes

first: Zoë

middle: W

last: Ohler


title: Reprogramming the spleen into a functioning “liver” in vivo I

first: Chunyan

last: Liu

first: Lei

last: Dong

first: Chunming

last: Wang

first: Junfeng

last: Zhang


title: Whole transcriptome analysis of lung tissue from mice after thoraxtrauma with and without sEV biogenesis inhibitor GW4869

first: Tim

last: Eiseler

summary: To assess trauma associated gene expression signatures in lungs after thorax trauma mediated by small extracellular vesicles (sEVs) total RNA was isolated from lung lysates of mice after experimental blunt chest trauma with/without intravenous injection of GW4869 (2µg/g body weight).

overall_design: RNA Profiling of trauma-associated gene expression impacted by inhibition of sEV biogenesis with GW4869 4hrs after experimenal thorax trauma in mice.

first: Thomas

last: Seufferlein

first: Tanja

last: Seibold


title: Whole transcriptome analysis of endothelial cells (HUVECs) after treatment with plasma-sEVs from polytrauma patients

summary: To assess inflammation associated gene expression in endothelial cells mediated by small extracellular vesicles (sEVs), HUVECs were treated for 8hrs with plasma-Evs isolated from polytrauma patients 4 and 24hrs after trauma and healthy probands.

overall_design: RNA Profiling of trauma-associated gene expression impacted by sEVs after 8hrs treatment of polytrauma-sEVs vs. Healty control-sEVs


title: Small extracellular vesicles propagate the inflammatory response after trauma.

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Molecular and functional analysis of sunitinib resistance induction in human renal cell carcinoma cells

status: Public on Apr 16 2021

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

country: Switzerland

institute: University of Geneva

summary: We report that in response to chronic treatment with the small molecule-based targeted drug sunitinib, human Caki-1 cells alter their pheno- and genotype. We detected that the metabolism of sunitinib is still functional, but sunitinib and its N-desethyl metabolite are accumulated in the interios (lysosmes). Gene expression analysis revealed significant differential expression of genes related to mitosis, apoptosis and cell attachment. We detected potential upregulation of autophagy.

overall_design: The experiments have been designed to analyze the genetic changes induced in the human Caki-1 cell line acquiring resistance in response to chronic treatment with the small molecule-based targeted drug sunitinib.

first: Magdalena

last: Rausch

first: Adriano

last: Rutz

first: Pierre-Marie

last: Allard

first: Céline

last: Delucinge-Vivier

first: Myléne

last: Docquier

first: Olivier

last: Dormond

first: Jean-Luc

last: Wolfender

first: Patrycja

last: Nowak-Sliwinska


title: Roles of voltage-gated potassium channels in the maintenance of pancreatic cancer stem cells

city: Kyoto

first: Tomoki

last: Konishi

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Division of Digestive Surgery

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: The targeting of membrane proteins that are activated in cancer stem cells (CSCs) represents one of the key strategies in novel cancer therapy. The present study investigated ion channel expression profiles and functions in pancreatic CSCs (PCSCs). Cells strongly expressing aldehyde dehydrogenase 1 family member A1 (ALDH1A1) were separated from PK59 cells, a human pancreatic cancer cell line, using fluorescence-activated cell sorting (FACS), and PCSCs were identified based on tumorsphere formation. A microarray analysis was performed to investigate gene expression profiles in PCSCs. ALDH1A1 messenger RNA levels were higher in PCSCs. PCSCs were resistant to 5-fluorouracil (5-FU) and capable of re-differentiation. The microarray analysis revealed that gene expression related to ion channels, including voltage-gated potassium channels (Kv), was up-regulated. 4-Aminopyridine (4-AP), a potent Kv inhibitor, exhibited greater cytotoxicity in PCSCs. In a xenograft model in nude mice, tumor volumes were significantly smaller in mice injected with PK59 cells treated with 4-AP than in those injected with non-treated cells. The present results implicate Kv in the persistence of PCSCs, and the Kv inhibitor, 4-AP, has potential as a therapeutic agent for pancreatic carcinoma.

overall_design: Total RNA of PK59 cells and PK59 CSCs were extracted using an RNeasy kit (Qiagen, Valencia, CA). Quantitative real-time PCR (7300 Real-Time PCR System; Applied Biosystems, Foster City, CA) and TaqMan Gene Expression Assays (Applied Biosystems) were performed. We compared the differences in gene expression between PK59cell and PK59CSC using Microarray assay.

first: Atushi

last: Shiozaki

first: Toshiyuki

last: Kosuga

first: Michihiro

last: Kudou

first: Kento

last: Kurashima

first: Hiroyuki

last: Inoue

first: Katsutoshi

last: Shoda

first: Tomohiro

last: Arita

first: Hirotaka

first: Ryo

last: Morimura

first: Shuhei

last: Komatsu

first: Hisashi

last: Ikoma

first: Atsushi

last: Toma

first: Takeshi

last: Kubota

first: Hitoshi

last: Fujiwara

first: Kazuma

last: Okamoto

first: Eigo

last: Otsuji


title: Identifying a novel biological mechanism for alcohol addiction associated with circRNA networks acting as potential miRNA sponges.

city: New York

first: Eric

last: Vornholt

state: NY

address: 800 E. Leigh St. Box 980126

institute: Icahn School of Medicine

summary: Our lab and others have shown that chronic alcohol use leads to gene and miRNA expression changes across the mesocorticolimbic (MCL) system. Circular-RNA (circRNA) are noncoding RNA that form closed-looped structures and are reported to alter gene expression through miRNA sequestration, thus providing a potentially novel neurobiological mechanism for the development of alcohol dependence (AD). Genome-wide expression of circRNA was assessed in nucleus accumbens (NAc) from 32 AD matched cases/controls. Significant circRNA (unadj. p≤0.05) were identified via regression and clustered in circRNA networks via WGCNA. CircRNA interactions with previously generated mRNA and miRNA were detected via correlation and bioinformatic analyses. MatrixeQTL was used to identify eQTLs affecting circRNA expression. Genomic enrichment was used to detect overlap between eQTLs and recent GWAS of substance abuse. Significant circRNAs (N=542) clustered in 9 significant AD modules (FWER p≤0.05), within which we identified 137 circRNA hubs. We detected 23 significant circRNA:miRNA:mRNA interactions (FDR≤0.10). Among these, circRNA-406742 and miR-1200 significantly interact with the highest number of mRNA, including genes associated with neuronal functioning and alcohol addiction (HRAS, PRKCB, HOMER1, and PCLO). Finally, we identified 96 significant circRNA eQTLs (unadj. p≤0.002), showing significant enrichment within recent alcohol use disorder (AUD) and smoking GWAS. To our knowledge, this is the first study to examine the role of circRNA in the neuropathology of AD. We show that circRNA impact mRNA expression by interacting with miRNA in the NAc of AD subjects. We further identify genetic variants affecting circRNA expression impacting potential miRNA and mRNA interactions. More importantly, we provide indirect evidence for the clinical importance of circRNA in the development of AUD by detecting a significant enrichment of our circRNA eQTLs among GWAS of substance abuse.

overall_design:
Our study examines circular RNA expression differences between 32 matched Alcohol Dependence cases and controls within human postmortem NAc.
------------------------------
Dummy Coding Legend
Hemisphere: 0 = left; 1 = right
Neuropathology: 0 = normal, 1 = abnormal
Hepatology: 0 = normal; 1 = abnormal; 9 = N/A
Toxicology: 0 = normal; 1 = alcohol; 2 = other drugs; 9 = N/A
Smoking Status: 0 = never; 1 = smoker; 2 = ex-smoker; 9 = N/A

first: Vladimir

last: Vladimirov

first: John

last: Drake


title: RNAseq in BRD4 reporter KBM7 cells (REDS1 and REDS15) with purine metabolism perturbation

first: Kai-Chun

last: Li

summary: To investigate the transcriptional profile in two BRD4 reporter clones (REDS1 and REDS15) with purine metabolism perturbation

overall_design: 3'mRNA sequencing in REDS1 and RED15 clones with DMSO, 10 µM 6-mercaptopurine or 1 µM (+)-JQ1 treatment for 72 hours and with sgRen or SLC35F5/29A4/28A3 knockout 12 days post sgRNA delivery

first: Vitaly

last: Sedlyarov

first: Giulio

last: Superti-Furga


title: BRD4-chromatin interaction in reporter KBM7 cells (REDS15) with purine metabolism perturbation

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To investigate whether BRD4-chromatin binding is modulated by purine levels, we performed BRD4 ChIP-seq in cells with SLC nucleoside transporters knockout, or cells with de novo purine synthesis inhibitor 6-MP treatment. (+)-JQ1, an inhibitor which disrupts BRD4 and acetylated histone binding, was used as a positive control.

overall_design: BRD4-ChIP seq in REDS15 with sgRen, SLC35F5/SLC28A3/SLC29A4 triple knockout (SLC TKO) for 12 days, 10 micromilar 6-MP or 1 micromolar (+)-JQ1 treatment for 48 h

first: Sarah

last: Grosche

first: Sandra

last: Schick


title: Identification of novel DVL3 cancer-associated target genes [ChIP-seq]

city: Lubbock

first: Kevin

last: Pruitt

state: Texas

address: 3601 4th Street

department: Immunology & Molecular Microbiology

institute: Texas Tech University Health Sciences Center

summary: We report novel target genes of DVL3 in two breast cancer cell lines

overall_design: DVL3 ChIP-Seq in MDA-MB-468 and MCF7 cell lines


title: hPSC-derived cells to model Macrophage-mediated inflammation in COVID19 Hearts

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

summary: We systematically compared autopsy samples from non-COVID-19 donors and COVID-19 patients using RNA-seq and immunohistochemistry. We observed strikingly increased expression levels of CCL2 as well as macrophage infiltration in heart tissues of COVID-19 patients. We generated an immuno-cardiac co-culture platform containing human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) and macrophages. We found that macrophages induce increased reactive oxygen species (ROS) and apoptosis in CMs by secreting IL-6 and TNF-α after SARS-CoV-2 exposure. Using this immuno-cardiac co-culture platform, we performed a high content screen and identified ranolazine and tofacitinib as compounds that protect CMs from macrophage-induced cardiotoxicity. We established an immuno-host co-culture system to study macrophage-induced host cell damage following SARS-CoV-2 infection, and identified FDA-approved drug candidates that alleviate the macrophage-mediated hyper-inflammation and cellular injury.

overall_design: 23 total samples. At least three samples' replicates were done for each group.

first: Robert

last: Schwartz

first: Liuliu

last: Yang


title: mRNA sequencing of embryonic kidney at different stages from wild-type and heterozygous mutants of a novel mouse model carrying a human splicing point-mutation in the Hnf1b-gene

city: PARIS

first: Silvia

last: Cereghini

address: 9 Quai Saint Bernard BatC 7ET

department: Developmental Biology

country: France

institute: IBPS- UMR7622 CNRS -UPMC

summary: Heterozygous mutations in HNF1B cause the complex syndrome Renal Cysts and Diabetes (RCAD), characterized by developmental abnormalities of kidney, genital tracts and pancreas and a variety of renal, pancreas and liver dysfunctions. The pathogenesis underlying this syndrome remained unclear since mice with Hnf1b heterozygous null mutations have no phenotype, while constitutive/conditional Hnf1b-ablation led to more severe phenotypes. We generated a novel mouse model carrying an identified human mutation at the intron-2 splice donor-site. Reflecting the disease and unlike previous heterozygous, heterozygous for the splicing mutation exhibited decreased HNF1B protein levels and bilateral renal cysts from embryonic stage E15, originated from glomeruli, early proximal tubules (PT) and intermediate nephron segments, concurrently with a delayed PT differentiation, hydronephrosis and rare genital tract anomalies. To further elucidate the cellular and molecular components sensitive to HNF1B levels, we performed RNA-sequencing on WT and heterozygous mutant kidneys at E14.5 (considered morphologically as pre-disease kidneys) and at disease stages (E15.5, E17.5 and P1).   Consistent with the histological and immunhistochemical findings, these analysis showed that most down-regulated genes in embryonic kidneys were primarily expressed in early PTs and Henle’s Loop and involved in ion/drug transport, organic acid and lipid metabolic processes, while previous targets identified upon Hnf1b-ablation, including the cystic disease genes, were weakly or no affected. Postnatal analyses revealed renal abnormalities, ranging from glomerular cysts to hydronephrosis and rarely multicystic dysplasia. Urinary proteomics uncovered a particular profile predictive of progressive decline in kidney function, injury and fibrosis, and displayed common features with a recently reported urine proteome in a RCAD pediatric cohort. Our results show that HNF1B reduced levels lead to developmental disease phenotypes associated with the deregulation of a subset of its targets and further suggests that this new model represents a unique clinical/pathological viable model of the RCAD disease.

overall_design: Stages analyzed: E14.5 (mutant kidneys were morphologically normal and considered as pre-disease stage) and at disease stages E15.5, E17.5 and postnatal day 1 (P1), presented various renal abnormalities (bilateral renal cysts from E15, originated from glomeruli, early proximal tubules (PT) and intermediate nephron segments, concurrently with a delayed PT differentiation, hydronephrosis. At E15.5 deep sequencing was from pooled samples of 3 WT and 3 Hnf1b Sp2/+ (6 kidneys each sample). At E17.5 kidneys were from embryos of 2 litters descendants of the same male and born de same day, allowing to pool n=3 (6 kidneys) for one of the two WT sample and the two heterozygous mutants   Total 14 samples (N : number of embryos or newborns (2 kidneys for each one) = E14.5: (4 samples) SCR10-E145-4wt( n=1), SCR13-E14.5wt (n=1), SCR12-E145 HET(n=1), SCR15-E145-HET (n=1); E15.5: (2 samples): SCR 2 WT(n=3), SCR1 Hnf1bSp2/+ ( n=3) ; E17.5 : (4 samples) GZS 17 WT (n=1), GZS 35WT(n=3), GSZ 34 Hnf1bSp2/+ (n=3), GSZ 36 Hnf1bSp2/+ (n=3) ; P1 : SCR20_P1_WT(n=1), SCR21_P1_WT (n=1), SCR22 P1 Hnf1bSp2/+ (n=1), SCR23_P1 Hnf1bSp2/+ (n=1).

first: Leticia

last: Niborski

first: Pierbruno

last: Ricci

first: Pantelis

last: Hatzis

first: Martin

last: Reczko


title: Next Generation Sequencing Facilitates Quantitative Analysis of Cystine-regulated Transcriptomes

city: Kunming

first: Jiao

last: Wu

state: Yunnan

address: No.519 at Kunzhou Road

department: Department of the Second Medical Oncology

institute: The Third Affiliated Hospital of Kunming Medical University

summary:
Purpose: To identify differentially expressed genes regulated by cystine.
Methods: HCT116 or RKO cells were cultured for 48 hours in cystine-free or 25μM cystine-containing conditional media, and three independent samples were collected by Trizol reagent and subjected to mRNA-sequencing by the LC Bio (Zhejiang, China) and data analysis
Results: we identified cystine upregulated 145 genes and downregulated 169 genes in both HCT116 and RKO cells. GO enrichment analysis revealed that cystine regulated biological functions of G1/S transition of mitotic cell cycle and regulation of DNA replication biosynthetic process.In addition,  KEGG enrichment analysis showed that mammalian target of rapamycin (mTOR) signaling pathway, a well-known nutrient sensor, was regulated by cystine. Furthermore,we noticed that SESN2 was one of the most significantly downregulated genes by cystine in both cell lines,  and confirmed that cystine activates mTORC1 via the GCN2-ATF4-SESN2 axis in colon cancer cells.
Conclusions: Our study established that cystine activates mTORC1 through GCN2-ATF4-SESN2 axis.

overall_design: The mRNA profiles of HCT116 and RKO cells cultured in cystine-free or 25μM cystine-contained media were generated for High-throughput sequencing, in triplicate, and analyzed the cystine-regulated transcriptomes

first: Runxiang


title: Identification of novel DVL3 cancer-associated target genes [RNA-seq]

summary:
The goal of this study is to identify novel target genes of DVL3 in two breast cancer cell lines
Methods:Total RNA was isolated using the Aurum™ Total RNA Mini Kit (Bio Rad) and library preparation and sequencing were performed at Center for Biotechnology & Genomics of Texas Tech University. RNA quality was determined using RNA Screen Tape (Agilent). Ribosomal RNA depletion was achieved using NEB Next rRNA Depletion Kit (Human/Mouse/Rat) (NEB # E6310X). RNA fragmentation, double stranded cDNA and adaptor ligation was generated using NEBNext Ultra II Directional RNA Library Prep according to the manufacturer’s protocol (NEB # E7760L). PCR enriched libraries were quantified by Qubit and equimolar indexed libraries (different samples had different indexes for multiplexing) were pooled. Pooled libraries were quantitatively checked using the Agilent Tapestation 2200 and quantified using Qubit. The libraries were then diluted to 200 pM and spiked with 2% phiX libraries (Illumina control). The transcriptome sequencing was performed on the barcoded stranded RNA-Seq libraries using Illumina NovaSeq 6000 SP flow cell, paired-end reads (2 × 50 bp).

overall_design: We compared non-target control (WT) vs. DVL3 KD (shB), and empty vector (EV) vs. DVL3-WT in 3 cell lines MDA-MB-468 and MCF7


title: Exercise inhibits tumor progression and improves the therapeutic efficacy of PD-1 blockade in colorectal cancer preclinical models

city: Nantong

first: zhao

last: yu

address: qixiu road 19

institute: Nantong university

summary: Exercise training (ExT) has shown antitumor effects in many preclinical cancer models. In the present study, we utilize MC38 and CT26 cells, which represent MSI and MSS colorectal carcinomas respectively, to study the effects and mechanisms of ExT alone or in combination with PD-1 based immunotherapy. Using treadmill running and PD-1/PD-L1 blockade, we demonstrated that post-implant exercise training has broad anticancer activities in murine models of CRC. Specifically, in MSI CRC models, ExT induces beneficial metabolic and immunological adaptations, leading to a more significant inhibition in tumors treated with PD-1/PD-L1 blockade, suggesting a genotype-directed combinatory therapy for the subgroup of CRC patients. Moreover, ExT might be a safe and alternative anticancer strategy for cancers resistant to the PD-1 based immunotherapy, such as patients with MSS CRC tumors.

overall_design: Gene expression profile of MC38 tumor tissue from  control, EXT, αPDL1, and the combination groups

first: Xiaorong

last: Zhou

first: Yuejiao

last: Cao

first: Yu

last: Zhao


title: Effect of infection with VSV-G pseudotyped HIV on the DNA damage response in HCT116 cells

city: Oxford

first: Maria

last: Jakobsdottir

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics

country: United Kingdom

institute: University of Oxford

summary: Effect of infection with VSV-G pseudotyped HIV partiles on HCT116 cells at different time points.

overall_design: Comparison of infected vs uninfecte cells at 0h (uninfected), 6 hours, 12 hours, and 24 hours after infection

first: Catherine

last: Green

first: David

last: Wedge


title: Tsga8 is required for spermatid morphogenesis and male fertility in mice

city: Yokohama

first: Keisuke

last: Minamizawa

address: Kanazawa

institute: Yokohama city university

summary: During spermatogenesis, intricate gene expression is coordinately regulated by epigenetic modifiers, which are required for differentiation of spermatogonial stem cells (SSCs) contained among undifferentiated spermatogonia. We previously found that KMT2B conveys H3K4me3 at bivalent and monovalent promoters in undifferentiated spermatogonia. Because these genes are expressed late in spermatogenesis or during embryogenesis, we expect that many of them are potentially programmed by KMT2B for future expression. Here, we show that one of the genes targeted by KMT2B, Tsga8, plays an essential role in spermatid morphogenesis. Loss of Tsga8 in mice leads to male infertility associated with abnormal chromosomal distribution in round spermatids, malformation of elongating spermatid heads and spermiation failure. Tsga8 depletion leads to dysregulation of thousands of genes, including the X chromosome genes that are reactivated in spermatids, and insufficient nuclear condensation accompanied by reductions of TNP1 and PRM1, key factors for histone-to-protamine transition. Intracytoplasmic sperm injection (ICSI) of spermatids rescued the infertility phenotype, suggesting competency of the spermatid genome for fertilization. Thus, Tsga8 is a KMT2B target that is vitally necessary for spermiogenesis and fertility.

overall_design: RNA-seq was performed using Tsga8 control (Tsga8+/Y) and knockout (Tsga8-/Y) mice (2 or 3 replicate animals). Collection of tissues enriched for spermatids was performed using laser capture microdissection (LCM).

first: Yuki

last: Kobayashi

first: Shin-ichi

last: Tomizawa

first: Michio

last: Ono

first: Kazuyuki

last: Ohbo


title: Gene expression profiling identifies different sub-types of retinoblastoma

city: Birmingham

first: Carmel

middle: M

last: McConville

state: UK

address: Vincent Drive

department: School of Cancer Sciences

institute: University of Birmingham

type:
Expression profiling by array
Third-party reanalysis

summary:
Background: Mutation of the RB1 gene is necessary but not sufficient for the development of retinoblastoma. The nature of events occurring subsequent to RB1 mutation is unclear, as is the retinal cell-of-origin of this tumour.
Methods: Gene expression profiling of 21 retinoblastomas was carried out to identify genetic events that contribute to tumorigenesis and to obtain information about tumour histogenesis.
Results: Expression analysis showed a clear separation of retinoblastomas into two groups. Group 1 retinoblastomas express genes associated with a range of different retinal cell types, suggesting derivation from a retinal progenitor cell type. Recurrent chromosomal alterations typical of retinoblastoma, for example, chromosome 1q and 6p gain and 16q loss were also a feature of this group, and clinically they were characterised by an invasive pattern of tumour growth. In contrast, group 2 retinoblastomas were found to retain many characteristics of cone photoreceptor cells and appear to exploit the high metabolic capacity of this cell type in order to promote tumour proliferation.
Conclusion: Retinoblastoma is a heterogeneous tumour with variable biology and clinical characteristics.
Kapatai, G et al. Br J Cancer (2013) 109, 512-525  doi: 10.1038/bjc.2013.283

overall_design:
Frozen tissue from 21 retinoblastomas, enucleated without prior treatment, was used for microarray analyses. A comparison was made with data from normal human fetal (GSM460264) and adult (GSM607947, GSM607948) retina.
The complete dataset with total 24 data columns (including three re-analyzed data from Series GSE18487, GSE24673) is linked below as a supplementary file.

first: Georgia

last: Kapatai


title: Deletion of the Hoxa Cluster in MLL-AF9 Is Incompatible with Leukemia Maintenance: RNAseq-based Quantitative Analysis of Wild Type and Hoxa-del Transcriptomes

city: Nottingham

first: Alexander

last: Thompson

address: University Park

department: Cancer and Stem Cells

institute: University of Nottingham

summary: High HOXA expression correlates with poor clinical outcome in AML, particularly those harboring MLL rearrangements (MLLr).  The necessity of the HOXA cluster for the maintenance of MLLr-leukemia has not been elucidated.  Primary leukemias were generated by transduction of MLL-AF9 (MA9) into hematopoietic stem and progenitor cells from compound Cre responsive transgenic mice for conditional deletion of the Hoxa locus. Hoxa deletion resulted in reduced proliferation, colony formation and repopulating ability in transplanted mice in which surviving leukemic cells retained at least one copy of the Hoxa cluster (Hoxa-del). Comparative RNA-seq analysis of leukemic MA9-Hoxa-wild type (WT) and MA9-Hoxa-del cells identified a unique gene signature.

overall_design: RNA profiles obtained from leukemic (MA9) stem and progenitor cells in wild type (WT), Hoxa cluster floxed (Hoxa-flox) or Hoxa cluster deleted (Hoxa-del) backgrounds.

last: Simpson


title: Identification of novel DVL3 cancer-associated target genes

first: Kevin

last: Pruitt


title: Occupancies of tissue-specific cis-regulatory modules by Spemann-Mangold organizer-specific transcription factors for embryonic head specification

status: Public on Apr 15 2021

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

institute: Cincinnati Children's Hospital and Medical Center

summary: Spemann-Mangold organizer-specific transcription factors (TFs), Otx2, Lim1/Lhx1, and Gsc, are essential for embryonic head specification. However, the molecular mechanisms by which those TFs interact with the genome to direct head formation are largely unknown. Here we employed ChIP-seq and RNA-seq approaches in Xenopus tropicalis gastrulae and found that occupancy of the corepressor, TLE/Groucho, is a better indicator of tissue-specific cis-regulatory modules (CRMs) than the coactivator p300, during early embryonic stages. On the basis of TLE binding and comprehensive CRM profiling, we defined two distinct types of Otx2- and TLE-occupied CRMs. Using these devices, Otx2 and Lim1/Lhx1 (activator) or Goosecoid (repressor) are able to upregulate or downregulate a large battery of target genes in the head organizer. An underlying principle is that Otx marks target genes for head specification to be regulated positively or negatively by partner TFs through specific types of CRMs.

overall_design: ChIP-seq analyses using Xenopus tropicalis embryos.

first: Yuuri

last: Yasuoka

first: Yutaka

last: Suzuki

first: Shuji

last: Takahashi

first: Norihiro

last: Sudou

first: Yoshikazu

last: Haramoto

first: Ken

last: Cho

first: Makoto

last: Asashima

first: Sumio

last: Sugano

first: Masanori

last: Taira


title: RNA Expression Profile of normal fibroblasts (NFs) and cancer-associated fibroblasts (CAFs) derived from human Pancreatic Ductal Adenocarcinoma.

city: Guangzhou

first: Chonghui

last: Hu

state: Guangdong

address: 106 Zhongshan Er Road

department: Department of General Surgery

institute: Guangdong Provincial People's Hospital

summary: Although how CAFs impact the tumor epithelium is being progressively unveiled, transcriptional processes of lineage plasticity in fibroblasts govern the acquisition and transition of the CAF phenotype are much less understood. Here, to explore the potential involvement of the circular RNAs (circRNAs) in fibroblast activation and phenotype acquisition, we isolated CAFs and NFs from human pancreatic cancer and paired normal pancreatic tissue. Next, we conducted circRNA profiling five CAFs and three paired NFs by high throughput sequencing. Our results showed that clusters of circRNAs were aberrantly expressed in CAFs compared with NFs, and provided potential targets for future treatment of PDAC and novel insights into PDAC microenvironment.

overall_design: Analyze circular RNA expression in CAFs and NFs by Next-generation sequencing

first: Shangyou

last: Zheng

first: Hongcao

last: Lin


title: Diversity of developing peripheral glia revealed by single cell RNA sequencing

city: Boston

first: Rosalind

last: Segal

state: MA

address: 450 Brookline Ave

institute: Harvard Medical School

summary: We collected dorsal root ganglion (DRG), sciatic nerve (SN) and cochlea tissues from each E14, E18 and P14 plp-GFP+ mice. This allowed for a comparison of plp-GFP+ glia from lumbar (DRG+SN) and cochlea tissues within the same mice. The transcriptional composition of all samples was assessed using single-cell RNA-seq (scRNA-seq).

overall_design: Lumbar tissues (DRG+SN) and cochlea were enzymatically dissociated, GFP+ glia were FACS sorted and profiled by Indrop Single cell v3 method.

first: Ozge

last: Tasdemir Yilmaz

first: Noah

last: Druckenbrod

first: Olubusola

middle: O

last: Olukoya

first: Andrea

last: Yung

first: Isle

last: Bastille

first: Maria

middle: F

last: Pazyra-Murphy

first: Austen

last: Sitko

first: Evan

middle: B

last: Hale

first: Weixiu

last: Dong

first: Sebastien

last: Vigneau

middle: A

last: Gimelbrant

first: Peter

last: Kharchenko

first: Lisa

middle: V

last: Goodrich


title: Experience modulates the effects of histone deacetylase inhibitors on gene and protein expression in the hippocampus: Impaired plasticity in aging

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The therapeutic potential of histone deacetylase inhibitor (HDACi) treatment has attracted considerable attention in the emerging area of cognitive neuroepigenetics. The possibility that ongoing cognitive experience importantly regulates the cell biological effects of HDACi administration, however, has not been systematically examined. In an initial experiment addressing this issue, we tested whether water maze training influences the gene expression response to acute systemic HDACi administration in the young adult rat hippocampus. Training powerfully modulated the response to HDACi treatment, increasing the total number of genes regulated to nearly 3000, including many not typically linked to neural plasticity, compared with <300 following HDACi administration alone. Although water maze training itself also regulated nearly 1800 genes, the specific mRNAs, gene networks, and biological pathways involved were largely distinct when the same experience was provided together with HDACi administration. Next, we tested whether the synaptic protein response to HDACi treatment is similarly dependent on recent cognitive experience, and whether this plasticity is altered in aged rats with memory impairment. Whereas synaptic protein labeling in the young hippocampus was selectively increased when HDACi administration was provided in conjunction with water maze training, combined treatment had no effect on synaptic proteins in the aged hippocampus. Our findings indicate that ongoing experience potently regulates the molecular consequences of HDACi treatment and that the interaction of recent cognitive experience with histone acetylation dynamics is disrupted in the aged hippocampus.

overall_design: Twenty-eight young (7 months old) male Fischer 344 × Brown Norway F1 hybrid rats (F344xBN) were divided into four groups (N=7/group) with three hippocampal subregions (CA1, CA3, and DG) queried, for a total of 84 microarray samples. Home cage controls were compared to animals receiving a single session of a redundant place-cue (RPC) variant of the water maze as an inducing event for examining hippocampal mRNA just prior to sacrifice (a week after basic water maze training for these animals). Animals were treated either with vehicle (100% DMSO) or the histone deacetylase inhibitor SAHA (50 mg/kg, delivered as 50 mg/ml i.p.) prior to any RPC-treatment, and 90 minutes prior to sacrifice for all animals.

first: Angila

middle: S

last: Sewal

first: Holger

last: Patzke

first: Evelyn

last: Perez

first: Pul

last: Park

first: Elin

last: Lehrmann

first: Yongqing

last: Zhang

first: Kevin

middle: G

last: Becker

first: Bonnie

last: Fletcher

first: Jeffrey

last: Long

last: Rapp


title: Integrative analysis of microRNA-mRNA of muscle tissues in Qianhua Mutton Merino and Small Tail Han sheep

city: Changchun

first: Limin

last: Sun

state: Jilin

address: Xincheng Street 2888,Jingyue Distric

institute: Jilin Agricultural University

summary: We aimed to evaluated the key microRNA-mRNA network associated with sheep muscle growth and development. We used RNA-Seq to obtain the smallRNA profiles of the longissimus muscle from the QHMM and STH. The results showed that a total of 153 known sheep miRNAs were identified, and 4 known sheep miRNAs were differently expressed. Combining mRNA library data, 26 target genes of 4 known miRNAs were selected and the miRNA–mRNA network was successfully built. GO and KEGG analysis showed that 26 target genes were significantly enriched in 86 biological processes, including muscle organogenesis, myoblast migration, cell proliferation, and adipose tissue development, and nine metabolic pathways, including carbohydrate, nucleotide, and amino acid metabolic pathways. The oar-miR-655-3p and target gene ACSM3, and oar-miR-381-5p and target gene ABAT were selected for subsequent analysis based on GO and KEGG analyses. The results suggested that the DEmiRNAs, especially oar-miR-655-3p and oar-miR-381-5p play crucial roles in muscle growth and development processes. This Integrative analysis of microRNA-mRNA analysis of QHMM and STH muscle is reported for the first time.

overall_design: Muscle miRNA profiles of Qianhua Mutton Merino (QHMM) and  Small Tail Han (STH) sheep were generated by deep sequencing, three replicates in each sheep breed, using ABI Ion Proton instrument .

first: Huaizhi

last: Jiang


title: Interplay between H2A.Z and epigenome in PANC-1

city: Ciudad de México

first: Pedro

middle: Antonio

last: Avila

state: CDMX

address: Av. Instituto Politécnico Nacional 2508, Col. San Pedro Zacatenco

department: Molecular Biomedicine

country: Mexico

institute: CINVESTAV

summary: The oncogenic process is regulated by a complex network of different regulatory elements in charge of regulate the cancer epigenome. The histone variant H2A.Z is involved in the regulation of different regulatory elements such as promoters and enhancers in different types of cancer, however, the interplay between the H2A.Z and the cancer epigenome is poorly understood. Here, we investigate the functional role of H2A.Z at promoters, enhancers, super enhancers and topologically associating domains in the pancreatic cancer cell line PANC-1. We found an oncogenic role of H2A.Z regulated by acetylation and deacetylation as well as the potential interactions with epigenetic regulators such as EZH2 and CTCF. Specifically, we found that the presence of H2A.Z facilitates the recruitment of RNA polymerase II and other transcription factors such as ZNF384 at promoters, enhancers and super enhancers, allowing the gene expression. On the other hand, the absence of acetylation is associated with an enrichment of EZH2 allowing transcriptional repression of transcription factors associated with cancer development. Also, we identified that H2A.Z is a component of the TAD boundaries in PANC-1, and its enrichment is associated with the presence of transcription factors such as CTCF, ZNF143 and ZNF384. Together, these data show new mechanisms associated with the interplay between H2A.Z and the epigenome in pancreatic cancer.

overall_design: ChIP-seq of H2A.Z and acH2A.Z in the pancreatic cancer cell line PANC-1, and RNA-seq  from  H2A.Z knock-down clone named PZT-1 generated with shRNA in the PANC-1

last: Ávila-López

first: Félix

last: Recillas-Targa

first: Rosaura

last: Hernández-Rivas


title: Developmental chromatin programs determine oncogenic competence in melanoma [Cut&Run]

first: Richard

middle: Mark

last: White

address: 1275 York Avenue MB 424

department: Cancer Biology & Genetics

institute: Memorial Sloan Kettering Cancer Center

summary: We perfomed Cut&Run for ATAD2, MYC and SOX10 in 3xKO ATAD2 dox melanocytes and 3xKO dox melanocytes. We used 10'000 cells per condition and the protocol was performed as in Skene et al., 2018. We could show that,  in the 3xKO ATAD2 dox melanocytes,  ATAD2, MYC and SOX10 have common targets. Many of those targets  belong to a developmental signature typical of the neural crest and to the MAPK pathway.

overall_design: Examination of the target genes of ATAD2, MYC and SOX10 in hPSC-derived melanocytes

first: Lorenz

last: Studer

last: Koche

first: Arianna

last: Baggiolini


title: All-Trans-Retinoic Acid Treatment of IDH Mutant Astrocytes

city: Pittsburgh

first: Xiaoran

address: 16 Sheridan Court

institute: upmc

summary: Immortalized human astrocytes were stably transfected to express IDH1 R132H. These cells were treated with 1uM ATRA

overall_design: Astrocytes expressing IDH1 R132H were treated with 1uM ATRA or equal volume DMSO for 48 hrs.

first: Aparna

last: Rao


title: Single-cell RNA-seq of human peripheral blood mononuclear cells in COVID-19

city: Durham

first: Daniel

last: Saban

state: NC

address: 2351 Erwin Rd, Duke Eye Center

institute: Duke University

summary: We carried out sex-balanced sampling of peripheral blood mononuclear cells (PBMCs) from confirmed COVID-19 inpatients (hospitalized) and outpatients (infected), uninfected close contacts (exposed), and healthy controls.

overall_design: We collected 48 PBMC samples from 24 participants in this study. In exposed and infected cohorts, 13 subjects were sampled longitudinally with 2 or 3 samples per individual. Each sample is associated with 3 files of processed data and 12 files of raw data.

first: Chen

last: Yu

first: Sejiro

last: Littleton

first: Nicholas

last: Giroux

first: Xiling

last: Shen


title: Germline deletion of Krüppel-like factor 14 does not increase risk of diet-induced metabolic syndrome in male C57BL/6 mice

city: New York

first: Sander

last: Houten

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The transcription factor Krüppel-like factor 14 (KLF14) has been associated with type 2 diabetes and high-density lipoprotein-cholesterol (HDL-C) through genome-wide association studies. The mechanistic underpinnings of KLF14's control of metabolic processes remain largely unknown. We studied the physiological roles of KLF14 in a knockout (KO) mouse model.

overall_design: 10 samples from pituitary (5 WT and 5 KLF14 KO) and 10 samples from inguinal white adipose tissue (5 WT and 5 KLF14 KO) were analyzed

first: Carmen

last: Argmann

first: Eric

last: Schadt


title: Developmental chromatin programs determine oncogenic competence in melanoma [ATAC-seq]

summary: Oncogenes are only transforming in certain cellular contexts, a phenomenon called oncogenic competence. Here, using a combination of a human pluripotent stem cell-derived cancer model along with zebrafish transgenesis, we demonstrate that the transforming ability of BRAFV600E along with additional mutations depends upon the intrinsic transcriptional program present in the cell of origin. In both systems, melanocytes are largely resistant to mutations, whereas both neural crest and melanoblast populations are readily transformed. Profiling reveals that progenitors have higher expression of chromatin modifying enzymes such as ATAD2, a melanoma competence factor that forms a complex with SOX10 and allows for expression of downstream oncogenic and neural crest programs. These data suggest that oncogenic competence is mediated by regulation of developmental chromatin factors, which then allow for proper response to those oncogenes.

overall_design: ATAC-seq


title: Transcriptomic Analysis on Oncogene STYK1/NOK transfected Baby Hamster Kidney BHK21 Cells

city: Beijing

first: Li

last: Liu

state: State...

address: #5 Dong Dan San Tiao

institute: Peking Union Medical College

summary: RNAseq analysis identified 837 differential gene expressions (DEGs) with 423 up-regulated and 414 down-regulated after transfecting STYK1/NOK into BHK21 cells. GEO and KEGG enrichment analysis indicated that several entries such as ribosome, aging related diseases, oxidative phosphorylation and apoptosis played major roles during this cellular process. PPI analysis showed that four top down-regulated proteins (TOMM7, Uba52, Rpl28 and XP_005077076.1 (ribosomal protein S29)) localized within the highly interaction region might play key roles.

overall_design: mRNA profiles of STYK1/NOK transfeced versus empty vector transfected BHK21 cells


title: Developmental chromatin programs determine oncogenic competence in melanoma [Zebrafish]

summary: Transcriptional profile of BRAFV600E driven melanoma driven under either the SOX10 or MITFA promoter, both in a p53 deficient background

overall_design: Transgenic F0 zebrafish were created by 1-cell injection of plasmids for either sox10-BRAFV600E or mitfa-BRAFV600E in a p53-/- background

first: Nathaniel

last: Campbell


title: Developmental chromatin programs determine oncogenic competence in melanoma [RNA-seq]

summary: Transcriptional profile of human ES-cell (hPSC) derived melanoma cell models

overall_design: Human ES cells were differentiated into neural crest (NC), melanoblast (MB) or melanocytes (MC). These were either WT or triple knockout (3xKO) for p53, p16, RB1. A dox-inducible cassette was integrated into the cells to activate the BRAFV600E oncogene upon addition of doxycyline.


title: Gene expression in clavicular cortical hyperostosis

city: Zagreb

first: Kristina

last: Gotovac Jerčić

address: Šalata 2

department: Department for functional genomics

country: Croatia

institute: Center for translational and clinical research

summary: Clavicular cortical hyperostosis (CCH) is a sterile inflammatory bone disorder of unknown etiology, clinically characterized  by pain and/or swelling of the clavicle. The aim of the study was to identify and confirm specific gene expression patterns in patients with CCH.

overall_design: Total RNA was isolated from whole blood of 18 children with diagnosis of CCH, as well as 8 age and sex matched control participants without diagnosis of chronic inflammatory disease. Of those, 5 patients and 4 controls were utilized in the microarray experiments, while the rest were used in the qPCR analysis.

first: F

last: Borovecki

first: M

last: Harjacek

first: L

last: Lamot

first: K

last: Jercic


title: Developmental chromatin programs determine oncogenic competence in melanoma

first: Richard

last: White

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

sample_organism:
Danio rerio
Homo sapiens

platform_organism:
Danio rerio
Homo sapiens

overall_design: Refer to individual Series


title: Effect of Effect of lytic replication on EBV and cell gene expression

city: Salt Lake City

first: Sankar

last: Swaminathan

state: UT

institute: University of Utah

summary: The effect of Epstein Barr virus replication on cellular gene expression was studied using AGSiZ epithelial cells which are derived from a gastric carcinoma. The cell line is infected with a recombinant strain of EBV known as Akata BX-1.  The cell line was further stably transduced with an inducible EBV Zta transactivator gene.  When cells are treated with doxycycline, robust lytic replication of EBV is achieved.  Cells made permissive for lytic replication in this manner were harvested for RNA suitable for deep sequencing at 24 and 48 hours post induction in parallel with cells that were mock induced with doxycycline to serve as a control for cells not undergoing EBV replication.

overall_design: Two different treatments were applied to cells:doxycline to induce replication or mock treatment.  Dox treatments were done with 24h and 48 hr treatment times. Each treatment ws done in duplicate


title: Integrative assessment of classical and molecular phenotypes in MCF10A cells

city: Portland

first: Laura

last: Heiser

state: OR

address: 2730 S Moody Ave

department: Biomedical Engineering

institute: Oregon Health and Science University


title: Genome-wide analysis of histone incorporation into the chromatin of permeabilized cells

city: Shinagawa-ku

first: Hiroaki

last: Tachiwana

state: Tokyo

institute: Hoshi University

summary: Histone proteins, including their variants, play indispensable roles in chromatin structure and function. The specific histone incorporation is the key to epigenetic features and contributes to cell differentiation and development. To understand how each histone is targeted to and incorporated into the specific chromatin region, we used a new method, in which we introduced epitope-tagged histone complexes in permeabilized cells and let them incorporated into the chromatin. The newly incorporated histone complex is easily distinguished from the parental histones by the epitope-tag. We name this as RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay. We analyzed the correlation between the histone incorporation and the chromatin structure, using the H2A-H2B and H2A.Z-H2B complexes. The histone incorporation mainly occurred at less condensed chromatin (open), suggesting that the condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. This led to the genome-wide distribution of H2A and the exclusion of H2A.Z from the closed chromatin.

overall_design: RhIP-ChIP-seq of H2A.Z under ANP32E or ATP depletion condition


title: Channel Nuclear Pore Complex subunits are required for transposon silencing in Drosophila

city: Cambridge

first: Marzia

last: Munafo

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

institute: University of Cambridge

summary: We investigate the transcription and export of the uni-strand piRNA cluster flamenco and report the involvement of Nuclear Pore Complex subunits in its nuclear export and specification as a piRNA precursor.

overall_design: Characterization of NPC subunits involvement in piRNA biogenesis.

first: Victoria

last: Lawless

first: Alessandro

last: Passera

first: Serena

last: MacMillan

first: Susanne

last: Bornelöv

first: Irmgard

middle: U

last: Haussmann

first: Matthias

last: Soller

first: Gregory

middle: J

last: Hannon

first: Benjamin

last: Czech


title: BCOR modulates transcriptional activity of a subset of glucocorticoid receptor target genes involved in cell growth and mobility

city: Kuopio

first: Einari

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: The effect of BCL6 corepressor (BCOR) on glucocorticoid signaling and was analyzed in HEK293-based cell lines using ChIP-seq and RNA-seq.

overall_design: Chromatin binding of BCOR was analyzed using ChIP-seq from two biological replicates of HEK293 cells constitutively expressing GR (HEK293-GR; Paakinaho et al., 2014). Fragmented de-crosslinked chromatin was used as an input control. Gene expression was analyzed from three (rep1-3) biological replicates using RNA-seq. Poly-A RNA was extracted from BCOR depleted (siBCOR) or control siRNA-transfected (siNON) HEK293-GR cells treated with vehicle (ethanol, EtOH) or dexamethasone (100nM, 6h).

first: Kaiser

last: Manjur

first: Jorma

last: Palvimo

first: Marjo

last: Malinen

first: Joanna

middle: K

last: Lempiäinen


title: Integrative assessment of classical and molecular phenotypes in MCF10A cells [RNA-seq]

summary: Maintenance of proper phenotypic state of mammary epithelial cells is crucial for normal function, however the molecular networks underlying control of various cellular phenotypes are not well understood. To date most studies have assessed the impact of extracellular signals on a single phenotypic response, such as proliferation, or have focused on elucidation of molecular changes associated with single perturbations. However, these approaches ignore that ligands frequently induce multiple phenotypic changes and that similar phenotypic responses can be induced by multiple ligands. As a consequence, little is known about the core molecular mechanisms that drive cells to different phenotypic states. Here we deeply profiled the phenotypic and molecular responses of MCF10A mammary epithelial cells to a diverse panel of ligands known to have a role in the normal mammary gland. These ligands elicited multiple phenotypic responses, including changes in proliferation, migration, and differentiation status. Analysis of companion RNAseq, ATACseq, and proteomic data identified distinct molecular features associated with ligand treatments and phenotypic changes. These data provide a robust resource to address questions about how environmental signals are encoded into molecular and phenotypic responses, the associations between molecular modalities, and temporal encoding of molecular and phenotypic responses.

overall_design: Gene expression profiles of biological triplicate MCF10A cells in 7 conditions (6 ligand treatments and 1 control), measured at 0, 24, and 48 hours post-treatment. 48 samples total.

first: Daniel

last: Derrick


title: RNA-seq analysis of NSC-34 mouse motor neuron-like cells treated with Negative Control siRNA#2 (siNC#2), miR-125b-5p mimic, mmu-miR-124-3p mimic and siRNA (-) control

status: Public on Apr 19 2021

city: Fujisawa

first: MASAHIRO

last: NOGAMI

state: Kanagawa

address: 26-1, Muraoka-Higashi 2-Chome

department: Research

institute: Takeda Pharmaceutical Company Limited

summary: Fused in sarcoma/translated in liposarcoma (FUS) is a causative gene of familial amyotrophic lateral sclerosis (fALS). Mutated FUS causes accumulation of DNA damage and stress granule (SG) formation, etc., thereby motor neuron (MN) death. However, key molecular aetiology of mutated FUS-dependent fALS (fALS-FUS) remains unclear. Here, both regular bioinformatics and Bayesian gene regulatory networks (GRN) analyses were applied to large-scale transcriptome datasets of induced pluripotent stem cell (iPSC)-derived MNs possessing wild-type form of FUS and mutated FUSH517D (FUSH517D MNs). From regular bioinformatics provided DNA damage response (DDR)-related genes were uniformly down-regulated in FUSH517D MNs. Bayesian GRN calculated by Super-Computer identified miR-125b-5p, TIMELESS and PRKDC as "hub genes/miRNA" which influence the GRNs. miR-125b-5p was up-regulated in FUSH517D MNs and negatively correlated with FUS, TIMELESS and miR-125b-5p target mRNAs. Introduction of miR-125b-5p suppressed Fus, Timeless and DDR-related genes in addition to miR-125b-5p targets in expression, and caused DNA damage. Furthermore, knocking-down Timeless expression caused DNA damage. PRKDC was down-regulated in FUSH517D MNs and the cellular model analyses validated DNA damage under impaired DNA-PK activity promoted FUS mis-localization to SGs. Collectively, our strategy with Bayesian GRNs based on the iPSC model would provide the first compelling evidence to elucidate fALS-FUSH517D molecular aetiology.

overall_design:
To explore the specific target mRNA molecules of miR-125b-5p in motor neuron, NSC-34 were treated with siNC#2, miR-125b-5p mimic, mmu-miR-124-3p mimic and siRNA (-) control and standard RNA-seq was performed.
12 samples were analyzed. 3 samples of "(-) siRNA" and 3 samples of "siNC#2" are control.

first: Masahiro

last: Nogami

first: Takahisa

last: Ogasawara

first: Masato

last: Yano

first: Hideyuki

last: Okano


title: Integrative assessment of classical and molecular phenotypes in MCF10A cells [ATAC-seq]

first: Laura

last: Heiser

overall_design: Chromatin accessibility profiles of MCF10A cells in 7 conditions (6 ligand treatments and 1 control), measured at 0, 24, and 48 hours post-treatment. 48 samples total.


title: Single cell gene expression analysis of mouse melanoma tumor infiltrating leukocytes

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: The tumor immune cell composition dictates cancer outcomes. To capture this tumor immune cell diversity, we isolated tumor infiltrating leukocytes from tamoxifen induced tumors of Tyr::CreER;BRAFCAPTENloxp mice for single cell RNA sequencing

overall_design: Single cell RNA sequencing of tumor-infiltrating leukocytes from two tamoxifen induced tumors to investigate intratumor immune cell heterogeneity and to capture individual cell gene expression.

first: Nicolas

last: Jacquelot

first: Yang

last: Liao

first: Gabrielle

last: Belz


title: Quantitative analysis of differential expressed genes and pathways in AB8 cells overexpressing Crb2 S267A variant for 48h (+dox) compared to non-induced control cells (-dox) using next-generation sequencing (NGS)

city: Münster

first: Annika

last: Möller-Kerutt

address: Albert-Schweitzer-Campus 1, A14

department: Medical Dept. D

institute: University Clinics of Münster

summary:
Purpose: NGS can be used for system-based analysis of cellular pathways. The goal of this study was to identify genes and pathways which are activated in AB8 podocytes due to Crb2 S267A overexpression.
Methods: AB8 cells were modified using lentiviral transduction with pIND21_hCrb2+GFP_S267A. After selection with puromycin, cells were induced with doxycycline for 48h to overexpress Crb2 S267A variant. Non-induced cells were used as controls. RNA-seq data from AB8 cells overexpressing Crb2 S267A variant for 48h (+dox) were compared with non-induced control cells (-dox) (n=4). Activated pathways (GO terms) were identified with DAVID bioinformatics tool.
Results: RNAseq data revealed activation of ER stress response, chaperon folding genes and pathways. Misfolded Crb2 variant induces cellular ER stress compared to control cells.

overall_design: AB8 cells expressing Crb2+GFP_S267A were compared to non-expressing control cells.

first: Thomas

last: Weide

first: Andreas

last: Huge


title: MicroRNA expression profle in bovine mammary gland parenchyma infected by coagulase-positive or coagulase-negative staphylococci.

status: Public on Apr 14 2021

city: Balice near Krakow

first: Klaudia

last: Pawlina-Tyszko

address: Krakowska 1

department: Deaprtment of Animal Genomics and Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

summary:
Purpose: The aim of the study was to compare the miRNA expression in non-infected (H) mammary gland parenchyma samples with that of glands infected with coagulase-positive staphy  lococci (CoPS) or coagulase-negative staphylococci (CoNS) using next-generation sequencing.
Methods: miRNA-seq analysis was performed on mammary gland parenchyma samples collected from non-infected cows and those infected with coagulase-positive or -negative staphylococci. The miRNA libraries were constructed from total RNA using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer protocol. The quantification of the obtained libraries was performed on a Qubit 2.0 spectrophotometer (Invitrogen, Life Technologies), while a quality control on a TapeStation 2200 instrument (D1000 ScreenTape; Agilent). Single-end cycle sequencing was performed on the HiScanSQ platform (Illumina) with the use of TruSeq SR Cluster Kit v3- CBOT-HS and TruSeq SBS Kit v 3 - HS (Illumina). MicroRNA differentially expressed between investigated groups were identified with the DESeq2 software.
Results: Comparing the CoPS and H groups, 256 known and 260 potentially new miRNAs were identifed, including 32 that were diferentially expressed (p≤0.05), of which 27 were upregulated and 5 downregulated. Comparing the CoNS and H groups, 242 known and 171 new unique miRNAs were identifed: 10 were upregulated (p≤0.05), and 2 downregulated (p≤0.05). Comparing CoPS with H and CoNS with H, 5 Kyoto Encyclopedia of Genes and Genomes pathways were identifed; in both comparisons, diferentially-expressed miRNAs were associated with the bacterial invasion of epithelial cells and focal adhesion pathways. Four gene ontology terms were identifed in each comparison, with 2 being common to both immune system processes and signal transduction.
Conclusions: Obtained results enabled us to characterize the miRNA profile of the mammary gland parenchyma tissue, not only the healthy one but also the tissue infected with coagulase-positive and negative staphylococci as well as allowed identification of miRNAs differing the examined groups and characteristic for the staphylococci infection. They also indicated that miRNAs, especially miR-99 and miR-182, play an essential role in the epigenetic regulation of a range of cellular processes, including immunological systems bacterial growth in dendritic cells and disease pathogenesis (miR-99), DNA repair and tumor progression (miR-182).

overall_design: MicroRNA next generation sequencing of healthy mammary gland parenchyma samples and infected by coagulase-positive or coagulase-negative staphylococci performed using Illumina HiScanSQ.

first: Emilia

last: Bagnicka

first: Ewelina

last: Kawecka-Grochocka

first: Magdalena

last: Zalewska

first: Aleksandra

last: Kapusta

first: Ewa

last: Kościuczuk

first: Sylwester

last: Marczak

first: Tomasz

last: Ząbek


title: Chimeric contribution of human extended pluripotent stem cells to monkey embryos

city: 昆明市

first: shaoxing

last: Dai

state: 云南

address: No.1 boda road chenggong, Kunming 650500 Yunnan,China

institute: Kunming University of Science and Technology

summary: Pluripotent stem cells (PSCs) represent the earliest stages of organismal development, and have the potential to differentiate into cell types from all three primary germ layers. To date, however, chimeric competency of human EPS cells has not been determined in other animal hosts. Leveraging on a recently developed in vitro culture system that enabled the development of monkey embryos up to 20 days in vitro, in this study, we injected human PSCs (hPSCs) cells into cynomolgus monkeys (Macaca fascicularis) morula embryos and examined their contribution to different lineages at different timepoints during in vitro culture.

sample_organism:
Macaca fascicularis
Homo sapiens

platform_organism:
Macaca fascicularis
Homo sapiens

overall_design: We first injected human PSCs (hPSCs) cells into cynomolgus monkeys. Then in vitro culture of  chimeric embryos to study chimeric contribution of human extended pluripotent stem cells to monkey embryos

first: Tao

last: Tan

first: Jun

last: Wu

first: Chenyang

last: Si

first: Shaoxing


title: Implication of EZH2 in the hyper-proliferative and apoptosis-resistant phenotype of pulmonary artery smooth muscle cells in PAH: a transcriptomic and proteomic approach

city: Spring House

first: Vinod

last: Krishna

state: Pennsylvania

address: 1400 McKean Road

institute: Janssen R&D LLC

summary: The aim of this study was to determine whether EZH2 represents a new factor critically involved in the cancer-like phenotype of PAH-PASMCs. We found that EZH2 is overexpressed in human lung tissues and isolated PASMCs from PAH patients compared to controls as well as in two animal models mimicking the disease. Through loss- and gain-of-function approaches, we showed that EZH2 promotes PAH-PASMC proliferation and survival. By combining quantitative transcriptomic and proteomic approaches in PAH-PASMCs subjected or not to EZH2 knockdown, we found that inhibition of EZH2 downregulates many factors involved in cell cycle progression, including E2F targets, and contributes to maintain energy production. Notably, we found that EZH2 promotes expression of several nuclear-encoded components of the mitochondrial translation machinery and TCA cycle genes. Overall, this study provides evidence that, by overexpressing EZH2, PAH-PASMCs remove the physiological breaks that normally restrain their proliferation and susceptibility to apoptosis and suggests that EZH2 or downstream factors may serve as therapeutic targets to combat pulmonary vascular remodeling.

overall_design: Paired end RNA sequencing of PASMC samples treated with control and EZH2 siRNA (four of each)

first: Jey

last: Jeyaseelan

first: Olivier

last: Boucherot


title: iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinement

city: Guangzhou

first: Yuchen

last: Yang

address: Xingangxi Road 135

institute: Sun Yat-sen University

summary: In the current study, we present iSMNN, a supervised batch effect correction method for scRNA-seq data via multiple iterations of mutual nearest neighbor refinement. To validate the performance of iSMNN, we performed single-cell RNA-seq for adult murine heart using 10X Chromium platform.

overall_design: Single-cell RNA-seq profile of cardiac cells isolated at two 10-12 week old mouse was generated by deep sequencing using 10x Genomics Chromium System.

first: Li

last: Wang

last: Qian


title: Gene expression changes following chronic antipsychotic exposure in single cells from mouse striatum

city: Madison

first: anthony

middle: shawn

last: abrantes

state: WI

address: 402 Paunack st apt 1

department: genetic medicine

institute: unc-chapel hill

summary: Background. Schizophrenia is an idiopathic psychiatric disorder with a high degree of polygenicity. Evidence from genetics, single-cell, and pharmacological studies suggest an important overlap between genes involved in the etiology of schizophrenia and the cellular mechanisms of action of antipsychotics in medium spiny neurons (MSNs). Methods. We applied single-cell RNA-sequencing to striatal samples from C57BL/6J mice chronically exposed to a typical antipsychotic (haloperidol), an atypical antipsychotic (olanzapine), or placebo. We implemented careful statistical analyses to identify differentially expressed genes in two cell populations identified from the single-cell RNA-sequencing (MSNs and microglia) and applied multiple analysis pipelines to contextualize these findings. Results. Differential expression analysis showed that there was a larger share of differentially expressed genes (DEGs) in MSNs from mice treated with olanzapine vs. haloperidol. DEGs were enriched in broad loci implicated by genetic studies of schizophrenia, and we highlighted nine genes with convergent evidence. Pathway analyses highlighted alternative splicing, mitochondrial function, and neuron and synapse development as particularly engaged by antipsychotics. In microglia, we identified pathways involved in microglial activation and inflammation as part of the antipsychotic response. Conclusions. Our goal was to evaluate connections between schizophrenia genetic findings and cellular gene expression changes following antipsychotic exposure. We found that differential gene expression in MSNs from mice chronically treated with olanzapine converges on similar pathways and gene sets.

overall_design: Radomized case/control.  Case1: 5 animals. Case2: 5 animals. Control: 5 animals.

first: Anthony

last: Abrantes

first: Paola

last: Giusti-Rodriguez

first: NaEshia

last: Ancalade

first: Marcus

last: Basiri

first: Garret

last: Stuber

first: Patrick

last: Sullivan

first: Rainbo

last: Hultman

first: Shadia

last: Sekle


title: RNA-Sequencing analysis of in vitro generated IL-22+ CD4+ T cells from wild-type and Riok2 haploinsufficient (Riok2hKO) mice.

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

summary: Patients with myelodysplastic syndromes (MDS) display severe anemia but the mechanisms underlying this phenotype are incompletely understood. Right open-reading-frame kinase 2 (RIOK2) encodes a protein kinase located at 5q15, a region frequently lost in MDS del(5q) patients. Here, we show that hematopoietic cell-specific haploinsufficient deletion of Riok2 (Riok2f/+Vav1cre) led to reduced erythroid precursor frequency leading to anemia. Proteomic analysis of Riok2f/+Vav1cre erythroid precursors suggested immune system activation and transcriptomic analysis revealed an increase in p53-dependent interleukin-22 (IL-22) in Riok2f/+Vav1cre CD4+ T cells (TH22). Further, we discovered that the IL-22 receptor, IL-22RA1, was unexpectedly present on erythroid precursors. Blockade of IL-22 signaling alleviated anemia not only in Riok2f/+Vav1cre mice but also in wild-type mice. Serum concentrations of IL-22 were increased in the subset of del(5q) MDS patients as well as patients with anemia secondary to chronic kidney disease (CKD). This work reveals a possible therapeutic opportunity for reversing many stress-induced anemias by targeting IL-22 signaling.

overall_design: RNA-Seq comparision of wild-type (n = 5) and Riok2 haploinsufficient (n = 5) IL-22+ CD4+ T cells from in vitro generated Th22 cultures.

first: Mahesh

last: Raundhal

first: Laurie

last: Glimcher


title: SPAAC-NAD-seq, a sensitive and accurate method to profile NAD+-capped transcripts

city: Riverside

first: HAO

last: HU

state: California

address: 16 Round Table Dr.

institute: University of California, Riverside

summary: We developed a Copper-free, strain-promoted azide-alkyne cycloaddition reaction (SPAAC) to capture NAD-RNAs without RNA degradation. We examined the specificity of CuAAC and SPAAC reactions towards NAD+ vs. m7G, and found that both prefer NAD+ but also act on m7G. We show that m7G-capped RNA can be immuno-depleted, allowing for the specific identification of NAD-RNA via the SPAAC reaction and sequencing, which we name SPAAC-NAD-seq. Subjecting Arabidopsis RNA to both the original NAD captureSeq and SPAAC-NAD-seq, we found that more NAD+-capped RNA was identified by the latter, particularly those with low abundance. This led to the discovery of new gene ontology terms such as starch biosynthsis, intracellular protein transport and response to cadmium stress associated with genes that produce NAD-RNA. Furthermore, reads were uniformly distributed along gene bodies, which suggested that SPAAC-NAD-seq retained full-length sequence information. SPAAC-NAD-seq enables specific and efficient discovery of NAD-RNA in prokaryotes, and when combined with m7G-RNA depletion, in eukaryotes.

overall_design: NAD capped transcripts profiled by CuAAC-NAD-seq and SPAAC-NAD-seq in Arabidopsis

first: Xuemei

last: Chen

first: Hao

last: Hu


title: ChIP-seq of Ndt80 in a C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different media

city: Irapuato

first: Eugenio

last: Mancera

state: Guanajuato

address: Km. 9.6 Libramiento Norte Carretera Irapuato-Leon

department: Ingenieria Genetica

institute: Cinvestav

summary: The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in C. albicans, C. dubliniensis and C. tropicalis during biofilm formation in different growth media. Ndt80 was tagged with a c-myc epitope in the three species and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain in two different media for each species.

sample_organism:
Candida albicans
Candida tropicalis
Candida dubliniensis

overall_design: myc tagged Ndt80 vs. untagged control with two technical replicates in two different media for each species


title: Adalimumab Induces a Wound Healing Profile in Patients with Hidradenitis Suppurativa by Regulating Macrophage Differentiation and Matrix Metalloproteinase Expression

city: Worcester

first: Jing

last: Wang

state: MA

address: 100 Research Drive

institute: AbbVie

summary: Adalimumab (ADA) is the only FDA-approved treatment for moderate-to-severe hidradenitis suppurativa (HS), whereas etanercept (ETN) and certolizumab-pegol (CZP) have been shown to be ineffective, suggesting that the mechanism of action of ADA is distinct in HS and may contribute to improved wound healing. Given that macrophages (Mφ) play pivotal roles throughout the wound healing process, an in-vitro Mφ differentiation assay was carried out to assess the impact of TNF-anti-TNF complexes on these cells. TNF-ADA complexes exhibited stronger inhibitory effects on inflammatory Mφ differentiation. Moreover, RNA sequencing revealed several unique wound healing profiles for TNF-ADA-treated inflammatory Mφs, which were not observed for those treated with either TNF-ETN or TNF-CZP, including the inhibition of the matrix metallopeptidase (MMP) pathway. In addition, ADA administration was found to significantly reduce the levels of inflammatory MMPs -1 and -9 while promoting wound healing MMP-13 and tissue inhibitor of metalloproteinases 2 (TIMP-2) levels in the circulation of those HS patients who responded to treatment. Our in-vitro findings demonstrate that TNF-ADA-treated inflammatory Mφs exhibit a distinct profile resembling wound healing. Moreover, ADA not only differentially regulates MMP expression in HS patients responding to the therapy but potentially induces a transition to a profile suggestive of wound healing.

overall_design: Gene expression profiles of human M1 macrophages exposed to TNF-anti-TNF biologics

first: Yonghao

last: Cao

first: Bohdan

middle: P

last: Harvey

first: Feng

last: Hong

first: Melanie

last: Ruzek

first: Erin

last: Murphy

first: Zehra

last: Kaymakcalan


title: Developmental chromatin programs determine oncogenic competence in melanoma [RNA-seq II]

city: New York

first: Richard

last: White

state: NY

address: 1275 York Avenue MB 424

institute: Memorial Sloan Kettering Cancer Center

summary: Transcriptional profile of 3xKO dox melanocytes and 3xKO ATAD2 dox melanocytes

overall_design: hPSC-derived melanocytes were infected with a lentivirus (Tomato or ATAD2) and selected for 1 week with blastocidin. After selection, the hPSC-derived melanocytes were treated for 72h with doxycycline to induce expression of BRAFV600E. Roughly 500'000 cells were collected per condition.

first: Lorenz

last: Studer

last: Koche

first: Arianna

last: Baggiolini


title: MLL3 suppresses tumorigenesis through regulating TNS3 enhancer activity [RNA-seq]

city: Wuhan

first: Jun-Yi

last: Zheng

address: No. 299 Of Bayi Road

institute: Wuhan Univisity

summary: MLL3 is a histone H3K4 methyltransferase which is frequently mutated in cancer, but the underlying molecular mechanisms remain elusive. Here, we found that MLL3 knockout by CRISPR/sgRNA did not elevate proliferation rate of cancer cells, but significantly enhanced cell migration. Through RNA-Seq and ChIP-Seq approaches, we identified TNS3 as the potential target gene for MLL3. MLL3 depletion caused down regulation of H3K4me1 and H3K27ac on an enhancer ~ 8 kb ahead of TNS3. 3C assay indicated the identified enhancer interacts with TNS3 promoter, and repression of enhancer with dCas9-KRAB system impaired TNS3 expression. Exogenous expression of TNS3 in MLL3 deficient cells completely blocked the enhanced cell migration phenotype. Taken together, our study revealed a novel mechanism for MLL3 in suppressing cancer, which may provide novel targets for diagnosis or drug development.

overall_design: mRNA profiles of U2OS cells after MLL3 knockdown and p53 activation

first: Chen-Yu

first: Chuan

last: Gao

first: Qiong

last: Xiao

first: Cheng-Wei

last: Huang

first: Min

last: Wu

first: Lian-Yun

last: Li


title: MLL3 suppresses tumorigenesis through regulating TNS3 enhancer activity

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

overall_design: Refer to individual Series


title: ChIP-seq of biofilm master regulators in four species of Candida

first: Eugenio

last: Mancera

summary: The purpose of this experiment was to identify the genes bound by the biofilm master regulators (Bcr1, Brg1, Efg1, Ndt80, Rob1 and Tec2) in Candida albicans, C. dubliniensis, C. tropicalis and C. parapsilosis during biofilm formation. The regulators were tagged with a c-myc epitope and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain.

sample_organism:
Candida albicans
Candida parapsilosis
Candida tropicalis
Candida dubliniensis

overall_design: myc tagged regulator vs. untagged control with two technical replicates for each regulator in each species


title: Genome-wide DNA methylation analysis of pancreatic tissue samples obtained from patients with pancreatic ductal adenocarcinoma.

city: Shinjyuku-ku

first: Yae

last: Kanai

address: 35, Shinano-machi

institute: Keio University School of Medicine

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip in 34 samples of non-cancerous pancreatic tissue and 82 samples of cancerous tissue samples obtained from 82 patients with pancreatic ductal adenocarcinoma.

overall_design: From fresh frozen tissue samples, high-molecular-weight DNA was extracted using phenol-chloroform followed by dialysis. Five-hundred nanogram of genomic DNA was subjected to bisulfite treatment using an EpiTect Bisulfite Kit (QIAGEN), in accordance with the manufacturer’s protocol. After bisulfite treatment, DNA methylation status at 485,764 probe sites was examined at single-CpG resolution using the Infinium HumanMethylation450K BeadChip (Illumina, San Diego, CA), according to the manufacturer’s instructions. Hybridization fluorescence signals were read by the iScan reader (Illumina). The data were assembled using GenomeStudio methylation software (Illumina). At each CpG site, the ratio of the fluorescent signal was measured using a methylated probe relative to the sum of the methylated and unmethylated probes, i.e. the so-called β-value, which ranges from 0.00 to 1.00, representing the fully unmethylated and fully methylated values of an individual CpG site, respectively.

first: Eri

last: Arai

first: Yutaka

last: Endo


title: ChIP-seq analysis of  MED1 and FOSL1 in SCC1 cells after depletion of FOSL1

city: Richmond

first: Jiong

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

summary: To explore genome-wide alteration MED1 and FOSL1 after depletion of FOSL1, we performed chromatin immunoprecipitation sequencing (ChIP-seq) of SCC1 cells to examine genome-wide recruitment of MED1 and FOSL1 following FOSL1 knockdown. Depletion of FOSL1 led to dramatically loss of the recruitment of MED1 and FOSL1 at a cohort of key oncogenes associate with tumorigenesis and metastasis.

overall_design: Examination of ChIP-seq of  HNSCC cells treated with FOSL1 siRNA.


title: ChIP-seq of Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation

summary: The purpose of this experiment was to identify the genes bound by the regulator Ndt80 in a C. albicans x C. dubliniensis hybrid during biofilm formation. C. albicans or C. dubliniensis Ndt80 was tagged with a c-myc epitope in a C. albicans x C. dubliniensis hybrid and the immunoprecipitation of the tagged strain was compared to that of an untagged control hybrid strain.

overall_design: myc tagged Ndt80 vs. untagged control with two technical replicates in either a hybrid were C. albicans Ndt80 is tagged or C. dubliniensis Ndt80 is tagged


title: Gene Expression Arrays comparing C. tropicalis CEM010 during planktonic and biofilm growth in different media

summary: The goal was to identify genes that change their expression in biofilm vs. planktonic growth.  Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.

overall_design: Expression was measured relative to pooled references, two replicates of each experiment were performed.


title: Gene Expression Arrays comparing C. albicans CEM175 during planktonic and biofilm growth in different media

summary: The goal was to identify genes that change their expression in biofilm vs. planktonic growth.  Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose and Spider. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.


title: Gene expression-profiling to predict induction chemotherapy efficacy in locoregionally advanced nasopharyngeal carcinoma

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Gene expression signature can be used to predict treatment efficacy in various types of tumour. We aim to identify a gene expression signature to predict efficacy of induction chemotherapy (IC) in patients with locoregionally advanced nasopharyngeal carcinoma (LA-NPC).

overall_design: Using Affymetrix Human Transcriptome Arrays 2.0, we profiled the gene expression between 71 LA-NPC tumor tissues with response to induction chemotherapy  and 24 LA-NPC tumor tissues with no-response to induction chemotherapy to identify induction chemotherapy efficacy-related genes.

first: Y

last: Lei

middle: Q

first: N

last: Liu

first: J


title: Gene expression profile of human trabecular meshwork cells with silenced expression of autophagy genes Atg5 and Atg7 subjected to cyclic mechanical stretch

city: Durham

first: Paloma

last: Liton

address: DUMC Box 3802

institute: Duke University

summary: In order to investigate the effects of downregulated autophagy in TM cells response to mechanical stretch, we conducted gene expression analysis in human TM cells deficient in autophagy and subjected to cyclic mechanical stretch. For this, three independent strains of primary human TM cells were transfected with a cocktail of siRNAs to specifically silence the expression of the autophagy genes Atg5 and Atg7 (siAtg5/7), and subjected to cyclic mechanical stress (15% elongation, 1 cycle/sec, 24h).

overall_design: siRNA transfection was performed as described previously with minor modifications (Kristine M Porter, Jeyabalan, & Liton, 2014). In brief, primary human TM cells were plated on 24-well plate, with 60-80% confluence, in 0.5 mL of the growth media.  After 24 h, the cells were transfected with either 5 pmol of siRNA against ATG5 (siAtg5, sc-41445) and ATG7 (siAtg7, sc-41447) or 5 pmol of non-targeting siRNA (siNC, sc-37007) using Lipofectamin® RNAiMAX Reagent, according to the manufacturer’s instructions. At 72 h post-transfection, cells were subjected to cyclic mechanical stress for 24 h using the Flexcell System. A regime of 15% cyclic stretch, 1 cycle/sec was applied. Non-stretched control cells were maintained under same culture conditions, but no mechanical forces were applied. Cells were washed with cold PBS and fixed in RNAlater (Qiagen). Total RNA was isolated using RNeasy kit (Qiagen, Valencia, CA), following the manufacturer's protocol, and treated in-column with DNase I. RNA concentration and quality were determined using the Agilent 2100 Bioanalyzer. Total RNA (5 µg) from human TM primary cultures with transient silenced autophagy and controls were independently hybridized to human Clariom D microarrays (ThermoFisher) following the manufacturer's instructions at the Duke Microarray Core Facility. Data analysis was performed using the Partek Flow and Partek Genome Suite statistical analysis software (Partek Incorporated).


title: Gene expression changes during aging in polyploid and diploid hepatocytes

city: Suita

first: Tomonori

last: Matsumoto

state: Osaka

address: 3-1 Yamadaoka

institute: Osaka University

summary: To examine gene expression changes duging aging in polyploid and diploid hepatocytes, diploid and polyploid hepatocytes were sorted from young and aged multi-reporter mice and their gene expressions were analyzed by high-throughput RNA sequence.

overall_design: Diploid and polyploid hepatocytes were collected from three young and three aged mice.

first: Markus

last: Grompe


title: Gene Expression Arrays comparing C. albicans SN250 during planktonic and biofilm growth in different media

summary: The goal was to identify genes that change their expression in biofilm vs. planktonic growth.  Cultures for the extraction of total RNA under biofilm growth conditions were performed on biofilms grown on the bottom of 6-well polystyrene plates for 48 hours at 37°C and 200 rpm as previously described (Nobile et al. 2012). The media used was Spider 1% glucose, Spider and RPMI 1% glucose. Planktonic cultures for total RNA were grown in the same media by inoculating with cells from an overnight 30°C YPD culture to an OD600 of 0.05. Cultures were then grown in flasks at 37°C with shaking at 225 rpm until they reached an OD600 of 1.0.


title: Gene Expression Arrays comparing C. dubliniensis CEM002 during planktonic and biofilm growth in different media


title: Analysis of the transcriptomic profile of WT mouse embryonic fibroblast (MEF WT) and Nf2-knockout mouse embryonic fibroblast (MEF Nf2 KO) cell lines

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

summary: Merlin is the tumor suppressor protein encoded by the NF2 gene. The expression of Merlin is remarkably decreased in metastatic breast cancer tissues irrespective of the breast cancer subtype. In order to ascribe clinical relevance, we re-capitulated the loss of Merlin in breast cancer cells. Merlin deficiency elicited a markedly invasive phenotype. In order to overcome the challenge of embryonic lethality of a total Nf2-knockout, we generated a unique mammary-specific Nf2-knockout mouse mammary tumor model. Both, the Nf2-knockout mouse embryonic fibroblasts (MEF) and Merlin-deficient breast tumor cells displayed a robust invasive phenotype. Transcriptomic assessment of Nf2-knockout MEFs revealed notable alterations in glutathione transferase and antioxidant networks indicating a role for Merlin in redox biology. This programmatic alteration resonated with the pathways that emerged from breast tumor cells engineered for Merlin deficiency.

overall_design: Examination of total RNA from 3 replicates of MEF WT (control)  and  3 replicates of MEF Nf2 KO

first: Mateus

last: Mota

first: Lalita

last: Samant


title: DNAJC9 Integrates Heat Shock Molecular Chaperones into the Histone Chaperone Network

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

summary: From biosynthesis to assembly into nucleosomes, histones are handed through a cascade of histone chaperones, which shield histones from non-specific interactions. Whether mechanisms exist to safeguard the histone fold during histone chaperone handover events or to release trapped intermediates is unclear. Using structure-guided and functional proteomics, we identify and characterize a histone chaperone function of DNAJC9, a heat shock co-chaperone that promotes HSP70-mediated catalysis. We elucidate the structure of DNAJC9, in a histone H3-H4 co-chaperone complex with MCM2, revealing how this dual histone and heat shock co-chaperone binds histone substrates. We show that DNAJC9 recruits HSP70-type enzymes via its J domain to fold histone H3-H4 substrates: upstream in the histone supply chain, during replication- and transcription-coupled nucleosome assembly, and to clean up spurious interactions. With its dual functionality, DNAJC9 integrates ATP-resourced protein folding into the histone supply pathway to resolve aberrant intermediates throughout the dynamic lives of histones.

overall_design:
Quantitative ChIP-seq analysis of DNAJC9 distribution and abundance from cells expressing DNAJC9-MYC-Flag WT, J or 4A mutants, and control cells . All experiments were done in duplicates. Chromatin of Drosophila melanogater S2 cells were used as spike-in for normalization purpose.
Please note that each processed data was generated from both replicates (R1 and R2) and is linked to the corresponding R1 sample records.

first: Colin

last: Hammond

first: Nazaret

last: Reverón-Gómez


title: Non-canonical immune response to inhibition of DNA methylation via stabilization of dsRNAs from endogenous retroviruses

city: Daejeon

first: Ku

last: yongsuk

address: KAIST, 291, Daehak-ro, Yuseong-gu

department: Department of Chemical and Biomolecular Engineering

country: South Korea

institute: KAIST

summary: 5-Aza-2'-deoxycytidine, also known as decitabine, is a DNA hypomethylating agent (HMA) used to treat acute myeloid leukemia (AML) and pre-leukemic disorder myelodysplastic syndrome (MDS). Decitabine activates the transcription of endogenous retroviruses (ERV), which can induce immune response by acting as cellular double-stranded RNAs. Here, we employ an image-based screening system to identify dsRNA-binding factors that mediate the downstream effect of ERV induction. We find that STAUFEN1 (STAU1) knockdown decreases the interferon signature and rescues decitabine-mediated cell death. Our subsequent analyses reveal that STAU1 directly binds to ERV RNAs and stabilizes the RNAs together with a long noncoding RNA, TINCR. Analysis of a clinical patient cohort further supports that MDS and AML patients with low STAU1 and TINCR expressions exhibited poor response to the HMA therapy. Our study reveals that decitabine-mediated cell death is a consequence of complex interactions among different dsRNA binding proteins for access to their common dsRNA targets.

overall_design: ncRNA and total RNA profiles of WT HCT116 and Staufen1-deficient HCT116.

first: Yoosik

last: Kim

first: Yongsuk

last: Ku

first: Ryeongeun

last: Cho

first: Hyoung-Min

last: Park


title: MLL3 suppresses tumorigenesis through regulating TNS3 enhancer activity [ChIP-seq]

first: Jun-Yi

last: Zheng

overall_design: Examination of 2 different histone modifications in U2OS cells after MLL3 knockdown.

first: Chen-Yu

last: Wang

first: Chuan

last: Gao

first: Qiong

last: Xiao

first: Cheng-Wei

last: Huang

first: Min

last: Wu

first: Lian-Yun

last: Li