title: U2OS shE4F1 transcriptome

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Zinc finger (ZnF) proteins represent one of the largest families of human proteins, although most remain uncharacterized. Given that numerous ZnF proteins are able to interact with DNA and poly(ADP-ribose), there is a growing interest in the understanding of their mechanism of action in the maintenance of genome integrity. We now report that the ZnF protein E4F1 is an actor of DNA repair. Indeed, E4F1 is rapidly recruited, in a PARP-dependent manner, to DNA breaks and promotes ATR/CHK1 signaling, DNA-end resection and subsequent homologous recombination. Moreover, we identified E4F1 as a new regulator of the ATP-dependent chromatin remodeling SWI/SNF complex in DNA repair. E4F1 binds to the catalytic subunit BRG1/SMARCA4, and together with PARP-1, mediates its recruitment to DNA lesions. We also report that a proportion of human breast cancers show amplification and overexpression of E4F1 or BRG1 that are mutually exclusive with BRCA1/2 alterations. Together, these results reveal a novel function of E4F1 in the DNA damage response that orchestrates proper signaling and repair of double strand breaks and document a molecular mechanism for its essential role in maintaining genome integrity and cell survival.

overall_design: U2OS cells (3 independent pool)  were cultured in DMEM 10% FBS and infected with shRNA ctrl or E4F1. RNA were extracted 72h after infection  and sequences were obtained with an Illumina NextSeq 500 sequencer.

first: Céline

last: Moison


title: n-3 LCPUFA intervention during pregnancy alters placental microRNA expression, potential miR-99a/mRNA interactions, involving mTOR, LAT1 and TauT, and maternal and fetal blood plasma amino acid levels

status: Public on Mar 11 2021

city: Freising-Weihenstephan

first: Bernhard

middle: L

last: Bader

address: Gregor-Mendel Straße 2

department: Clinical Nutritional Unit - ZIEL-Research Center for Nutrition and Food Sciences

country: Germany

institute: Technische Universität München

summary: Our previous analyses of placentas revealed sexually dimorphic mRNA expression and responsiveness to maternal dietary supplementation with n-3 long chain polyunsaturated fatty acids (LCPUFA). In this secondary analysis we aimed to explore the respective placental microRNA expression and putative microRNA-mRNA target interactions, and their associations with offspring body composition.

overall_design: Considering our previous data showing mRNA expression changes predominantly in female placentas following the n-3 LCPUFA intervention Sedlmeier et al. 2014, we analyzed for the initial explorative microRNA profiling total RNA containing small RNA of a pool of female placentas assigned to the control (n=3) or a pool of the n-3 LCPUFA intervention group (n=3).

first: Eva-Maria

last: Sedlmeier

first: Dorothy

middle: M

last: Meyer

first: Lynne

last: Stecher

first: Manuela

last: Sailer

first: Hannelore

last: Daniel

first: Hans

last: Hauner


title: CLL plasma circRNA microarray

city: Nanjing

first: Zijuan

last: Wu

state: Jiangsu

address: 300 Guangzhou Road, Nanjing, 210029, China

country: China

institute: The First Affiliated Hospital of Nanjing  Medical University, Jiangsu Province Hospital

summary: To identify a novel circRNA which could serve as a plasma biomarker and explore its function and molecular mechanism as well as clinical significance in chronic lymphocytic leukemia (CLL) we performed circRNA microarray analysis.

overall_design: To analyse circRNAs expression profiles in CLL, plasma samples from three untreated CLL patients  and five normal donors (age- and sex-matched) were collected for circRNA microarray.

first: Jianyong

last: Li

first: Hui

last: jin


title: T cell receptor repertoire analysis of tumor-infiltrating T cells in non-small cell lung cancer

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

country: USA

institute: Rutgers Cancer Institute of New Jersey

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Multi-omics Characterization of WNT Pathway Reactivation to ameliorate BET Inhibitor Resistance in Liver Cancer Cells

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

summary: The goals of this study are to find drug response genes to different drug combinations in BET inhibitor resistant HepG2 cells. RSEM is taken for consequent data analysis, mapping each sample to the human genome (build hg19) to determine expressions of 57773 transcripts.

overall_design:
First, HepG2 and Hep3B cells were seeded into 15 cm dish in 2 replicates after treatments with a BET inhibitor (215 nM) or Control (vehicle DMSO) for 24h.

Then a series of mRNA profile in HepG2 cells is generated from different inhibitor combination treated samples during 72h by deep sequencing, in duplicate, using Illumina HiSeq 3000. NC represents control, treated with DMSO; 74 means treatments with BET inhibitor at 4000nM; 94 means treatments with CHIR98014 at 4000nM;749 means treatments with BET inhibitor at 4000nM and CHIR98014 at 72nM;794 means treatments with BET inhibitor at 25nM and CHIR98014 at 4000nM.

first: Yuwei

last: Liu


title: Sulfur-dependent translational regulation via methylation multiplicity of 18S rRNA

city: Dallas

first: Kuanqing

state: Texas

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern Medical Center

summary: N6-methyladenosine (m6A) is a conserved nucleoside modification that regulates many facets of RNA metabolism and cellular physiology. Using quantitative mass spectrometry, we find that the universally conserved tandem adenosines at the 3’ end of 18S rRNA (A1781 and A1782 in Saccharomyces cerevisiae), which were thought to be constitutively di-methylated (i.e. N6, N6-dimethyladenosine or m62A), are also mono-methylated (i.e. m6A). Although present at substoichiometric amounts, m6A at these positions increases significantly and specifically in response to sulfur starvation in both yeast and mammalian cells. Combining yeast genetics and ribosome-profiling, we further demonstrate that ribosomes bearing different numbers of methyl groups (zero, one, and two) at these tandem adenosines exhibit distinct translation profiles in a sulfur-dependent fashion. Our work thus reveals methylation multiplicity as a mechanism to regulate translation and also uncovers the functional importance of the ubiquitous m62A modification in 18S rRNA.

overall_design: We performed ribosome profiling and RNA-seq on three Saccharomyces cerevisiae strains growing with and without methionine

first: Daniel

middle: A

last: Santos

first: Jeffrey

last: Hussmann

first: Yun

last: Wang

first: Benjamin

last: Sutter

first: Jonathan

middle: S

last: Weissman

middle: P

last: Tu


title: Effects of root applied glutathione (GSH) on gene expression profile in the root of Brassica napus

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

country: Japan

institute: Hirosaki University

summary: Glutathione (GSH) is a tripeptide involved in controlling heavy metal movement in plants. Our previous study demonstrated that GSH, applied to plant roots site-specifically, inhibited Cd translocation from roots to shoots in oilseed rape plants (Brassica napus) cultured hydroponically. One of the factors of this inhibitory effect was due to activation of Cd efflux from root cells. To investigate the molecular mechanism triggered by root applied GSH in more detail, the Cd movement was monitored non-invasively using a positron-emitting tracer imaging system (PETIS). The Cd absorption and efflux process in roots were visualized successfully. The effects of GSH on Cd efflux from root cells were estimated by analyzing obtained imaging data. Another image analysis suggested that Cd return was activated by GSH, applied to roots, at the shoot base. Cutting the shoot base of oilseed rape plants significantly inhibited Cd efflux from root cells. These experimental results demonstrated the shoot base is playing important roles in distributing Cd in the plant bodies. Furthermore, DNA microarray analysis revealed that over 300 genes in the roots of oilseed rape plants responded to root applied GSH. Among them, transporter proteins, related to heavy metal movement in plants, and proteins related to changing the structure of cell walls were involved.

overall_design: Seeds of oilseed rape (Brassica napus L. cv. Nourin No.16, Kaneko Seed Co. Ltd., Gumma, Japan) were germinated in submerged vermiculite. The solution used for the bottom flooding is a nutrient solution for hydroponics. This solution is containing 0.5 mM NH4H2PO4, 3.0 mM KNO3,  2.0 mM Ca(NO3)2, 1.0 mM MgSO4, 90 µM Na2EDTA (ethylenediamine-N, N, N’, N’-tetra acetic acid disodium), 90 µM FeSO4, 22.5 µM H3BO3, 10 µM MnSO4, 0.1 µM (NH4)6Mo7O24, 0.35 µM ZnCl2, 0.20 µM CuCl2 (Nakamura et al., 2008). The pH of this solution was adjusted to 5.5 using KOH solution. After one week, plants were transferred to hydroponic culture condition in 3 L plastic containers (6 plants per one container) with 2 L of Hoagland solution and aeration. The Nutrient solution was freshly replaced once a week. 2 – 3 week old seedlings were used for each experiment. The plants were cultivated in 10 µM CdCl2-containing hydroponics solution with or without 100 mM GSH (glutathione, reduced form) for 2 days.

first: Jun

first: Nobuo

last: Suzui

first: Yon

middle: G

last: Yin

first: Satomi

last: Ishii

first: Shu

last: Fujimaki

first: Naoki

last: Kawachi

first: Hiroki

last: Rai

first: Takashi

last: Matsumoto

first: Kanna

last: Sato-Izawa

first: Naoko

last: Ohkama-Ohtsu

first: Shin

last: Nakamura


title: RNAseq of freshly isolated and ex vivo expanded peripheral blood NK cells

status: Public on Mar 10 2021

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: NK cells were isolated from the perpheral blood of healthy donors (n=6) and expanded ex vivo in the presence of feeder cells and IL-2. RNA  from fresh and expanded cells was isolated, sequenced, and gene expression of the cell populations were compared.

overall_design: Examiniation of gene transcription by FPKM

first: Emily

middle: R

last: Levy

first: Richard

middle: W

last: Childs


title: Nef dimerization defect abrogates HIV viremia and associated immune dysregulation in the Bone Marrow-Liver-Thymus-Spleen (BLTS) humanized mouse model.

city: Pittsburgh

first: SHIVKUMAR

middle: of

last: BIRADAR

state: PA

address: 130 De Soto St

department: Infectious Diseases and Microbiology

institute: University of Pittsburgh

summary: Loss of function mutations in the human immunodeficiency virus (HIV)-negative factor (Nef) gene are associated with reduced viremia, robust T cell immune response, and delayed acquired immunodeficiency syndrome (AIDS) progression in humans. Additionally, in vitro studies have shown that mutations in Nef's dimerization interface may play a significant role in modulating viral replication and impairing host defense. However, in vivo, mechanistic studies on the role of Nef dimerization in HIV infection are lacking. Humanized rodent models with human immune cells are robust platforms for investigating the interactions between HIV and the human immune system. We recently developed the bone marrow-liver-thymus-spleen (BLTS) humanized mouse model, which carries human immune cells, as well as primary and secondary lymphoid tissues that facilitate anti-viral immune responses. Here, we employed the BLTS-humanized mouse model to demonstrate that preventing Nef dimerization abrogates HIV viremia and the associated induction of immune dysregulation (immune activation and exhaustion). This suggests that Nef dimerization may be a therapeutic target for future HIV cure strategies, which can be explored in humanized mouse models.

overall_design: Human immune cells reconstituted BLTS humanized mice were infected with HIV-WT/ HIV dNef/ HIV-Y115D/ PBS. Three mice were assigned per group. HIV infected, and PBS-inoculated humanized mice were sacrificed at 5-7 weeks post HIV infection and total RNA was isolated from engrafted spleen tissue of humanized mice using Qiagen RNA isolation kit Cat# 74104. Nanostring profiling of host response was performed at the University of Pittsburgh Genomic Core facility using the nCounter Human Immunology v2 Panel, Cat #-XT-CSO-HIM2-12. Total RNA (50ng) was hybridized to reporter and capture probe sets at 65°C for 24 h. Hybridized samples were loaded on the nCounter cartridge and post-hybridization steps and scanning was performed on the nCounter Profiler. RCC files were analyzed using nSolver analysis software (Version 4.0) as per the manufacturer's protocols. Negative and positive controls included in probe sets were used for background thresholding, and normalizing samples for differences in hybridization or sample input respectively.

first: Shivkumar

last: Biradar

first: Moses

middle: T

last: Bility


title: Single-Cell RNA-Seq Analysis of long-term transplanted single-cell-derived mouse DASC in host lung

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: Distal airway stem cell (DASC) expressing basal cell restrictive transcription factor p63 and keratin-5 (Krt5) has a strong ability of regeneration after lung injury. Such cells are originated from primitive progenitors in distal airways and could expand/migrate to inflamed damaged lung parenchymal region to form ‘KRT5 pods’ once activated by various types of tissue injury. We isolated the mouse DASC and transplanted the GFP-labelled mDASC into the bleomycin-injured mouse lung by intratracheal instillation. Mice were sacrificed at 30 and 90 days post transplantation and their lung tissue were harvest to detect GFP signal by fluorescence stereomicroscope, the region of which was dissect for single cell-RNA-seq (scRNA-seq). We utilized scRNA-seq to trace the fate of transplanted mDASCs at 30 days and 90 days post transplantation, which revealed cell types differentiated from the transplanted DASCs.

overall_design: Bleomycin was intratracheally administrated to isoflurane-anesthetized mice at a concentration of 3U/kg 7 days prior transplantation (n=8). DASCs suspended in PBS (106 cells per mouse) were transplanted via trachea. At 30dpt and 90dpt, mice were sacrificed and their lung tissue were harvest to detect GFP signal by fluorescence stereomicroscope (MVX10, Olympus, Japan), the region of which was dissect for further work (30dpt= 3, 90dpt= 4). Firstly, the GFP+ tissues of lung were collected and immersed in cold F12 medium with 5% FBS, followed by being minced into small pieces and digested with dissociation buffer  on shaker for 1~1.5h. Dissociated cells were filtered through 100 μm cell strainer, and Red Blood Cell Lysis Buffer was used to remove erythrocyte. Cell pellets were resuspended in DMEM containing with 1% FBS following washing twice, and then passed through 30 μm strainers. Sorting and subsequent quantification were performed on BD FACS Aria ll cytometers.

first: Daniel

last: Henry


title: T cell receptor repertoire analysis of tumor-infiltrating T cells in non-small cell lung cancer [tumor_T_cells]

first: Shin-Heng

last: Chiou

summary: We analyzed 778,938 T cell receptor (TCR) CDR3b sequences from 178 non-small cell lung cancer (NSCLC) patients using GLIPH2 (Grouping of Lymphocyte Interactions with Paratope Hotspots 2). We identified over 66,000 TCR shared specificity groups, of which over 400 were enriched in tumor vs. adjacent lung. We focused on one tumor-enriched specificity group and used a yeast display library to identify the peptide epitopes. These include peptides from TMEM161A, which is an overexpressed antigen in NSCLC, and homologous peptides from Epstein-Barr virus (EBV) and E. coli, aligning with recent reports of virus-specific T cells in tumor infiltrates. Overall, we analyzed a very large dataset of TCR sequences from NSCLC patients and found thousands of specificities shared by three or more patients. This creates a database of TCR shared specificity groups in NSCLC, and also a template for mining and understanding the specificity of infiltrating T cells for any cancer.

overall_design: Single-cell RNA-Seq data collected with FACS sorted T cells from tumors of treatment-naive lung cancer patients (LUAD).

first: Diane

last: Tseng


title: Blood microRNA signatures serve as potential diagnostic biomarkers for hepatic sinusoidal obstruction syndrome caused by Gynura japonica containing pyrrolizidine alkaloids

first: Xunjiang

last: Wang

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

department: Shanghai R & D Center for Standardization of Traditional Chinese Medicines

institute: Shanghai University of Traditional Chinese Medicine

summary:
Background & Aims: Gynura japonica-induced hepatic sinusoidal obstruction syndrome (HSOS) is closely related with pyrrolizidine alkaloids (PAs) and the prevalence is on the rise worldwide in recent years. However, there is no effective therapy for PA-induced HSOS in clinic, which is partially caused by the failure of quick diagnosis. The aim of the present study was to identify blood miRNAs signatures as the potential biomarkers for PA-induced HSOS in clinic.
Methods: Microarray-based miRNA profiling was performed on blood samples of the discovery cohort, i.e. 9 HSOS patients and 9 healthy donors. The differentially expressed miRNAs were further confirmed using a validation cohort of 20 independent HSOS patients. In addition, rat model was also established by orally administration of total alkaloids extract (TA) from G. japonica to investigate the association of miRNAs biomarkers with the progression of HSOS. Bioinformatic analysis, including GO and KEGG enrichment analyses, receiver operating characteristics curve (ROC) analysis, correlation analysis, etc., were conducted to evaluate the accuracy of the potential miRNA biomarkers.
Results: Three miRNAs, namely miR-148a-3p, miR-362-5p, and miR-194-5p, were over-expressed in PA-induced HSOS patients and rats. They were positively related to the severity of liver injury and displayed considerable diagnostic accuracy for HSOS patients with areas under the curve (AUC) over 0.87. Conclusions: In summary, the present study demonstrated that 3 miRNAs, i.e. hsa-miR-148a-3p, hsa-miR-362-5p, and hsa-miR-194-5p, might serve as potential biomarkers for PA-induced HSOS in clinic.
Conclusions: In summary, the present study demonstrated that 3 miRNAs, i.e. hsa-miR-148a-3p, hsa-miR-362-5p, and hsa-miR-194-5p, might serve as potential biomarkers for PA-induced HSOS in clinic.

first: Yuzheng

last: Zhuge

first: Aizhen

last: Xiong

first: Li

last: Yang

first: Zhengtao


title: CD47 modulates the interaction of γ-catenin with E-cadherin and participates in epithelial–mesenchymal transformation in lipid nephrotoxicity

city: jiangsu

first: li

last: Gao

address: 639 longmian avenue

institute: China pharmaceutical university

summary: Hyperlipidemia, an important risk factor for cardiovascular diseases and end-stage renal disease, often increases renal injury and compromises kidney function. In the present study, the kidney histology analysis in human samples showed that high lipid levels induced renal fibrosis. However, the mechanism of lipid nephrotoxicity remains unknown. We employed mice models of two kinds to further experiments. The kidney histology analysis in mouse showed that high lipid levels induced renal fibrosis that was further confirmed by Western blot and real-time PCR of fibrotic indexes (fibronection, collagenI and α-SMA). In Vitro analysis also supported that OX-LDL significantly induced fibrotic response in HK-2 tubular epithelial cells. To further ascertain the mechanism of high lipid-induced fibrosis, RNA-sequencing (RNA-Seq) was performed. Combined the Gene Ontology (GO) analysis results of differentially expressed mRNAs obtained by RNA-Seq with the results of LC-MS/MS and STRING Functional Association Networks showed that CD47 modulated the interaction of γ-catenin with E-cadherin and participated in epithelial–mesenchymal transformation in lipid nephrotoxicity. The inhibition of CD47 expression by transfected with shRNA plasmid or treated with anti-CD47 antibody in OX-LDL-treated tubular epithelial cells restored the expression of E-cadherin and attenuated renal injury including fibrosis and inflammatory response. These findings indicate that CD47 may be a therapeutic potential target for long-term lipid abuse-induced kidney injury.

overall_design: mRNA profiles of HK-2 cells treated with control and OX-LDL stimulation.

first: Ting-ting

first: Jun-sheng

last: Zhang


title: Gene expression profiling of fucose-deficient Fx-/- mice cDC1-enriched splenocytes

city: Cleveland

first: Ernest

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

summary:
Analysis of the top differentially regulated genes in cDC1 in response to fucose treatment revealed genes enriched in pathways such as immune-effector processes, myeloid leukocyte activation, exocytosis, and secretion.
We used microarrays to detail the global programme of gene expression underlying fucosylation deficiency in mouse cDC1 cells

overall_design: cDC1 cells were isolated from mouse spleens by negative selection with biotinylated B220 and CD11b antibody and anti-Biotin MicroBeads followed by positive selection with CD11c MicroBeads. Total RNA was extracted from spleen cDC1 cells, reverse transcribed and labeled according to the instruction of Affymetrix WT Pico protocol

first: Lan

last: Zhou


title: Harvested primary hepatocytes exposed to either normoxia or hypoxia (1% O2)

city: Heidelberg

first: Ahmed

last: Sadik

address: Im Neunheimer Feld 280

department: Metabolic Crosstalk in Cancer

institute: DKFZ

summary: Hepatocytes endogenously express high levels of the enzyme tryptophan dehydrogenase (TDO2), in the current study we explore the effect of reduced oxygen on hepatocyte Tryptophan metabolism

overall_design: Primary hepatoctes were harvested from 8 to 12 week old wildtype C57BL/6 mice and taken into culture, following which they were either cultured under normoxic (19.5%) or hypoxic (1% O2) conditions for 72 hours before harvest for microarray analysis.

first: Soumya

last: Mohapatra

first: Christiane

last: Opitz


title: Transcriptome analysis of mercury chloride (HgCl2) treated H1299 human non-small cell lung carcinoma cells

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

summary:
Purpose:  finding differential transcripts usage in environmentally harzardous chemical, mercury chloride (HgCl2) in human non-small cell lung carcinoma cells
Methods: transcriptome analysis by the RNA-seq via mRNA pull-down
Results: We found that HgCl2 increases cellular toxicity by the increasing of apoptosis via caspase-3 independent pathway in H12999 cells. Also, over thounds of altered gene expression pattern were detected from the RNA-seq analysis.
Conclusions: mercury chloride (HgCl2) increases cytotoxic effects and apoptosis in H1299 cells through the caspase-3 independent pathway and changes the context of trascript

overall_design: H1299 cells were treated with various concentration of mercury chloride and all experiments were duplicated.


title: Expression Dataset of Ectopic expression of the TAp73 in Hep3B cells

city: Izmir

first: Mehmet

last: Ozturk

address: Dokuz Eylul University Health Campus

department: Izmir Biomedicine and Genome Center

country: Turkey

institute: Izmir Biomedicine and Genome Center

summary:
Hepatocyte dedifferentiation is a major source of hepatocellular carcinoma (HCC), but its mechanisms are unknown. We explored the p73 expression in HCC tumors and studied the effects of transcriptionally active p73 (TAp73) in HCC cells. Expression profiles of p73 and patient clinical data were collected from the Genomic Data Commons (GDC) data portal and the TSVdb database, respectively. Global gene expression profiles were determined by pan-genomic 54K microarrays. The Gene Set Enrichment Analysis was used to identify TAp73-regulated gene sets. The effects of TAp73 were analyzed in monolayer cell culture, 3D-tumoroid and xenograft models in zebrafish using western blot, flow cytometry, fluorescence imaging, real-time polymerase chain reaction (RT-PCR), immunohistochemistry and morphological examination. TAp73 was significantly upregulated in HCC, and its high expression indicated poor patient survival. The induced expression of TAp73 caused landscape expression changes including genes involved in growth signaling, cell cycle, stress response, immunity, metabolism and development. HCC cells overexpressing TAp73 had lost hepatocyte lineage biomarkers including ALB, CYP3A4, AFP, HNF4α. In contrast, TAp73 upregulated genes promoting cholangiocyte lineage such as YAP, JAG1 and ZO-1, accompanied with an increase in metastatic ability. Our findings strongly suggest that TAp73 is a major promoter of malignant dedifferentiation of HCC cells
Hepatocellular carcinoma (HCC) is a highly complex and heterogeneous type of cancer. Hepatocyte dedifferentiation is one of the important steps in the development of HCC. However, its molecular mechanisms are not well known. In this study, we report that TAp73 which is the major transcriptionally active form of p73 is overexpressed in HCC. Mechanically, TAp73 suppresses the expression of the hepatocyte markers including CYP3A4, AFP, ALB, HNF4a, while increasing the expression of several cholangiocyte markers in HCC cell lines. In conclusion, this report reveals a pro-oncogenic role for TAp73 in liver cancer.

overall_design: Cells were treated and/or untreated (control) with 1ug/ml doxyclline for 12h, 24h (duplicates) and 48h in triplicates

last: OZTURK

first: Evin

last: ISCAN


title: Exosome derived from liver humanized mice

first: Haiming

last: Cao

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

summary: HepaCur™serum from liver humanized FRG®KO mice was obtained from Yecuris and subsequently sent to System Biosciences for Exo-NGS exosomal RNA-sequencing. Exosome isolation and subsequent RNA-sequencing were performed by System Biosciences.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing profiles were generated for exosome derived from liver humanized mice.

first: Yu

last: Shi

first: Ping

last: Li

first: Cheng-fei

last: Jiang

first: Yi

last: Chen

first: Yonghe

last: Ma

first: Nikhil

last: Gupta

first: Xiangbo

last: Ruan


title: Nutrigenomic response to Omega-3 fatty acid in human primary hepatocytes

summary: Primary human hepatocytes were treated with 200µM DHA/EPA/OA or vehicle(ethanol) for 16 hours before cells were harvested for RNA extraction. Total RNA was isolated from primary human hepatocytes using KingFisher PURE RNA tissue Kit. The eluted RNA was subjected for strand specific sequencing libraries construction with illumina TruSeq RNA sample Prep Kit and subsequently sequenced by NHLBI DNA sequencing and Genomic Core using Illumina HiSeq 3000 paired-end sequencing platform.

overall_design: RNA sequencing profiles were generated for primary human hepatocytes treated with omega-3 fatty acids.


title: Pneumococcal colonization impairs nasal and lung mucosal immune responses to Live Attenuated Influenza Vaccination in adults

city: Liverpool

first: Jesús

last: Reiné

state: Merseyside

address: Pembroke Place

department: Clinical Sciences

country: United Kingdom

institute: Liverpool School of Tropical Medicine

summary:
Purpose: Influenza virus infections affect millions of people annually. Current available vaccines provide varying rates of protection. There is a knowledge gap on how the nasal microbiota, particularly established pneumococcal colonization, shapes the response to influenza vaccination.
Methods: In this study, we inoculated healthy adults with live S. pneumoniae and vaccinated them three days later with either TIV or LAIV. Vaccine-induced immune responses were assessed in nose, blood and lung.
Results: Nasal pneumococcal colonization had no impact upon TIV-induced antibody responses to influenza, which manifested in all compartments. However, pre-existing pneumococcal colonization dampened LAIV-mediated mucosal antibody responses, primarily IgA in the nose and IgG in the lung. Pulmonary influenza-specific cellular responses were more apparent in the LAIV group compared to either TIV or an unvaccinated group.
Conclusions: These results indicate that TIV and LAIV elicit differential immunity to adults and that LAIV immunogenicity is diminished by the nasal presence of S. pneumoniae. This important confounder should be considered when assessing LAIV efficacy.

overall_design: Healthy adults were inoculated with live S. pneumoniae and vaccinated three days later with either TIV or LAIV.

first: Beatriz

middle: F

last: Carniel

first: Fernando

last: Marcon

first: Jamie

last: Rylance

first: Seher

last: Zaidi

first: Edessa

last: Negera

first: Elissavet

last: Nikolaou

first: Sherin

last: Pojar

first: Carla

last: Solórzano

first: Andrea

last: Collins

first: Victoria

last: Connor

first: Debby

last: Bogaert

first: Stephen

middle: B

last: Gordon

first: Helder

last: Nakaya

first: Daniela

last: Ferreira

first: Simon

last: Jochems

first: Elena

last: Mitsi


title: The Transcriptomic Landscape in Asian Medulloblastomas

city: Cincinnati

first: Zaili

last: Luo

address: 3333 Burnet Ave.

institute: CCHMC

summary: We report the transcriptomic profiles of 59 Asian medulloblastoma and 4 normal tissues (para-tumor) including WNT, SHH, Group 3 and Group 4  medublastoma patients.

overall_design: RNA-seq of 64 Asian medulloblatoma turmor or para-tumor tissues

first: Xinran

last: Dong

first: Jianzhong

last: Yu

first: Yong

last: Xia

first: Wenhao

last: Zhou

first: Q

last: Lu


title: A genome-wide RNAi screen to identify human factors essential for SARS-CoV-2 infection

city: Hong Kong

first: Philip

last: Yeung

address: Queen Mary Hospital Compound, Pokfulam

country: Hong Kong

institute: The University of Hong Kong

summary: We performed high-throughput sequencing to identify virus-dependency factors that are targeted by shRNAs after challenged with SARS-CoV-2

overall_design: Identificaiton of enriched host factors-targeting shRNAs in SARS-CoV-2-infected cells when compared with that in mock-infected cells.

first: Man


title: RNA-seq analysis of SF3B2-depleted and pladienolide B-treated prostate cancer PC3 cells.

city: Ariake, Koto-ku, Tokyo

first: Kyoko

last: Matsumoto

department: Cancer Chemotherapy Center

institute: Japanese Foundation for Cancer Research

summary:
Purpose: Small interfering RNA (siRNA)-mediated knockdown of SF3B2, a component of U2 snRNP subcomplex in the spliceosome, suppresses innate immune gene expression. To examine whether pladienolide B, a pre-mRNA inhibitor, phenocopies SF3BP2 knockdown, we compared the RNA-seq profiles of SF3B2-depleted and pladienolide B-treated PC3 cells.
Method: Total RNAs were extracted from the cells and treated with DNase I. After RNA-seq libraries were constructed, next-generation sequencing and Differential Expressed Gene (DEG) analysis were performed. The library was sequenced on an Illumina NextSeq 6000 as paired-end 101 bp reads. The sequence reads were aligned to the GRCh38 reference genome using HISAT2 version 2.1.0, Bowtie2 2.3.5.1. All reads were assembled with StringTie software version 2.1.3b, using annotated genes from the NCBI database. Low quality transcripts are filtered. Afterwards, TMM Normalization are performed. Statistical analysis is performed using Fold Change, exactTest using edgeR per comparison pair. The significant results are selected on conditions of |fc|>=2 & exactTest raw p-value<0.05. DEG analysis was performed on 3 comparisons pairs using edgeR. The results showed 11,306 genes which satisfied |fc|>=2 & exactTest raw p-value<0.05 conditions in at least one of comparison pairs. For Enrichment test which based on Gene Ontology (GO) DB was conducted with significant gene list using g:Profiler tool.
Result: Gene signatures of SF3B2-depleted cells were compared with those of control siRNA-treated cells. GO analysis of the down-regulated genes in SF3B2-depleted cells identified GO terms related with innate immunity. Next, gene signatures of pladienolide B-treated cells were compared with those of DMSO-treated cells. GO analysis of genes altered in pladienolide B-treated cells identified GO terms related with RNA splicing. However, innate immunity-related GO terms were classified statistically not significant.
Conclusion: These observations indicate that SF3B2 knockdown and pladienolide B differentially affect the gene expression signature in PC3 cells.

first: Hiroyuki

last: Seimiya


title: Genome-wide analysis of differentially expressed miRNAs and their associated regulatory networks in lenses deficient for the congenital cataract-linked tudor domain containing protein TDRD7

city: Newark

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: Mutations/deficiency of TDRD7, which encodes a tudor domain containing protein involved in post-transcriptional gene expression control, causes early-onset cataract in humans and animal models.  While Tdrd7 is implicated in the control of key lens mRNAs, the impact of Tdrd7 deficiency on microRNAs (miRNAs), and how this contributes to cataracts, is undefined.  Here, we address this critical knowledge-gap by investigating Tdrd7-targeted knockout (Tdrd7-/-) mice that exhibit fully penetrant juvenile cataracts.  To gain global insights into miRNA profile alterations, we performed Affymetrix miRNA 3.0 microarray analysis on Tdrd7-/- mouse lenses at postnatal day (P) 4, because this stage precedes cataract formation and thus informs on early miRNA misexpression while minimizing detection of secondary changes.

overall_design: miRNA microarray comparision of lenses fromTdrd7 targeted germline knockout (KO) mouse line (Tdrd7tm1.1Chum, or Tdrd7-/-), and wild-type control

first: Salil

last: Lachke


title: Genomic characterization of well differentiated/dedifferentiated retroperitoneal liposarcoma

city: Milano

first: Stefano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

country: Italy

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

summary: An integrated profiling approach was performed to define molecular alterations associated to the aggressive behavior of retroperitoneal dedifferentiated liposarcoma. In particular, matched well and dedifferentiated components as well as normal adipose tissues, obtained from the same tumor sites, were comparatively investigated to higlight differences in gene expression.

overall_design: Gene expression of dedifferentiated, well differentiated and normal adipose tissue was generated using clarioms array

first: Valentina

last: Zuco


title: Epigenetic mechanisms mediating the transition from proliferating into hypertrophic chondrocytes. [RNA-Seq]

city: Essen

first: Manuela

last: Wuelling

address: Universitätsstrasse 2

department: Developmental Biology

institute: University Duisburg-Essen

summary: Correlation of RNA-seq and ChIP-seq data from proliferating (PC)  and hypertrophic chondrocytes (HC).

overall_design: RNA sequencing of proliferating and hypertrophic chondrocytes isolated by laser-microdissection from cryosections of E14.5 (PC) an dE15.5 (HC) mouse forelimbs.

first: Christoph

last: Neu

first: Andrea

last: Thiesen

first: Simo

last: Kitanowski

first: Yingying

last: Cao

first: Anja

last: Lange

first: Daniel

last: Hoffmann

last: Vortkamp


title: Epigenetic mechanisms mediating cell state transitions in chondrocytes.

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design:
Chromatin Immunopreciptiation followed by sequencing (ChIP-seq) of histone modifications H3K4me3, H3K9ac, H3K9me3, H3K27ac, H3K27me3 and H3K36me3 from primary proliferating (PC) and hypertrophic chondrocytes (HC) isolated from teh axial and appendicular skeleton of E13.5 and E15.5 embryonic mice (GSE155399).
RNA sequencing (RNA-seq) of proliferating and hypertrophic chondrocytes isolated by laser-microdissection from cryosections of E14.5 (PC) and E15.5 (HC) mouse forelimbs (GSE155400).


title: Epigenetic mechanisms mediating the transition from proliferating into hypertrophic chondrocytes. [ChIP-Seq]

summary: Chromatin Immunopreciptiation of histone modifications in primary proliferating (PC) and hypertrophic chondrocytes (HC) from embryonic mice

overall_design: Analysis of 5 different histone modifications in chondrocytes.


title: Whole-organ analysis of TGF-b-mediated remodelling of the tumour microenvironment

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

institute: Wakayama Medical University

summary: Tissue clearing technique may be one of the most powerful strategies for a comprehensive and unbiased analysis of disease progression. Here, we improved a tissue clearing protocol and explored its application in a mouse tumour model of experimental lung metastasis. We established an integrated pipeline for 3D profiling of the tumour microenvironment in combination with our new clearing protocol and machine learning. This pipeline distinguished each cellular component within the tumour microenvironment, and provided information on their spatial relationships. We further explored the role of TGF-b in the tumour microenvironment using this integrated pipeline. TGF-b-stimulated cancer cells enhanced metastatic colonization of unstimulated-cancer cells in vivo when both cells were mixed. RNA-sequencing analysis showed that expression of the genes related to coagulation and inflammation were up-regulated in TGF-b-stimulated cancer cells. Further, 3D profiling of the tumour microenvironments revealed accumulation of platelets or macrophages with TGF-b-stimulated cancer cells, suggesting that TGF-b might promote remodelling of the tumour microenvironment through the activation of these cellular components at the metastatic sites, which further enhances the colonization of cancer cells. Hence, an integrated pipeline that combines tissue clearing, 3D imaging, and machine learning will help further the understanding of the role of the tumour microenvironment.

overall_design: Target genes for TGF-b in A549 cells were identified.

first: Shimpei

last: I. Kubota

first: Kei

last: Takahashi

first: Tomoyuki

last: Mano

first: Katsuhiko

first: Takahiro

last: Katsumata

first: Shoi

last: Shi

first: Kazuki

last: Tainaka

first: Hiroki

last: R. Ueda

first: Kohei

last: Miyazono


title: Experimental competition induces immediate and lasting effects on the neurogenome in free-living female birds

city: Bloomington

first: Kimberly

last: Rosvall

state: IN

address: 1001 E Third Street

department: Biology

institute: Indiana University

type: Methylation profiling by high throughput sequencing

summary: Periods of social instability can elicit adaptive phenotypic plasticity to promote success in future competition. However, the underlying molecular mechanisms have primarily been studied in captive and lab-reared animals, leaving uncertainty as to how natural competition among free-living animals affects gene activity. Here, we experimentally generated social competition among wild, cavity-nesting female birds (tree swallows, Tachycineta bicolor). After territorial settlement, we reduced the availability of key breeding resources (i.e., nest boxes), generating heightened competition; within 24 hr we reversed the manipulation, causing aggressive interactions to subside. We sampled females during the peak of competition and 48hr after it ended, along with date-matched controls. We measured transcriptomic and epigenomic responses to competition in two socially relevant brain regions (hypothalamus and ventromedial telencephalon). Gene network analyses suggest that processes related to energy mobilization and social aggression (e.g., dopamine synthesis) were upregulated during competition, the latter of which persisted 2 days after competition had ended. Cellular maintenance processes were also downregulated after competition. Competition additionally altered methylation patterns, particularly in pathways related to hormonal signaling, which appeared transcriptionally poised to respond to future competition . Thus, experimental competition among free-living animals shifts gene expression in ways that may facilitate the demands of competition  at the expense of self-maintenance. Further, some of these effects persisted after competition ended, demonstrating the potential for epigenetic biological embedding of the social environment in ways that could “prime” individuals for success in future social instability.

overall_design: 2 tissues (ventromedial telencephalon and hypothalamus) were collected from 20 female tree swallows during peak competition (Day 0; n=6 experimental and n=5 controls) and two days after (Day 2; n=4 experimental and n=5 controls); total RNA and DNA were extracted and run on a Nextseq platform.

first: Alexandra

last: Bentz

first: Elizabeth

last: George

first: Sarah

middle: E

last: Wolf

first: Douglas

last: Rusch

first: Ram

last: Podicheti

first: Aaron

last: Buechlein

first: Kenneth

last: Nephew


title: Genetic and transcriptomic identification of sensory neuron types underlying chronic pain in primates

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: Molecular characterization of the individual neuron types existing in the primate dorsal root ganglion and the relation to model organisms used for studying somatosensation and pain is critical for understanding the cellular origin of chronic pain and for translational aspects of biomedical research. However, molecular insights into the primate dorsal root ganglion are missing and a systematic comparison of strategies for somatosensation between the mouse and primates is lacking. Here we classify non-human primate sensory neurons based on their transcriptome and identify neuronal types with heritability to chronic pain. We identify nine neuronal types and use machine learning to expose an overall cross-species conserved strategy and shared taxonomy for nociception, although with differences at individual gene level, highlighting the importance of incorporating primate knowledge for the successful translation of discoveries in rodent model organisms. Genomic loci implicated in chronic pain were mapped onto specific primate sensory neuron types to identify the cellular origin of chronic pain. The common-variant genome-wide association results for chronic pain point to the same cells at the same pain sites and concentrate on two different neuronal types between pain disorders, suggesting that causative cell types and molecular mechanisms are different between different pain conditions.

overall_design: 6-8 Lumbar DRGs, 3 pairs of the biggest and one pair of anterior/posterior (L3-L7) extracted from two female Rhesus monkeys

first: Dmitry

last: Usoskin

first: Jussi

last: Kupari

first: Daohua

last: Lou

first: Marc

last: Parisien

first: Yizhou

last: Hu

first: Michael

last: Fatt

first: Peter

last: Lönnerberg

first: Mats

last: Spångberg

first: Bengt

last: Eriksson

last: Kharchenko

first: Gunilla

last: Karlsson Hedestam

first: Karin

last: Loré

first: Samar

last: Khoury

first: Luda

last: Diatchenko

first: Patrik

last: Ernfors


title: ALTERED DUODENAL MUCOSAL MITOCHONDRIAL GENE EXPRESSION IS ASSOCIATED WITH DELAYED GASTRIC EMPTYING IN DIABETIC GASTROENTEROPATHY

city: Rochester

first: Daniel

middle: Rothschild

last: OBrien

state: MN

address: 200 First St. SW

institute: The Mayo Clinic

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Refer to individual Series


title: ALTERED DUODENAL MUCOSAL MITOCHONDRIAL GENE EXPRESSION IS ASSOCIATED WITH DELAYED GASTRIC EMPTYING IN DIABETIC GASTROENTEROPATHY [miRNA-Seq]

summary:
Introduction. Hindered by a limited understanding of the molecular mechanisms responsible for diabetic gastroenteropathy (DGE), patients are managed by symptom-based therapies.  We investigated the duodenal mucosal expression of protein-coding genes and miRNAs in DGE and related these abnormalities to clinical features.
Methods. mRNA and micro RNA (miRNA) expression and ultrastructure of duodenal mucosal biopsies were investigated in 39 DGE patients and 21 healthy controls. Results were analyzed in the context of diabetic phenotype and gastric emptying.
Results. There were 3175 differentially-expressed genes (FDR<0.05), especially mitochondrial genes, in DGE versus controls.  Several mitochondrial (mt) DNA-encoded genes (12 of 13 protein coding genes mainly involved in oxidative phosphorylation (OXPHOS), both rRNAs and 9 of 22 tRNAs) were downregulated; conversely, nuclear (n) DNA-encoded mitochondrial genes (eg, OXPHOS, TCA cycle) were upregulated in DGE.  Motif analysis uncovered binding sites for transcription factors NRF1, GABPA and YY1, which regulate mitochondrial biogenesis, in the promoters of differentially expressed genes.  Seventeen of 30 differentially expressed miRNAs in DGE targeted differentially expressed mitochondrial genes.  Mitochondrial density was also reduced and correlated with the expression of 9 mt-DNA OXPHOS genes in DGE.  Uncovered by a principal component (PC) analysis of OXPHOS genes, PC1 was significantly associated with neuropathy (P = 0.01) and with delayed gastric emptying (P < 0.05).
Conclusion. In DGE, mtDNA- and nDNA-encoded mitochondrial genes are reduced and increased, respectively, associated with reduced mitochondrial density, neuropathy, and delayed gastric emptying, and correlated with cognate miRNA expression.  Together, these findings provide substantial evidence for clinically-relevant mitochondrial disturbances in DGE.

overall_design: Comparison of gene expression by RNA sequencing in the duodenal mucosa of patients with DM and healthy controls

first: Susrutha

last: Puthanmadhom Narayanan

first: Anshuman

last: Desai

last: O'Brien

first: Karl

last: Miller

first: Adil

last: Bharucha


title: CD36 ko and WT CD8 T Cells

city: Houston

first: xingzhe

last: ma

state: TX

address: 6565 fannin street

department: cancer center

institute: houston methodist hospital

summary: To investigate the role of cd36 on CD8 T cells,we did RNAseq to find the difference between CD36 ko and WT CD8 T Cells

overall_design:
endogenous B16 tumor infiltrating CD36 KO cd8 t cells and WT cd8 T cells
8_S25* samples (Sample 1-4) are wt cd8 t cells.


title: Transcriptome sequencing of in vivo cervical tissue revealed lncRNA-miRNA-mRNA co-regulatory functions in cervical cancer of Uygur women

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Background: Non-coding RNA has been shown to participate in numerous biological and pathological processes and has attracted increasing attention in recent years. Recent studies have demonstrated that long non-coding RNA and microRNA can interact through various mechanisms to regulate mRNA. Yet the gene-gene interaction has not been investigated in cervical cancer of Uygur woman. High throughput sequencing were used to identify differentially expressed lncRNA, miRNA, and mRNA profiles between normal, cervical intraepithelial neoplasia and cervix carcinoma tissues. Gene Oncology (GO), KEGG enrichment analysis were performed. Gene co-expression network were constructed and pivotal genes were screened out. A total of 1464 lncRNAs were differentially expressed between normal, cervical intraepithelial neoplasia and cervical cancer tissues. GO and KEGG analysis show that related molecular mechanisms and biological processes play a role in cervical cancer. The gene-gene interaction network was constructed and visualized based on Pearson correlation coefficients and TargetScan prediction. These results have shown the potential of lncRNA, miRNA, and mRNA as clinical biomarkers and in elucidating pathological mechanisms of cervical cancer from a transcriptomic perspective.

overall_design: Cervical cancer (Iia stage), Cervical intraepithelial neoplasia (stage III), and cervicitis tissues were obtained with three biological replicates. RNA-seq experiment was performed for these samples and bioinformatics analysis was performed for the sequencing data.

first: Cailing

last: Ma

first: Yi

last: Zhang


title: Differential gene expression analysis in liver, inguinal white adipose tissue (iWAT), skeletal muscle, and hypothalamus of mice with liver-specific Crif1 deficiency

city: Daejeon

first: Minho

last: Shong

address: 282, Munhwa-ro

institute: Chungnam National University

summary: CR6-interacting factor-1 (CRIF1) interacting with large mitoribosome subunits is essential for the maturation and insertion of oxidative phosphorylation (OxPhos) polypeptides into the mitochondrial inner membrane. Recently, it has reported that the genetic ablation of Crif1 in a tissue-specific manner results in mitochondrial stress response (MSR) including mitochondrial unfolded protein response (UPRmt). In this study, we aim to obtain a comprehensive understanding of systemic energy metabolism in response to hepatic mitochondrial dysfunction. Through the liver-specific Crif1 deficient mice (LKO), we explore the adaptive response not only in the liver but also in inguinal white adipose tissue (iWAT). Moreover, RNA sequencing in liver, iWAT, skeletal muscle, and hypothalamus suggest that hepatic mitochondrial dysfunction enhance metabolic pathways, including glycolysis, fatty acid elongation and degradation, and 1C metabolism in liver and insulin signaling in iWAT. RNA sequencing also suggests that hepato-mitokines, GDF15 and FGF21 are highly increased in liver of LKO mice. To identify the role of hepato-mitokines, we generate double knockout mice (LKO/Gdf15-/- and LKO/Fgf21-/-), suggesting that GDF15 is responsible for the regulation of the body and fat mass and FGF21 has a critical role for the insulin sensitivity and energy expenditure in this mice.

overall_design: RNA was isolated from liver, inguinal adipose tissue (iWAT), skeletal muscle, and hypothalamus of control (Ctrl) and liver-specific Crif1 deficient mice (LKO) fed a chow diet at 8 weeks old of age (n = 3 each per group).

first: Seulgi

last: Kang


title: Transcriptome profile of Bbs8/TTC8 Knockout mouse RPE Tissue

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem


title: Transcriptional analysis of naïve and central memory CD4 and CD8 T cells from healthy subjects treated with IL-27

city: Montréal

first: Nathalie

last: Arbour

state: Quebec

address: 900 Saint Denis Street

department: Neuroscience

country: Canada

institute: CHUM-University of Montreal

summary:
To examine the broad impact of IL-27 on human T lymphocytes, we performed a microarray analysis assessing >20,000 well annotated genes on purified naïve (CD45RA+CD45RO-CCR7+) and central memory (CD45RA-CD45RO+CCR7+) CD4+ and CD8+ T cells from three healthy donors that were activated in vitro (plate bound anti-CD3 and soluble anti-CD28) in the presence or absence of human recombinant IL-27 (100 ng/mL).
Our goal was to investigate the impact of interleukin-27 on the gene expression profil of human CD4 and CD8 T lymphocytes.

overall_design: Naive and central memory CD4 and CD8 T cells from 3 healthy donors were sorted and then stimulated for 3 days with αCD3-αCD28 in the presence or not of IL-27 (100 ng/mL). RNA was purified and transcriptome-wide analysis of gene expression was performed by Genome Québec using the Clariom S HT array.

first: M

last: Clénet

first: N


title: miR-21 plays a dual role in tumor formation and cytotoxic response in breast tumors

city: Philadelphia

first: Anuradha

last: Shastri

state: Pennsylvania

address: 233 S 10th Street

institute: Thomas Jefferson University

summary:
Breast cancer (BrCa) relies on specific microRNAs to drive disease progression. Oncogenic miR-21 is upregulated in many cancers including BrCa and is associated with poor survival and treatment resistance. We sought to determine the role of miR-21 in BrCa tumor initiation, progression and treatment response. In a triple-negative BrCA model, radiation exposure increased miR-21 in both primary tumor and metastases. In vitro, miR-21 knockdown decreased survival in all BrCa subtypes in presence of radiation. The role of miR-21 to BrCa initiation was evaluated by implanting wild-type miR-21 BrCa cells into genetically-engineered mouse models where miR-21 was intact, heterozygous or globally ablated. Tumors were unable to grow in mammary fat pads of miR-21-/- mice, grew in ~50% of miR-21+/- and 100% in miR-21+/+ mice. The contribution of miR-21 in progression and metastases was tested by crossing miR-21-/- mice with mice that spontaneously develop BrCa. Global ablation of miR-21 significantly decreased tumorigenesis and metastases of BrCa while sensitizing tumors to radio- and chemotherapeutic agents by a Fas/FasL-dependent apoptosis. Therefore, targeting miR-21 alone or in combination with various radio or cytotoxic therapies may represent novel and efficacious therapeutic modalities for the future treatment of BrCa patients.
We used microarray to identify gene expression associated with miR-21 function in breast development and metastasis.

overall_design: We analyzed miR-21+/+;MMTV-PyMT(WT) and miR-21-/-;MMTV-PyMT(KO) tumors with or without radiation treatment (RT) using Affymetrix gene expression array

first: Ajay

last: Palagani

first: Tu

last: Dan

first: Simone

last: Buraschi

first: Thomas

last: Neill

first: Jason

last: Savage

first: Aastha

last: Kapoor

first: Tiziana

last: DeAngelis

first: Sankar

last: Addya

first: Kevin

last: Camphausen

first: Renato

last: Iozzo

first: Nicole

last: Simone


title: Transcriptome profile of Bbs8/TTC8 Knockout mouse RPE Tissue [P29]

summary: To analyse gene expression differences between Wildtype and Bbs8 knockout mouse RPE tissues at two different developmental times points.

overall_design: Total RNA was extracted from n=4 Bbs8 Knock out mice and n=4 wild type mice (litter mate controls) at P29.

first: R

first: S

last: Schneider

first: H

last: May-Simera


title: ALTERED DUODENAL MUCOSAL MITOCHONDRIAL GENE EXPRESSION IS ASSOCIATED WITH DELAYED GASTRIC EMPTYING IN DIABETIC GASTROENTEROPATHY [mRNA-Seq]

first: Daniel

last: OBrien

first: Susrutha

last: Puthanmadhom Narayanan

first: Anshuman

last: Desai

last: O'Brien

first: Karl

last: Miller

first: Adil

last: Bharucha


title: Transcriptome profile of Bbs8/TTC8 Knockout mouse RPE Tissue [P11]

first: Rossella

last: De Cegli

overall_design: Total RNA was extracted from n=4 Bbs8 Knock out mice and n=4 wild type mice (litter mate controls) at P11.


title: Myeloma-modified 3T3-L1 adipocytes exhibit aberrant gene expression profiles [experiment 1]

city: Northfield

first: Heather

middle: Elizabeth

last: Driscoll

state: VT

address: 158 Harmon Drive

institute: Norwich University

summary:
Herein we compare mouse 3T3-L1 adipocyte gene expression after 7 days of adipogenic differentiation with and without exposure to MM.1S myeloma cells.
Microarray analysis was used to compare adipogenic gene expression either following exposure to MM.1S cells prior to differentiation (48h) or after differentiation (72h).

overall_design: Total RNA from 10 3T3-L1 adipocyte samples was extracted via Qiagen RNeasy Kit and run on Affymetrix® ClariomTM S Arrays. This dataset includes the 5 samples in the pre-exposure experiment.

last: Campbell

first: Michaela

last: Reagan


title: Myeloma-modified adipocytes exhibit a senescent-associated secretory phenotype

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: Bone marrow -adipocytes (BMAs) have recently been implicated in accelerating bone metastatic cancers such as AML and breast cancer. Importantly, bone marrow adipose tissue (BMAT) expands with aging and obesity- two key risk factors in multiple myeloma (MM) disease prevalence- suggesting that BMAs influence and are influenced by myeloma cells in the marrow. Here we examined how myeloma cells affect adipocytes and provide evidence that MM cells alter adipocyte gene expression and cytokine secretion profiles, creating a “MM-associated” adipocyte (MM-adipocyte) phenotype. Our findings indicate that: (1) Multiple myeloma cells decrease BM adiposity in vitro, in myeloma animal models, and in clinical samples, (2) myeloma induces widespread gene expression and phenotypic changes in adipocytes in vitro, most notable, the induction of a senescent-like phenotype in BMAs, (3) MM-adipocytes affect myeloma cell cycle, drug sensitivity, and aggressiveness, illuminating a new driver of MM cell evolution in a drug resistant clone. We demonstrate that myeloma cells exposed to MM-adipocytes are rescued from dexamethasone-induced cell cycle arrest and have increased expression of FKBP5, a potential drug resistance gene. Our findings in patients confirm that BMAs are dynamic during myeloma disease progression (decrease during MM initiation, recover during disease remission) and that the interactions between BMAs and MM cells have previously unappreciated implications in the understanding and treatment of myeloma.

overall_design: Primary human mesenchymal stromal cells (MSCs) were isolated from bone marrow samples received from deidentified male and female donors after total hip arthroplasty. MSCs were isolated by surface adherence, and seeded into 6-well plates at a density of 150,000 cells/well and grown until 80-90% confluent. To generate bone marrow adipocytes (BMAs), MSCs were differentiated for 21 days in hMSC adipogenic media consisting of DMEM/F12 supplemented with FBS, antibiotic/antimycotic, 500 µM IBMX, 50 µM indomethacin, 1 µM dexamethasone, and 1 µM insulin. After 21 days, cells were washed and myeloma cells (OPM-2, MM.1S, and RPMI-8226) were added via transwell co-culture (0.4 µm pores) at a density of 500,000 cells/well in RPMI-1640 media containing FBS and antibiotic/antimycotic for 72 hours. Following co-culture the individual cell types were then pooled (n=2 wells) prior to RNA extraction.

first: Andre

middle: J

last: van Wijnen

first: Amel

last: Dudakovic


title: CircRNA circTIAM1 promotes papillary thyroid cancer progression through the miR-646/HNRNPA1 signaling pathway

status: Public on Mar 09 2021

city: Hangzhou

first: Junjie

last: Chu

state: Zhejiang

address: 3 East Qingchun Road

department: Sir RUN RUN Shaw Hospital

institute: Zhejiang University

summary: Papillary thyroid cancer (PTC) is a common endocrine tumor with rapidly increasing incidence in recent years. Although the majority of PTC are relatively indolen and have a good prognosis, it still has a certain proportion of PTC which is highly aggressive with lymphatic metastasis, iodine resistance and easy to recur. Circular RNAs as an class of noncoding RNAs are linked to a variety of tumor processes including PTC. In the current study, a circRNA deep sequencing was performed to identify alterations in circRNA expression levels of PTC tissues. CircTIAM1 was then selected as its increased expression in PTC and associated with migration, apoptosis and proliferation of PTC in vivo and in vitro. Mechanistically, circTIAM1 acted as a sponge of miR-646 and functioned in PTC through targeting mir-646 and HNRNPA1. Fluorescence in situ hybridization (FISH) and luciferase reporter assays further conﬁrmed these connerctions. Overall, our results reveal an important oncogenic role of circTIAM1 in PTC and provide a potentially effective therapeutic strategy for PTC progression.

overall_design: To generate a circRNA profiling database, three pairs of representative PTC and paracarcinoma tissues（T） were selected for circular RNA microarray analysis.

first: Deguang

last: Zhang

first: Liang

last: Fang

first: Jian

last: Chen


title: LncRNA APTR promotes uterine leiomyoma cell proliferation by targeting ERα to activate the Wnt/β-catenin pathway

city: shanghai

first: Yongli

address: No.2699 Gaokexi Road, Shanghai

department: Obstetrics and Gynecology

institute: Shanghai First Maternity and Infant Hospital

summary: The molecular mechanisms by which uterine leiomyoma (UL) cells proliferate are unclear. Long noncoding RNA (lncRNA) is reported to participate in the occurrence and development of gynecological cancers. We investigated the molecular mechanisms that lncRNA uses in UL. We found that lncRNA Alu-mediated p21 transcriptional regulator (APTR) showed higher expression in UL tumor tissues compared with that in normal uterine tissues. APTR induced cell proliferation and colony formation both in vitro and in vivo. The JASPAR database showed that APTR was likely interacted with ERα, and these molecules were identified via laser scanning confocal microscopy and RNA immunoprecipitation analysis. To verify the correlation between APTR and ERα, we overexpressed and underexpressed APTR and simultaneously expressed ERα. The results showed that APTR function was suppressed. APTR increased the expressions of the proteins in the Wnt pathway, and inhibiting ERα eliminated these responses. In conclusion, our data suggest that APTR promoted leiomyoma cell proliferation through the Wnt pathway by targeting ERα, suggesting a new role of APTR in the Wnt signaling pathway in UL.

overall_design: Three patients were included in the study, and UL tumor tissue and adjacent normal uterine tissue specimens were acquired at the follicular phase. Inclusion criteria for this study were patients who (a) were nonmenopausal, (b) had undergone a hysterectomy because of UL between 12/2016 and 08/2017, (c) were without medical complications, and (d) had no history of hormone therapy.

first: Weiqiang

last: Zhou

first: Guocheng

last: Wang

first: Bilan

last: Li

last: Qu


title: Phosphorylation state of the histone variant H2A.X controls human stem and progenitor cell fate decisions

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

institute: McMaster University

summary: Stem cell fate decisions are tightly regulated by several processes, including epigenetic based histone modifications. Histone variants (HVs) represent a subfamily of epigenetic regulators implicated in early embryonic development, but their role in stem cell fate control has not been targeted. Here we reveal direct involvement of phosphorylation state of the histone variant H2A.X that allows control of self-renewal and differentiation of human pluripotent stem cells (hPSCs) and leukemic patient derived progenitors. Reduced levels of γH2A.X using either genetic approaches or chemical targeting allowed enhanced hPSC differentiation toward the mesodermal (hematopoietic) lineage with concomitant inhibition of ectodermal (neural) development. In contrast, activation and sustained levels of phosphorylated H2A.X enhanced hPSC ectodermal fate while suppressing mesodermal derived hematopoiesis. This controlled bifurcation of neural vs. hematopoietic differentiation correlated to occupancy of γH2A.X at gene loci associated with lineage selection. Drug modulation of H2A.X phosphorylation was extended to somatic cells to reveal the ability to induce differentiation of leukemic progenitors and serve as a biomarker in a cohort of adult leukemic patients. Our study uncovers a mechanism of cell-fate control of hPSCs extended to neoplastic progenitors through a histone variant epigenetic regulation

overall_design: Examination of H2A.X phosphorylation on human embryonic stem cells before and after lineage specific differentiation. Sample were sequenced in 2 back to back Hiseq runs 100% cover paired- end,  using 4 different lines  (about 31.5M clusters per sample).

first: Luca

last: Orlando

first: Borko

last: Tanasijevic

first: Mio

last: Nakanishi


title: Addition-elimination mechanism activated nucleotide transition sequencing for RNA dynamics profiling

city: Xi’an, Shaanxi

first: Feng

address: Xi’an Jiaotong University, Xianning West Road, Xi’an, Shaanxi, P. R. China

institute: Xi’an Jiaotong University,

summary: The temporal information of intracellular transcripts is essential to understand their functional roles, yet routine RNA-seq methods only measure RNA species at a steady state. Here we develop addition-elimination mechanism activated nucleotide transition sequencing (AENT-seq) for transcriptome-wide profiling of RNA dynamics. In AENT-seq, intracellular transcripts are metabolically labeled with 4-thiouridine (4sU), and then isolated total RNA are subjected to 4sU-to-cytosine (C) transition reactions based on a mild addition-elimination chemistry. N2H4•H2O is demonstrated to convert 4sU to 4-hydrazino cytosine (C*) in RNA-friendly aqueous conditions. The C* is recorded as natural C during extension reactions with a high efficiency of ~95%. This 4sU-to-C transition marks 4sU-containing nascent transcripts, and it enables subsequent sequencing analysis of RNA dynamics with single-nucleotide resolution. We applies our AENT-seq to simply investigate transcript dynamic information of several genes involved in cancer progression and metastasis. This method avoids harsh chemical conditions and harmful reagents involved in previous approaches, allowing rapid dissemination and extensive applications of the technique.

overall_design: Next generation sequencing (NGS) provided the numbers and locations of 4sU-to-C (T-to-C) transition in the mapping reads of mRNA transcripts

first: Li

last: Su


title: OCI-AML5-Cas9 EKO chemogenomic CRISPR screen

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

summary: Identify genes that show synthetic lethal and synthetic recue interactions with chemical compounds

overall_design: OCI-AML5-Cas9 EKO library cells were treated with compounds (UM171 and Dexamethasone) and DMSO as control for 14 days. Cells were pelleted every 2 days and DNA was extracted. ID sequences of the sgRNAs were amplified by PCR and the products were sent for sequencing in Illumina NextSeq 500

first: Laura

last: Simon

first: Jalila

last: Chagraoui

first: Jean-François

last: Spinella

first: Thierry

last: Bertomeu


title: Transglutaminase Type 2 regulates the Wnt/β-catenin pathway in vertebrates

city: Rome

first: Mauro

last: Piacentini

address: via della ricerca scientifica 1

department: Department of Biology

institute: University of Rome Tor Vergata

summary: In this study we analyzed the effect of TG2 on the modulation of gene expression by defining its effects on the cellular mRNA profile. To address this point we analyzed, by RNA seq, the effect of TG2 on the overall transcriptome after heat shock treatment. The data obtained reveal that TG2 markedly influences the overall cellular transcriptome profile and specifically the Wnt and HSF1 pathways. In particular, its ablation leads to a drastic downregulation of many key members of both these pathways.  We found that key components of the Wnt/β-catenin pathway are also downregulated in cells lacking HSF1, thus confirming that TG2 regulates the HSF1 and this axis controls the Wnt signaling.

overall_design: Analysis of the effect of TG2 on the overall transcriptome in basal condition and after activation of the heat shock response

first: Federica

last: Rossin

first: Roberto

last: Costa

first: Matteo

last: Bordi

first: Manuela

last: D’Eletto

last: Occhigrossi

first: Maria

last: Farrace

first: Nickolai

last: Barlev

first: Fabiola

last: Ciccosanti

first: Silvia

last: Muccioli

first: Leonardo

last: Chieregato

first: ldiko

last: Szabo

first: Gian

last: Fimia

first: Luigi

last: Leanza


title: Gene expression profiling of granulocytes from primary and secondary myelofibrosis

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

summary: Primary myelofibrosis (PMF) together with polycythemia vera (PV) and essential thrombocythemia (ET) belongs to the classic Philadelphia-negative myeloproliferative neoplasms (MPNs). PV and ET can evolve to secondary myelofibrosis (SMF) giving rise to post-PV (PPV) and post-ET (PET) myelofibrosis (MF). PMF and SMF patients are currently managed in the same way and prediction of survival is based on the same prognostic models, even if it has been demonstrated that they can’t accurately distinguish different risk categories in SMF. In the last few years interest grew concerning the ability of gene expression profiling (GEP) to provide valuable prognostic information for clinical decision making. To construct a molecular signature that can predict survival according to gene expression we studied GEP of granulocytes from 114 MF patients, including 35 prefibrotic/early PMF (Pre-PMF), 37 overt PMF (Overt-PMF), 26 PET and 16 PPV, using microarray platform.

overall_design: Granulocytes were isolated from 114 MF patients (35 prefibrotic/early PMF, 37 overt PMF, 26 PET and 16 PPV) and total cellular RNA was extracted. GEP was performed using Affymetrix platform and data were processed by means of Partek Genomics Suite Software.

first: Sebastiano

last: Rontauroli

first: Sara

last: Castellano

first: Paola

last: Guglielmelli

first: Roberta

last: Zini

first: Elisa

last: Bianchi

first: Elena

last: Genovese

first: Chiara

last: Carretta

first: Sandra

last: Parenti

first: Sebastian

last: Fantini

first: Selene

last: Mallia

first: Lara

last: Tavernari

first: Stefano

last: Sartini

first: Carmela

last: Mannarelli

first: Francesca

last: Gesullo

first: Annalisa

last: Pacilli

first: Daniela

last: Pietra

last: Rumi

last: Salmoiraghi

first: Barbara

last: Mora

first: Laura

last: Villani

first: Vittorio

last: Rosti

first: Giovanni

last: Barosi

first: Francesco

last: Passamonti

first: Alessandro

last: Rambaldi

first: Luca

last: Malcovati

first: Mario

last: Cazzola

first: Enrico

last: Tagliafico

last: Vannucchi


title: OCI-AML1-Cas9 EKO chemogenomic CRISPR screen

first: Guy

last: Sauvageau

overall_design: OCI-AML1-Cas9 EKO library cells were treated with compounds UM171 and DMSO as control for 14 days. Cells were pelleted every 2 days and DNA was extracted. ID sequences of the sgRNAs were amplified by PCR and the products were sent for sequencing in Illumina Nextseq500

last: Simon

first: Jalila

last: Chagraoui

first: Jean-François

last: Spinella

first: Thierry

last: Bertomeu


city: lanzhou

last: wang

address: No 204 Donggang West Road, Lanzhou city, Gansu province, China

institute: Lanzhou University

summary:
Exploring differentially expressed miRNAs (DEmiRNAs) in plasma sample between lung adenocarcinoma patients and healthy people using a small RNA (sRNA) sequencing,results showed that we could used these DEmiRNAs identified could discriminate healthy peoples from lung adenocarcinoma  patients.
In present study, we applied an RNA sequencing (RNA-seq) approach to explore the differentially expressed miRNAs (DEmiRNAs) in plasma sample between 6 lung adenocarcinoma patients and 4 healthy people.

overall_design: The miRNAs profiles of plasma sample between lung adenocarcinoma patients and healthy people

first: Xiao-Jun

last: Wang

first: Qin

last: Yu

first: Jing

last: Gao


title: RNA sequencing analysis of in vitro-derived early spinal cord progenitors

city: Napoli

first: Ilaria

last: Granata

address: Via Pietro Catellino, 111

department: Institute for high performance computing and networking (ICAR)

institute: National Research Council of Italy (CNR)

summary: human embryonic stem cells (hESCs) were treated with WNT and FGF agonists to generate NMP-like cells (D3) which were then subsequently treated with WNT and high levels of FGF signalling to produce early spinal cord progenitors (D7 of differentiation)

overall_design: Gene expression profiling utilised total RNA extracted from hECS cells (N=3); D3 axial progenitors (N=3); D7 spinal cord progenitors (N=3)

first: Anestis

last: Tsakiridis

first: Ichcha

last: Manipur


title: Mitophagy related expression profiling by high throughput sequencing for human induced pluripotent stem cells (iPSCs) derived astrocytes

city: Bergen

first: Kristina Xiao

last: Liang

state: Hordaland

address: Jonas Lies vei 87, P. O. Box 7804

country: Norway

institute: University of Bergen

summary: The pupose of this study is to explore the mitophagy related transcriptome profiling of the astrocytes differentiated from POLG patient iPSCs compared to the astrocytes generated from healthy control iPSCs.

overall_design:
Examination of mRNA profile in iPSC-derived astrocytes.
Note from submitter:  Human raw sequencing data (e.g.FASTQ) cannot be made publicly available due to their sensitive nature, as dictated by Norwegian law. This data can be made available on the basis of reasonable request and following permission from our Regional Ethics Committee (REC).

first: Kristina

middle: X

first: Anbin

last: Chen


title: USP7 CRISPR knock-out in T-ALL cells [Molt4_CRISPR_RNA-seq]

city: Memphis

first: Timothy

last: Shaw

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

summary: RNAseq analysis of USP7 CRISPR KO in T-ALL cell lines. Genetically modified T-ALL cells were generated using CRISPR-Cas9 technology.  Briefly, the sgRNA was designed with at least 3bp of mismatch to any other site in the human genome to mitigate the risk of off-target editing. To generate the modified cells, 400,000 cells were transiently co-transfected with / without 0.5 ug pmaxGFP plasmid (Lonza), with 33 pmol spCas9 protein, 100 pmol chemically modified sgRNA (Synthego), and 100 pmol of blocking ssODN (IDT) via nucleofection (Lonza), using solutions and programs according to the manufacturer’s recommended protocol. Five days post-nucleofection, cells were single-cell sorted by FACs into 96-well plates. Cells were clonally expanded and verified the desired modification via targeted deep sequencing

overall_design: Partial CRISPR KO of USP7 in Molt4 (n = 2); 100% CRISPR KO of USP7 in Molt4 (n = 2); Wild-type Molt4 (n = 1);

middle: I

first: Dong

last: Li

first: Jinghui

last: Zhang


title: CNV analysis of normal brain and glioma samples II

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

country: France

institute: GReD CNRS

summary: In human, the 39 coding HOX genes and 18 referenced non-coding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression-, DNA methylation- and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative "master" HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.

overall_design: copy-number assay has been performed using the Genome-Wide Human CytoScan HD Array (Affymetrix, CA, USA). DNA and array processing were performed by the Genomic Platform/ Curie Institute (France) according to the manufacturer's protocol.

first: Franck

last: Court

first: Philippe

last: Arnaud


title: Expression analysis of gene expression chang in Homo sapiens Esophageal squamous cell carcinoma cells KYSE30  after knock down MTA2 gene

city: Shijiazhuang,Hebei,China

first: Suli

last: Dai

address: No. 12 Jiankang Road, Shijiazhuang, Hebei

institute: The Fourth Hospital of Hebei Medical University

summary: Investigation of whole genome gene expression level changes in  Homo sapiens Esophageal squamous cell carcinoma cells KYSE30   after knock down of MTA2 gene expression

overall_design: A six chip study using total RNA extracted from  KYSE30 cells transfected with siRNA negative control and KYSE30 cells knock down of MTA2 with siRNA . Each chip measures the expression level of 34.558 genes  collected from the authoritative data source including NCBI

first: Dai

last: Suli


title: USP7 shRNA knock-down in T-ALL cells [Jurkat_HSB2_shRNA_RNA-seq]

summary: RNAseq analysis of USP7 shRNA KD in T-ALL cell lines. USP7 shRNAs lentivirus was generated by co-transfecting 293T cells with shRNA vectors (OriGene or Sigma). T-ALL cells were transduced with USP7 shRNA lentivirus and sorted for GFP positive cells five days after transduction or selected by puromycin.

overall_design: USP7 shRNA in Jurkat (n = 4); shRNA scramble in Jurkat (n = 2); Wild-type Jurkat (n = 2); USP7 shRNA in HSB-2 (n = 4); shRNA scramble in HSB-2 (n = 2); Wild-type HSB-2 (n = 2)


title: Heterozygous and Homozygous Knock-Out of USP7 mouse models [mouse_RNA-seq]

summary: RNAseq analysis of USP7 conditional knock-out (cKO) mice. They were designed to flox exon 6 of USP7 and to allow deletion of exon 6 upon expression of Cre recombinase 27. USP7FL/FL mice were bred with Vav1-Cre mice to obtain USP7FL/wt-Vav1-Cre mice (heterozygote). USP7FL/FL-Vav1-Cre mice (homozygote) were obtained via breeding of heterozygous cKO mice.

overall_design: Single allele KO (n = 3), bi-allelic KO (n = 3), wild-type with cre-induced (n = 2), wild-type without cre-induction (n = 2)


title: Adult High Grade B-cell Lymphoma with Burkitt Lymphoma Signature: Genomic features and Potential Therapeutic Targets

city: Omaha

first: Javeed

last: Iqbal

state: NE

address: 601 S 42nd St

institute: UNMC

summary: Gene expression profiling of RNA and SNP array profiling of DNA was performed on Burkitt lymphoma samples to identify genes and pathways affected by DNA copy number alterations and expression changes.

overall_design: Affymetrix 250K NspI SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved lymphoma tumor specimens.  Affymetrix U133 plus 2.0 array were performed according to the manufacturer's directions on RNA extracted from cryopreserved lymphoma tumor specimens.

first: Wing

middle: C

last: Chan


title: Dnmt1 deletion in Hmx3-positive POA-derived interneurons

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

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

overall_design: Refer to individual Series


title: Copy-number profiling by SNP array of 4 acute myeloid leukemia (AML) cell lines

city: Freiburg

first: Gabriele

last: Greve

address: Hugstetter Str 55

department: Department of Internal Medicine 1

institute: University of Freiburg Medical Center

summary: DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's protocol on DNA extracted from the cultured AML cell lines UCSD-AML1, ELF-153, KG-1 and U937.

first: Dietmar

last: Pfeifer


title: Dnmt1 deletion in Hmx3-positive POA-derived interneurons [MeDIP-seq]

summary: The proliferative niches in the subpallium generate a rich cellular variety fated for diverse telencephalic regions. The embryonic preoptic area (POA) represents one of these domains giving rise to the pool of cortical GABAergic interneurons and glial cells, in addition to striatal and residual POA cells. The migration from sites of origin within the subpallium to the distant targets like the cerebral cortex, accomplished by the adoption and maintenance of a particular migratory morphology, is a critical step during interneuron development, which seems to be regulated partially via DNA methylation-dependent gene expression. To identify genes that are altered by DNA methylation mediated by DNMT1 in POA-derived Hmx3-positive interneurons, we used an Hmx3-Cre/tdTomato/Dnmt1loxP mouse model and FAC-sorted the basal telencephalon at E16. RNA and MeDIP sequencing were performed. MeDIP data are assigned here.

overall_design: 4 samples in total; 2 biological replicates per WT and KO condition; cells were pooled from 12 individual wild type embryos and 6 individual knockout embryos.

first: Daniel

last: Pensold

first: Anne

last: Hahn

first: Thomas

last: Lingner

last: Salinas-Riester

first: Bryan

last: Downie

first: Fabian

last: Ludewig

first: Judit

last: Symmank

first: Nico

last: Andreas

first: Katrin

last: Schubert

first: Tomas

last: Pieler

first: Geraldine

last: Zimmer


title: Global transcriptomic profiling of microcystin-LR or -RR treated hepatocytes (HepaRG)

city: Durham

first: Weichun

last: Huang

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US EPA

summary: Microcystins (MC) are toxins found in harmful algal blooms.  The canonical MC mode of action (MOA) is the inhibition of protein phosphatases, but complete characterization of its toxicity pathway has yet to be identified.  The existence of 100s of MC structural congeners further complicates risk estimates.  This work employed RNA-seq to provide an unbiased and comprehensive characterization of cellular targets and impacted cellular processes of hepatocytes exposed to either MC-LR or MC-RR congeners. The human hepatocyte cell line, HepaRG, was treated with three concentrations of MC-LR or RR (1000, 100, 10 g/L) for two hours.  Significant reduction in cell survival was observed in the LR1000 and LR100 treatments.  RNA-seq was performed on the control groups and all concentrations of MC-LR and -RR and differentially expressed genes (DEGs) were identified.  Genes and pathways associated with oxidative and endoplasmic reticulum stress, and the unfolded protein response (UPR) were highly enriched by both congeners.  Enrichment of inflammatory pathways was also evident.  In the cytotoxic LR1000 treatment, apoptotic pathways and related genes were identified, suggesting cells pursue both inflammation and apoptosis simultaneously and that cellular fate may be determined by the activation kinetics of jun N-terminal kinase (JNK).  We present a model of MC toxicity where MCs cause the production of ROS and oxidative stress leading to ER stress and activation of the UPR.  Under non-cytotoxic conditions this leads to an inflammatory and pro-survival cellular response mediated through up-regulation and activation of NF- and its inhibition of JNK.  With acute MC exposure, increased ER stress results in the cellular program switching to favor apoptosis by inhibiting NF- resulting in sustained JNK activation and through the activation of C/EBP homologous protein (CHOP) via the protein kinase RNA-like endoplasmic reticulum kinase (PERK) arm of the UPR

overall_design: One control and total six treatment groups (three MC-LR groups at three different concentrations, and three corresponding MC-RR groups), each having multiple replicates from three experimental batches

first: Adam

middle: D

last: Biales

first: David

last: Bencic

first: Robert

last: Flick

first: Armah

middle: A

last: Delacruz

first: Denise

last: Gordon


title: Gene expression data of serially sorted primary AML patient blasts prior and after treatment with the DNMT inhibitor decitabine (DAC)

first: Gabriele

last: Greve

summary: DNMT inhibitors (DNMTi) are finally approved for AML/MDS, also based on their activity in patients with high-risk cytogenetics (often monosomal karyotype) such as -5/del(5q) or -7/del(7q), often - but not always - harboring TP53-mutations. Several studies provided evidence for aberrant hypermethylation/silencing on monoallelic gene loci, including tumor suppressor genes. We hypothesized that transcriptional repression on monosomal gene loci may be preferentially reversed by DNMTi. Using an unbiased RNA-seq approach we aimed to identify preferentially regulated genes in cells monoallelic for chromosome 7q. We validated these findings in serially sorted primary AML patient blasts at day 0 and day 8 of DNMTi treatment (within the DECIDER trial).

overall_design: Affymetrix HTA 2.0 expression arrays were performed in technical triplicates (duplicates for samples 02_d8, 04_d0, 17_d0 and 17_d8),  on primary AML blast of 14 patients at day 0 and day 8 of decitabine treatment

first: Nadja

last: Blagitko-Dorfs

first: Dietmar

last: Pfeifer

first: Olga

last: Grishina

first: Michael

last: Lübbert


title: Simultaneous Inhibition of LSD1 and TGF-β Enables Eradication of Poorly Immunogenic Tumors with anti-PD-1 Treatment

city: Hangzhou

first: Wanqiang

last: Sheng

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

summary: Epigenetic regulators are a class of promising targets in the combination with immune checkpoint inhibitors for cancer treatment, but the impact of the broad effects of perturbing epigenetic regulators on tumor immunotherapy remains to be fully explored. Here we show that ablation of the histone demethylase LSD1 in multiple tumor cells induces TGF-β expression, which exerts an inhibitory effect on T cell immunity through suppressing the cytotoxicity of intratumoral CD8+ T cells and consequently dampens the antitumor effect of LSD1 ablation-induced T cell infiltration. Importantly, concurrent depletion of LSD1 and TGF-β in combination with PD-1 blockade significantly increases both CD8+ T cell infiltration and cytotoxicity, leading to eradication of poorly immunogenic tumors and a long-term protection from tumor re-challenge. Thus, combining LSD1 inhibition with blockade of TGF-β and PD-1 may represent a promising triple combination therapy for treating certain refractory tumors.

overall_design: B16 tumors of different genetic settings (scramble, Lsd1 KO, Tgfb TKO and Lsd1/Tgfb QKO) were implanted to wild-type mice for 14 days. Tumors were harvested and tumor-infiltrating lymphocytes were enriched, then subjected to CD8+ T cells isolation by microbeads and positive selection. Afterwards, CD3+CD8+ cells were sorted by FACS. Total RNA was extracted and subjected to polyA+ RNA purification, before used for making library. The prepared libraries were sequenced at 150bp from both ends.

first: Yang

last: Shi


title: Dnmt1 deletion in Hmx3-positive POA-derived interneurons [RNA-seq]

first: Gabriela

last: Salinas

summary: The proliferative niches in the subpallium generate a rich cellular variety fated for diverse telencephalic regions. The embryonic preoptic area (POA) represents one of these domains giving rise to the pool of cortical GABAergic interneurons and glial cells, in addition to striatal and residual POA cells. The migration from sites of origin within the subpallium to the distant targets like the cerebral cortex, accomplished by the adoption and maintenance of a particular migratory morphology, is a critical step during interneuron development, which seems to be regulated partially via DNA methylation-dependent gene expression. To identify genes that are altered by DNA methylation mediated by DNMT1 in POA-derived Hmx3-positive interneurons, we used an Hmx3-Cre/tdTomato/Dnmt1loxP mouse model and FAC-sorted the basal telencephalon at E16. RNA and MeDIP sequencing were performed. RNA data are assigned here.

first: Daniel

last: Pensold

first: Anne

last: Hahn

first: Thomas

last: Lingner

last: Salinas-Riester

first: Bryan

last: Downie

first: Fabian

last: Ludewig

first: Judit

last: Symmank

first: Nico

last: Andreas


title: Heterochromatin lossening by Oct4 in somatic cell reprogramming

city: Guangzhou

first: Keshi

last: Chen

address: 190 Kai Yuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Science

summary: The success of Yamanaka factor reprogramming mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs) suggests that some factor(s) must remodel the nuclei from a condensed state to a relaxed state to facilitate factor binding to target genes. We asked how the Yamanaka factor-dependent chromatin opening occurs. We found Oct4, but neither Sox2 nor Klf4, is responsible for the loosening of the condensed state. Oct4 acts as a pioneer factor that facilitates the binding of Klf4 and the expression of epithelial genes in the early stage of reprogramming.

overall_design: Examination of chromatin status in 9 samples and a Flag control

first: Xingguo

last: Liu


title: Transcriptome profiling by RNA-sequencing of the AML cell lines UCSD-AML1 and ELF-153.

first: Gabriele

last: Greve

overall_design: The AML cell lines UCSD-AML1 and ELF-153 were treated with decitabine (DAC) in technical triplicates for 4 consecutive days (with daily change of media and DAC add-on). Cells were harvested and RNA was isolated after 96 hours and after 144 hours, Fragment Analyzer QC confirmed RIN values ≥9.7.  rRNA was removed and strand-specific libraries of each replicate were sequenced on an Illumina HiSeq 2500 with approximately 33 million reads per sample.

first: Björn

last: Grüning

first: Ulrike

last: Bönisch

last: Peifer


title: Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [CRISPR]

status: Public on Mar 08 2021

city: Shanghai

first: donghong

last: Cai

address: Yueyang Street

institute: PICB, CAS

summary: Aging changes global transcriptome including protein-coding and noncoding RNAs. Whether aging dependent lncRNAs undergo conserved regulation and function still remain unknown. We report aging dependent lncRNAs carry signature of evolutionary constraint and significantly enriched for targets of transcription factors and RNA binding proteins. Aging dependent lncRNAs is conservatively under NFκB pathway regulation. CRISPR screening for NFκB pathway found that aging dependent lncRNAs also extensively regulate NFκB pathway. The human LINC02085 is an evolutionary conserved lncRNA that can be traced to 29Mya before human. LINC02085 is induced during aging, inflammation and senescence through NFκB pathway. Reciprocally, LINC02085 directly regulates NFKBIZ in cis within same topological associated domain (TAD). LINC02085 binds to enhancer of NFKBIZ and recruits RELA to the NFKBIZ promoters and participates phase separation. These findings reveal that aging dependent lncRNAs are previously under-appreciated contributors to the evolutionary conservation and regulation of NFκB pathway.

overall_design: The CRISPR screening of aging dependent lncRNA in NFκB pathway

first: Donghong

first: Jing-Dong

last: Han


title: Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling


title: Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [RNA]

summary: Aging changes global transcriptome including protein-coding and noncoding RNAs. Whether aging dependent lncRNAs undergo conserved regulation and function still remain unknown. We report aging dependent lncRNAs carry signature of evolutionary constraint and significantly enriched for targets of transcription factors and RNA binding proteins. Aging dependent lncRNAs is conservatively under NFκB pathway regulation. CRISPR screening for NFκB pathway found that aging dependent lncRNAs also extensively regulate NFκB pathway. The human NFKBMARL-1 is an evolutionary conserved lncRNA that can be traced to 29Mya before human. NFKBMARL-1 is induced during aging, inflammation and senescence through NFκB pathway. Reciprocally, NFKBMARL-1 directly regulates NFKBIZ in cis within same topological associated domain (TAD). NFKBMARL-1 binds to enhancer of NFKBIZ and recruits RELA to the NFKBIZ promoters and participates phase separation. These findings reveal that aging dependent lncRNAs are previously under-appreciated contributors to the evolutionary conservation and regulation of NFκB pathway.

overall_design: The ribo- strand specific RNA-seq for NFKBMARL-1 ASO knock down in IMR90


title: Aging-associated lncRNAs carry evolutionary constraints and participate in NFκB signaling [ChIRP]

overall_design: The ChIRP-seq of NFKBMARL-1 in IMR90


title: Disulfiram mediated modulation of lung immune response during M. tuberculosis infection

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

summary: Methionine biosynthetic pathway, essential for the growth of Mycobacterium tuberculosis (Mtb) in the host, represents an attractive target for the development of novel anti-tuberculars. Here, we have biochemically characterized homoserine acetyl transferase (HSAT viz. MetA) of Mtb, which catalyses the first committed step of methionine and S-adenosylmethionine (SAM) biosynthesis. High-throughput screening of a 2300 compound library resulted in identification of thiram, an anti-fungal organosulfur compound, as the most potent MetA inhibitor. Further analysis of thiram analogs led to the identification of orally bioavailable disulfiram (DIS, an anti-alcoholism FDA approved drug) as a novel inhibitor of MetA. Both thiram and DIS restricted the growth of drug-sensitive and drug-resistant Mtb strains in a bactericidal manner. ThermoFlour assay demonstrated direct binding of DIS with MetA. Metabolomic and transcriptomic studies showed DIS mediated perturbation of methionine and redox homeostasis, respectively, in Mtb. In concordance, the effect of DIS on Mtb growth was partially rescued by supplementation with either L-methionine as well as N-acetyl cysteine, suggesting a multi-target killing mechanism. In Mtb-infected mice, DIS administration restricted bacterial growth, increased efficacy of isoniazid, ameliorated lung pathology,  modulated lung immune cell landscape and protective immune response. Taken together, our results demonstrate that DIS can be repurposed for designing an effective anti-tubercular therapy.

overall_design: To elucidate the effect of disulfiram on tuberculosis pathogenesis lungs from uninfected or Mtb-infected mice treated or not with disulfiram were processed for RNA isolation and transcriptomic analysis (using RNAseq). Drug treatment was started at day 7 post-infection and animals were sacrificed at 21 and 35 days post infection. Untreated mice  - day zero (D0)

first: Mardiana

last: Marzuki

first: Andrea

last: Lee

first: Josephine

last: Lum

first: Bernett

first: Amit

last: Singhal


title: De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives

city: Olsztyn

first: Maciej

last: Florczyk

address: Słoneczna 45G

country: Poland

institute: University of Warmia and Mazury in Olsztyn

summary: Microcystin-LR (MC-LR) is a potent hepatotoxin for which a substantial gap in knowledge persists regarding the underlying molecular mechanisms of liver toxicity and injury. Although long non-coding RNAs (lncRNAs) have been extensively studied in model organisms, our knowledge concerning the role of lncRNAs in liver injury is limited. Given that lncRNAs show low levels of sequence conservation, their role becomes even more unclear in non-model organisms without an annotated genome, like whitefish (Coregonus lavaretus). The objective of this study was to discover and profile aberrantly expressed polyadenylated lncRNAs that are involved in MC-LR-induced liver injury in whitefish. Using RNA sequencing (RNA-Seq) data, we de novo assembled a high-quality whitefish liver transcriptome. This enabled us to find 94 differentially expressed (DE) putative evolutionary conserved lncRNAs, such as MALAT1, HOTTIP, HOTAIR or HULC, and 4429 DE putative novel whitefish lncRNAs, which differed from annotated protein-coding transcripts (PCTs) in terms of minimum free energy, guanine-cytosine (GC) base-pair content and length. Additionally, we identified DE non-coding transcripts that might be 3′ autonomous untranslated regions (3′UTRs) of mRNAs. We found both evolutionary conserved lncRNAs as well as novel whitefish lncRNAs that could serve as biomarkers of liver injury.

overall_design: A total number of 52 individuals from the RNA-Seq of the whole project were used in order to assemble the reference transcriptome. However, 13 individuals from the project were used to assess MC-LR effects on expression of non-coding transcripts using RNA-Seq. RNA-Seq included four control samples (PBS_1d). Each treatment group (the dose of MC-LR 100 μg·kg−1 of body mass) included three individuals.

first: Paweł

last: Brzuzan

last: Woźny