title: Triptolide Targets Super-Enhancer Networks in Pancreatic Cancer Cells and Cancer Associated Fibroblasts

city: Allen

first: Wei

last: Lin

state: TX

address: 1525 Evanvale Dr.

institute: Translational Genomics Research Institute

summary: This study invesitgated the super-enhancer (SE) networks in pancreatic cancer cells and cancer associated fibroblasts (CAFs) as well as the effects of triptolide treatment on the SEs and the expression of the SE associated genes using ChIP-Seq and RNA-Seq.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: A panel of pancreatic cancer cell lines and cancer associated fibroblasts (CAFs) were profiled for super-enhancer (SE) activities using H3K27ac based ChIP-Seq analysis. RNA-seq analysis was also performed on the same cell lines to profile the expression of SE associated genes. Selected cell lines were treated with triptolide and profiled for SE changes using ChIP-seq and/or gene expression changes using RNA-seq.  The effects on the RNA expression profiled was compared to those of the  CDK7 inhibitor THZ1 (known to disrupt super-enhancers).

first: Shaimaa

last: Husein

first: Pawan

last: Noel

first: Yin

first: Haiyong

last: Han


title: Regulation of male fertility and accessory gland gene expression by the Drosophila DHR39 nuclear receptor

status: Public on Jan 01 2021

city: Salt Lake City

first: Carl

middle: S

last: Thummel

state: UTAH

address: 15 North 2030 East, Room 5200, University of Utah, Department of Human Genetics

department: Human Genetics

country: USA

institute: University of Utah

type: Expression profiling by high throughput sequencing

summary: Here we show that the Drosophila nuclear receptor DHR39 is necessary for male reproduction and acts as a global regulator of accessory gland gene expression. Mutants for the DHR39 transcription factor are sterile, with the majority of accessory gland genes expressed at reduced levels. Specific depletion of DHR39 within the accessory gland is sufficient to reduce male fecundity and accessory gland gene expression. Restoration of DHR39 in the accessory gland of DHR39 mutants rescues this sterility and transcriptional reduction. We conclude that DHR39 is a key regulator of most accessory gland genes, including ovulin and sex peptide, and is necessary for male fertility.

overall_design:
Comparison of mRNA levels in control and DHR39 mutant animals. n=3-5 replicates per genotype

**Please note that the control samples from GSE152031 are re-used in the current study and duplicated sample records are created for the convenient retrieval of the complete raw data from SRA.

first: Sophia

middle: A

last: Praggastis


title: RNA-binding protein RBM3 negatively regulates innate lymphoid cells (ILCs) and lung inflammation

city: San Diego

first: Taylor

last: Doherty

state: CA

address: 9500 Gilman Dr. 0678 La Jolla

department: Department of Medicine

institute: UC San Diego

summary: Innate lymphoid cells (ILCs) promote lung inflammation in diseases such as asthma through cytokine production.  RNA-binding proteins (RBPs) are critical post-transcriptional regulators of cellular function though the role of RBPs in innate lymphoid cells is unknown.  Here, we demonstrate that RNA-binding motif 3 protein (RBM3) is one of the most highly expressed RBPs in Thy1.2+ lung ILCs after fungal allergen challenge and is further induced by epithelial cytokines TSLP and IL-33 in both human and mouse ILCs.   Single (rbm3-/-) and double (rbm3-/-rag2-/-) knockout mice exposed via the airway to the asthma-associated fungal allergen Alternaria alternata displayed increases in eosinophilic lung inflammation and ILC activation compared to control mice.  In addition to increased Th2 cytokine production, rbm3-/- ILCs produced elevated IL-17A.  The negative regulation by RBM3 in ILC responses was direct as purified rbm3-/- ILCs were hyperinflammatory in vitro and in vivo after stimulation with IL-33.  Transcriptomic analysis by RNA-sequencing of rbm3-/- lung ILCs showed increased type 2 and 17 cytokines as well as global expression differences in critical cytokines, receptors, transcription factors, and survival transcripts compared with WT ILCs.  Importantly, these transcript changes were independent of the numbers of AU-rich elements (AREs) which RBM3 is known to bind.  Thus, regulation of ILC responses by RNA-binding proteins offers novel mechanistic insight into lung ILC biology and ILC-driven inflammatory diseases.

overall_design: RNA-seq for Lin-Thy1.2+ Innate Lymphoid Cells (ILC) from WT and rbm3 KO mice. WT and RBM3KO mice were challenged with 25µg Alternaria Alternata 3 times over 7 days. WT and RBM3KO ILCs were sorted with the BD FACSAria II or the BD FACSAria Fusion at the UCSD Human Embryonic Stem Cell Core Facility. Lin-Thy1.2+ ILCs were sorted directly into TrizolLS.

first: Jana

middle: H

last: Badrani

first: Monalisa

last: Mondal

first: Gregory

last: Seumois


title: Transcriptomic study of C4-2 prostate cancer cells under the treatment of direct HSF1 inhibitor DTHIB (E12)

city: Durham

first: Bushu

last: Dong

state: NC

address: 308 Research Dr.

department: Biochemistry

institute: Duke University

summary: This is a RNA-Seq analysis aiming to study the transcriptomic changes of C4-2 prostate cancer cells induced by HSF1 inhibitor DTHIB (E12)

overall_design: mRNA transcriptomic profile of C4-2 prostate cancer cells under the treatment of direct HSF1 inhibitor DTHIB (E12)

first: Dennis

middle: J

last: Thiele


title: Single-cell RNA sequencing of golden hamster upper respiratory tract (nasal mucosa and trachea), lung, kidney and small intestine

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

summary:
Full understanding of the pathophysiology of COVID-19 is critical for adequate treatment and development of vaccine and therapeutics. Although Golden hamster has been emerged as animal model of COVID-19, it is unknown how SARS-CoV-2 enters and infects targeted epithelial cells at molecular and cellular levels. Here, by applying single cell RNA sequencing in the upper respiratory tract, lung, kidney and intestine of golden hamster, we show that the expression profiles of host factors for SARS-CoV-2 infection in specific cell types are similar to that of human.
These data can be applied to a larger investigation (data not provided here) into the expression patterns of host cell entry factors of SARS-CoV-2 in golden hamster organs.

overall_design: To investigate the expression patterns of host cell entry factors of SARS-CoV-2 in golden hamster organs. Single cells from dedicated organs were isolated and single-cell transcriptome libraries were generated.

first: Gou

middle: Y

last: Koh

first: Myung


title: Host transcriptional analysis to improve the diagnosis of group A streptococcal pharyngitis.

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Current diagnostic methods used to evaluate patients with pharyngitis for the presence of group A Streptococcus (GAS) do not discriminate between acute infection and asymptomatic carriage, potentially resulting in overuse of antibiotics. Host response as measured by the transcriptomic profile of peripheral blood leukocytes could make this distinction, and could also distinguish between GAS and viral infection. We used RNA sequencing to generate transcriptomes from whole blood samples from 37 children, including 10 with acute GAS pharyngitis, 5 asymptomatic GAS carriers, 3 with adenoviral pharyngitis, 3 with pharyngitis of unknown etiology, and 16 asymptomatic children negative for GAS. Transcriptional profiles from each group were distinct . 1357  genes were upregulated in the children with symptomatic GAS compared to those with asymptomatic carriage. A panel of 13 genes distinguished between children with acute GAS and all others with 91% accuracy. The gene encoding CD177, a marker of neutrophil activation, was markedly overexpressed  in children with acute GAS and has potential as a diagnostic biomarker. We conclude that measurement of host response is highly promising to improve the diagnosis of GAS pharyngitis and could help limit unnecessary antibiotic use.

overall_design: A total of 37 subjects were included in the RNA-seq transcriptional analysis, of which 10 cases were with group A Streptococcus (GAS) infection, 3 cases with adenovirus infection, 3 other cases with pharyngitis by other cause, 5 controls with GAS colonized, 3 controls with positive of non-adenovirus, and 13 controls with negative of viruses tested. We comparied the GAS cases with controls and with all other subjects in terms of transcriptional changes.

first: Eric

last: Tycksen

first: Thomas

last: Mariani

first: Ann

last: Falsey

first: Soumyaroop

last: Bhattacharya

last: Storch


title: single cell RNA sequencing of hematopoietic stem cells aged in old and young niches

city: los angeles

first: Du

last: Jiang

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

summary:
Purpose: Compare the transcriptome of hematopoietic stem cells (HSCs) that were aged in old and young niches
Methods: barcoded GFP+ HSCs were FACS-sorted from a) three recipient mice 15 months post transplantation, and b) six serial transplantation recipient mice 5 months after the 8th transplantation, then subjected to processed using the Chromium Single-cell 3′ v2 Library Kit (10× Genomics, Pleasanton, CA) following the manufacturer’s instructions
Results: we obtained transcriptomes of about 12k HSCs aged in young niche, and about 10k HSCs aged in old niche, with the average sequencing depth at close to 50k reads per cell
Conclusions: we identified striking differences in gene expression profiles 1) between HSCs aged in young niches from mice with early aging and from mice with delayed aging, and 2) between HSCs aged in old niches and young niches  when mice exhibited hematopoietic aging phenotype

overall_design: single cell gene expression profiles of individual HSCs were generated from different aging onsets

first: Anna

last: Nogalska


title: Expression data of microRNA from human stem cells from apical papilla

city: Jinan

first: Junqing

last: Liu

address: No.44-1 Wenhua Road West

country: China

institute: Shandong University

summary:
Osteo/odontogenic differentiation is a key process of human stem cells from apical papilla (SCAP) in tooth root development. Emerging evidence indicates microRNAs (miRNAs) play diverse roles in osteogenesis. However, their functions in osteo/odontogenic differentiation of SCAP remain to be elucidated.
We used miRNA microarray to analysis differentially expressed miRNAs in order to investigate the role of miRNAs in SCAP osteo/odontogenic differentiation and underlying mechanism.

overall_design: Stem cells from apical papilla of human immature third molar were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous stem cells from apical papilla (SCAP) at each osteogenic differentiation stage in order to increase the temporal resolution of expression profiles. To that end, we selected SCAP at two time-points: before osteogenic differentiation (c) and osteogenic differentiation for 7 days (k).Biological replicates: 3 control replicates (1c, 2c, 3c), 3 testing replicates (1k, 2k, 3k).

first: Yan

last: Wang

first: Jing

last: Du


title: Elevated ETV6 expression in glioma promotes an aggressive in vitro phenotype associated with shorter patient survival

city: Shanghai

first: Fengjiao

last: LI

address: 131 Dong'an Rd., Xuhui District

institute: Fudan University

summary:
Purpose
It has been postulated that glioblastoma (GBM) has the ability to hijack neural progenitor migration mechanisms to facilitate tumor progression. Our previous data show that ETS variant 6 (ETV6) is highly expressed in human GBM and fetal astrocytes compared to normal mature astrocytes. We hypothesized that ETV6 played a role in GBM tumor progression.
Methods
Expression of ETV6 was first examined in 2 American and 3 Chinese tissue microarrays. The correlation between ETV6 staining intensity and patient survival was calculated, followed by validation using public databases-TCGA and REMBRANDT. The effect of ETV6 knockdown on glioma cell proliferation (EdU), viability (AnnexinV labeling), clonogenic growth (colony formation), and migration/invasion (transwell assays) in GBM cells was tested. RNA sequencing was performed to ellucidate the underlying molecular mechanisms.
Results
ETV6 was highly expressed in GBM and associated with an unfavorable prognosis. ETV6 silencing in glioma cells led to increased apoptosis and decreased proliferation, clonogenicity, migration, and invasion. RNA-Seq based gene expression and pathway analyses revealed that ETV6 knockdown in U251 cells led to the upregulation of genes involved in extracellular matrix organization, NF-κB signaling, TNFmediated signaling and downregulation of genes in regulation of cell motility, cell proliferation, PI3KAKT and Ras pathways.
Conclusion
Our findings suggested that ETV6 was highly expressed in GBM and its high expression correlated with poor survival. ETV6 silencing decreased an aggressive in vitro phenotype. The study encourages further investigation of ETV6 as a potential therapeutic target of GBM.

overall_design: Glioblastoma (GBM) was postulated to have the ability to hijack neural progenitor migration programs to promote tumor progression. Our previous data show that ETS variant 6 (ETV6) is highly expressed in human GBM and fetal astrocytes compared to normal mature astrocytes. We hypothesized a role of ETV6 in GBM tumor progression and investigated it in three aspects. First, the expression of ETV6 was examined in 2 American and 3 Chinese tissue microarrays including totally 192 glioma samples to reveal positive correlation of ETV6 expression with glioma WHO grade and inversed correlation with patient survival. This finding was consolidated by similar correlation in public databases-TCGA and REMBRANDT with totally 1071 glioma samples. Second, the effect of ETV6 knockdown on GBM cellular behaviors such as proliferation, apoptosis, clonogenic growth, migration and invasion was tested in three GBM cell lines. The results showed ETV6 silencing led to increased apoptosis and decreased proliferation, clonogenicity, migration and invasion. At last, RNA-Seq based gene expression and pathway analyses were performed to reveal that the in vitro ETV6-dependent GBM phenotype may partially due to PI3K-AKT and Ras signaling, which is consistent with the effect of ETV6-NTRK3 oncogenic fusion on the two pathways. Our study encourages further investigation of ETV6 as a potential therapeutic target of GBM.

first: Shuai

last: Wu

first: Feng-jiao

last: Li

first: Chen

last: Luo

first: Qiu-yan

last: Jin

first: Ian

middle: D

last: Connolly

first: Melanie

last: Gephart

first: Linya

last: You


title: Expression data from DMSO- and ATRA-treated human multiple myeloma (MM) cells

city: Houston

first: Qiang

state: Texas

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

summary:
All-trans retinoic acid (ATRA) is important for sensitizing MM cells to carfilzomib (Cfz). To determine what signalling pathways are affected by ATRA in Cfz-treated MM cells, MM.1S MM cell line was pulsed with Cfz and then cultured with DMSO or 10µM ATRA for 12 h. Total RNAs of 2 x 106 MM.1S cells were extracted by RNeasy Mini Kit (Qiagen). 5-10 µg RNA samples were sent to Gene Expression and Genotyping Facility at Case Western Reserve University (Cleveland, OH) for genearray followed by data analysis.
We use microarray data to determine differential expression of genes in Cfz-treated MM cells in culture with DMSO and ATRA.

overall_design: Examination of gene-profiling data in DMSO- and ATRA-treated MM cells after treatment with Cfz.


title: Expression data from Head and neck squamous cell carcinoma cell lines cell line Cal27 after TCF19 knockout mediated by CRISPR/CAS9

city: Nanjing

first: Xiaoyu

last: Wei

state: Jiangsu

address: 101 Longmian Avenue, Nanjing, Jiangsu 211166, P.R. China

institute: Nanjing Medical University

summary: The deletion of TCF19 in CAL27,oral squamous cell carcinoma cell line,was conducted by using CRISPR/Cas9 system. For WT and TCF19 KO CAL27 cell lines, samples were done in triplicates. A total of 3μg of high-quality RNA per sample was used for ribosomal RNA removal by the Epicentre Ribo-zero rRNA Removal Kit (Epicentre, USA) and the sequencing library was prepared using the rRNA-depleted RNA by the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, San Diego, CA, USA), followed by the 150-bp paired-end sequencing on the HiSeq X Ten instrument (Illumina, San Diego, CA, USA) according to the manufacturer’s protocols.

overall_design: TCF19 may act as a putative head and neck squamous cell carcinoma susceptibility gene in our previous in vitro study. This in vivo study was designed to confirm the role of TCF19 and explore some more detail function in head and neck squamous cell carcinoma .Cells mRNA profiles of  WT and TCF19 KO CAL27 cell lines were provided.

first: Hongxia

last: Ma


title: THC prevents mortality from ARDS through induction of immune cell apoptosis

city: Columbia

first: Mitzi

last: Nagarkatti

state: SC

address: 6439 Garners Ferry Rd

department: PMI

institute: University of South Carolina School of Medicine

summary: We used 10X Genomic and NextSeq sequencer to identify dysregulated genes in single cell suspension isolated from lungs of SEB-induced ARDS mice treated with vehicle or THC.

overall_design: Single cell suspension was isolated from lungs of SEB-induced ARDS mice treated with vehicle or THC at the peak of the disease, 72 hours post Staphylococcal enterotoxin-B exposure.

first: Amira

last: Mohammed

first: Kathryn

last: Miranda

first: Kiesha

last: Wilson

first: Prakash


title: RNA-Seq expression analysis of chronic asthmatic mice with Bu-Shen-Yi-Qi formula treatment and prediction of regulated gene targets of anti-airway remodeling

first: Jie

last: Cui

address: 12 Middle Urumqi Road, Shanghai

institute: HuaShan Hospital, Fudan University

summary: Airway remodeling is one of the typical pathological characteristics of asthma. While, the structural changes of the airways in asthma are complex, which impedes the development of novel asthma targeted therapy. Our previous study have shown that Bu-Shen-Yi-Qi formula (BSYQF) could ameliorate airway remodeling in chronic asthmatic mice by modulating airway inflammation and oxidative stress in the lung. To further explore the molecular mechanism of BSYQF, in this study we analyzed the lung transcriptome of control, asthma mice with/without BSYQF treatment. Using RNA-sequencing analysis, we found that BSYQF treatment completely or partial reversed a group of genes that induced expression changes in asthma. Additionally, based on previous result we identified 21 differential expression genes (DEGs). Then through inputting 21 DEGs into Ingenuity Pathway Analysis (IPA) database to construct gene network, we inferred Adipoq, SPP1 and TNC which are located at critical nodes in the network, may be key regulators of BSYQF's anti-remodeling effect. Our results provide a preliminary clue to the molecular mechanism of anti-remodeling of BSYQF in asthma.

overall_design: In this study we analyzed the lung transcriptome of control, asthma mice with/without BSYQF treatment.

first: Zexi

last: Lv

first: Ying

first: Jingcheng

last: Dong


title: Effect of XCT790 on Aortic Valves (AV) in NOTCH1 (N1)-Haploinsufficient Mice

city: San Francisco

first: Christina

last: Theodoris

state: California

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

summary: RNA-seq on aortic valves from WT vs N1-haploinsufficient telomere-shortened (generation 2 Terc-/-) mice with either healthy AVs or AV stenosis treated with control solvent or XCT790

middle: V

first: Casey

last: Gifford

first: Deepak

last: Srivastava


title: Drosophila E78A nuclear receptor regulates intestinal dietary triacylglyceride uptake and systemic lipid levels

first: Carl

last: Thummel

summary: Here we show that the Drosophila nuclear receptor E78A regulates transcription in adult animals facilitating dietary lipid uptake. E78A mutant adults are viable with normal developmental timing, locomotor activity, female fecundity, but have significantly reduced stored triglycerides. This reduction in whole body triglyceride stores appears to originate from the midgut, using neutral lipid stainings we determined lipid levels in the midgut were greatly reduced. Upon examining our RNA-seq analysis we found that a gastric lipase, CG17192, is transcriptionally coordinated by E78A. CG17192 is expressed in an adult, intestinal specific fashion within control flies, and has a human ortholog. Through dietary supplementation and genetic testing we determined that the whole body hypolipidemia seen within E78A mutants is dependent on CG17192 expression within the intestine. Restoration of this lipase in the intestine of mutant flies is sufficient to restore normal lipid levels. Our data support the model that E78A contributes to a transcriptional regulation of the gastric lipase, CG17192, thus directing dietary triglyceride uptake in the adult fly.

overall_design: Comparison of mRNA levels in control and E78A mutant animals. n=4-5 replicates per genotype

first: Sophia

last: Praggastis


title: Novel Rare Copy Number Variants Associated with Tetralogy of Fallot in the Han Chinese Population

city: Tianjin

first: huanxin

last: chen

address: No.61, third avenue, tianjin economic and technolo

institute: Teda International Cardiovascular Hospital

summary: Tetralogy of Fallot (TOF), the most frequent cyanotic congenital heart disease, occurs as a simplex trait of unknown etiology in the majority of cases. Studies of non-Asian populations suggest that approximately 10% of TOF cases carry a de novo rare copy number variant (CNV) thought to underlie the malformation. A genome-wide CNV analysis was performed in 303 TOF and 302 controls of Han Chinese as well as compared to 1,000 common Chinese database and revealed 166 rare CNVs identified in TOF patients with 119 CNVs further evaluated as potential “TOF-specific CNVs”; 98 were validated by qPCR, and 44 CNVs showed positive results on validation (positive rate 46.9%, 44/98).  The genes related to the clinical phenotypes (subpulmonary VSD, bicuspid pulmonary valve, aortic valve overriding more than 75%, and right aortic arch) and the specific CNVs were included in integrating gene-gene interaction network analysis that identified the genes covering the specific CNVs directly or indirectly correlated to TOF and the signaling pathways.  Thus, this study identified novel TOF-specific/associate CNVs in the Han Chinese that occurring at higher frequency in the Han Chinese (28.4% in Chr 1-20 and 42.9% in all chromosomes) is reflective of the increased prevalence of TOF in China.  These novel CNVs identify new candidate genes for TOF.  Our findings provide new insight into the contribution of CNVs to the genetic basis of TOF and identify new genetic loci potentially important to the pathogenesis of TOF

overall_design: A total of 303 isolated TOF patients and 302 normal control subjects (Control-1) were recruited (the first batch of 466 samples is included in the current records). An informed consent form was obtained from their parents or guardians. All TOF patients were Chinese children from TEDA International Cardiovascular Hospital and associated hospitals（Guangzhou Women and Children Medical Center and Qingdao Children’s Hospital. Age-matched control subjects (between 2 month to 15 years) were assembled from healthy children or children without congenital or cardiac disease.  The project was approved by the Institutional Review Board (Ethics Committee) of TEDA International Cardiovascular Hospital.  Informed consent was obtained from all subjects or their guardians. A diagnosis of TOF was made with echocardiography or echocardiography plus catheterization, MRI, or CT scan and was confirmed in corrective cardiac surgery. Clinical records were reviewed before recruitment.

first: Guo-Wei

last: He

first: Cheryl

middle: L

last: Maslen


title: Single-cell RNA sequencing facilitates quantitative analysis of mouse hematopoietic stem/progenitor cells and SCF/2i expanded cells

first: Du

last: Jiang

summary:
Purpose: The goal of this study is to compare the transcriptome profiling of SCF/2i expanded cells to freshly sorted hemtopoietic stem/progenitor cells (HSPCs) at single cell level.
Methods: Mouse bone marrow HSPCs (HSC, MEP, CLP, CMP, GMP) and alive SCF/2i expanded cells were sorted by FACS. The FACS-sorted single cell suspensions were washed with ice cold 0.04% BSA in PBS, then loaded onto 3’ library chips as per the manufacturer’s protocol for the Chromium Single Cell 3’ Library (10X Genomics, V2). The 10× Genomics libraries were first sequenced on an Illumina NextSeq 500 aiming at a coverage of 5,000 raw reads per cell to estimate the cell numbers, before being sequenced deeper on an Illumina HiSeq 2500 aiming at a coverage of 50,000 raw reads per cell. (paired-end; read1: 26 cycles; i7 index: 8 cycles; read 2: 98 cycles). Raw sequencing data were pre-processed using the Cell Ranger pipeline (10× Genomics, v 2.1.0). The raw-count datasets from difference cell types were integrated and analyzed by Seurat3 R package.
Results: tSNE plot showed that the transcriptome of SCF/2i cells overlapped with that of freshly sorted GMPs. The top 50 highly expressed genes from each comparison were used for analysis by heatmap, which showed that the SCF/2i cells shared a similar gene expression pattern with GMPs, but not other hematopoietic cell lineages.
Conclusion: The SCF/2i expanded cells are GMPs.

overall_design: Comparation of the transcriptome between SCF/2i expanded cells and HSPCs

first: Shi

last: Yue

first: Litao

last: Tao


title: Single cell RNA-seq of psoriatic skin identifies pathogenic Tc17 subsets and reveals distinctions between CD8+ T cells in autoimmunity and cancer

status: Public on Jan 05 2021

first: Wilson

last: Liao

address: 2340 Sutter St.

department: Dermatology

institute: University of California, San Francisco

summary: Psoriasis is an inflammatory, IL-17-driven skin disease in which autoantigen-induced CD8+ T cells have been identified as pathogenic drivers. In this study, we used single-cell RNA-seq to identify 11 transcriptionally diverse CD8+ T cell subsets in psoriatic and healthy skin. Among several inflammatory subsets enriched in psoriatic skin, we observed two Tc17 subsets that were metabolically divergent, developmentally related, and expressed CXCL13, which we found to be a biomarker of psoriasis severity. Despite high co-inhibitory receptor expression in the Tc17 clusters, a comparison of these cells with melanoma-infiltrating CD8+ T cells revealed upregulated cytokine, cytolytic, and metabolic transcriptional activity in the psoriatic cells that differed from an exhaustion program. Our findings provide a high-resolution view of cutaneous CD8+ T cells in psoriasis and healthy skin and shed light on their functional distinctions within the chronic pathologies of autoimmunity and cancer.

overall_design: transcriptomic comparison of CD8+ T cells in 11 psoriatic and 5 healthy skin samples

first: Jared

last: Liu

first: Hsin-Wen

last: Chang

first: Zhi-Ming

last: Huang

first: Mio

last: Nakamura

first: Sahil

last: Sekhon

first: Richard

last: Ahn

first: Priscila

last: Munoz-Sandoval

first: Shrishti

last: Bhattarai

first: Kristen

middle: M

last: Beck

first: Isabelle

last: Sanchez

first: Eric

last: Yang

first: Mariela

last: Pauli

first: Sarah

middle: T

last: Arron

first: Wai-Ping

last: Fung-Leung

first: Ernesto

last: Munoz

first: Xuejun

first: Tina

last: Bhutani

first: Jeffrey

last: North

first: Anne

last: Fourie

first: Michael

last: Rosenblum


title: Gene expression profile of zebrafish synpo2 mutant

city: North York

first: Vinothkumar

last: Rajan

state: ON

address: 2075 Bayview Ave, Room # M7-413

department: Biological Sciences

country: Canada

institute: Sunnybrook Research Institute

summary: Embryonic zebrafish synpo2 mutants were compared to wild-type (22 hpf)

overall_design: RNAseq in three biological replicates and 2 genotypes

first: Nandini

last: Margam


title: Single cell RNA sequencing reveals fetal ovary development in Macaca fascicularis

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: The germ cells are vital for reproduction and heredity. However, the mechanisms for female germ cell development in primates, especially in late embryonic stage, has remained elusive. Here, we performed single-cell RNA sequencing of 12471 cells from fetal ovaries. We identified five cell types (germ cell, granulosa cell, theca cell, endothelial cell, macrophage cell), and explored the interactions between germ cells and niche cells. Interestingly, we demonstrated that two waves of oogenesis occur during fetal ovary development and ZGLP1 could activate oogenic program and is essential for meiosis initiation. Furthermore, late formed double strand breaks (DSBs) mediated by PRDM9 may lead to the apoptosis of germ cells during cyst breakdown process. Moreover, our study identified the origin of theca cells that may derive from Leydig cell like cells in fetal ovaries. Overall, our work provides new insights into the molecular and cellular basis of fetal ovary development at single-cell resolution.

overall_design: Single cell RNA sequencing on fetal ovary cells was performed from  Macaca fascicularis.

first: Zheng-Hui

last: Zhao

first: Qing-Yuan


title: Expression data of liver tissue from wild type and Cdc42 liver-specific knockout mice at 2-month-old

first: Peng

last: Zhang

state: Shanghai

address: 320 Yue-Yang Road

institute: Shanghai Institutes for Biological Sciences

summary:
Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death. However, the mechanism for HCC initiation remains poorly known. Cdc42, a small Rho GTPase, with multiple cellular functions has been shown involved in variant types of human cancers, but its role in HCC initiation remains unclear.
Cdc42 liver-specific knockout mice (Cdc42LK) developed HCC at 6-month-old. We used microarrays to detail the global programme of gene expression induced by Cdc42 deletion and identified distinct classes of up or down-regulated genes during HCC initial time.

overall_design: The liver tissues of wild type and Cdc42LK mice were harvested at 2-month-old for RNA extraction and hybridization on Affymetrix microarrays. 4 biological replicates of wild type and Cdc42LK mice.

first: Lan

last: Yu


title: Proteomic and Transcriptomic Analysis of Neural Cell Fate in Developing Xenopus laevis Embryos and Explants

city: Notre Dame

first: Paul

last: Huber

state: Indiana

address: 251 Nieuwland Science Hall

department: Chemistry & Biochemistry

institute: University of Notre Dame

summary:
Purpose: Study the developing neural cell fate of the D1 blastomere in the 8-cell embryo. Determine what transcripts are dependant on cell/cell signaling and which are inherit to the single cell and do not depend on the rest of the embryo.
Methods: D1 blastomere was either injected with fluorescent dye or explanted away from the developing embryo. Transcript profile was taken at 7 time points: 8-cell, 16-cell, 32-cell, blastula, gastrula, early neurula, and mid/late neurula. 3 biological triplicates were taken at each time point for both the dissect and explant condition.
Results: Up until blastula stage, dissect and explant transcript profiles remain fairly similar. But following this the profiles completely diverge, with the dissect tissue heading towards the neural fate while the explant samples head towards an ectoderm/epithelial fate.

overall_design: Dissect tissue or explant mRNA profiles at 7 critical developmental timepoints, in triplicate, using Illumina NextSeq.

first: Kyle

last: Dubiak

middle: W


title: Polyomavirus and neuroendocrine regulomes converge to establish tumor dependencies

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Merkel Cell carcinoma (MCC) is an aggressive neuroendocrine skin cancer often driven by Merkel cell polyomavirus T antigens. The epigenomic mechanisms driving MCC are poorly understood. We show that virus positive MCC (VP-MCC) super enhancer networks are committed to and controlled by lineage-specific neuroendocrine transcription factors (TFs) including LHX3, ISL1, ATOH1, INSM1, SOX2 and POU4F3.  These VP-MCC TFs are central to core regulatory (CR) transcriptional circuitry, essential for growth, and co-bind enhancers with polyomavirus small T antigen. We establish that T antigen expression is directly regulated by LHX3 and ISL1, establishing a positive feedback autoregulatory circuitry for a neuroendocrine state.

overall_design: Virus positive and virus negative MCC cell lines were assayed for enhancers by H3K27ac ChIP-seq (3 VN MCC and 4 VP MCC), open chromatin by DNase hypersensitivity (same cell lines, most in duplicate), and TF binding by ChIP-seq for the top 6 core regulatory TFs (2 cell lines).

first: Berkley

middle: E

last: Gryder

first: Xinyu

last: Wen


title: Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: We systematically probed which cell types in the colon are permissive to SARS-CoV-2 infection. Transcriptomic analysis following SARS-CoV-2 infection of hPSC-derived colon organoids revealed upregulation of chemokines but not type I/III interferon signaling. A large small molecule screen was also performed.

overall_design: Transcriptomic analysis of stem cell derived colon organoids

first: Robert

last: Schwartz

first: Shuibing

last: Chen

first: Todd

last: Evans


title: Coordinated Regulation of Smooth Muscle Cell Remodeling by Non-coding and Coding products of Phenotype Switching Regulator Gene.

city: Chongqing

first: Junyi

address: 10th Changjiangzhilu Road, Yuzhong District

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University, Chongqing, P.R. China.

summary: We identified a novel nuclear peptide Arteridin encoded by an annotated lncRNA Phenotype Swithching Regulator (PSR). To test the DNA binding capacity of Arteridin, we perfomed Arteridin ChIP-seq. We found both Arteridin and lncPSR transcript could induce vascular smooth muscle cell phenothype switching. We also found the interaction between Arteridin, lncPSR and transcription factor YBX1. To further illustrate how Arteridin and lncPSR work coordinately, we performed YBX1 ChIP-seq in VSMCs with Arteridin-FLAG overexpression or lncPSR ATT mutant overexpression.

overall_design: Arteridin ChIP-seq was performed in VSMC A10 cells with or without Arteridin overexpression. YBX1 ChIP-seq was performed in VSMC A10 cells without treatment, with Arteridin-FLAG overexpression , and with lncPSR ATT mutant overexpression.

first: Bing


title: Transcriptomic analysis of BMP4/GREM1 stimulation on primary myoblasts

city: Lyon

first: Fabien

last: Le Grand

address: 8 avenue Rockefeller

department: Melis

country: France

institute: Institut Neuromyogene

summary:
The capacity of muscle to grow or to regenerate is provided by adult stem cells, called satellite cells. Satellite cells can generate proliferating myoblasts, sensitive to MP signaling. To understand the role of this signaling pathway in adult myogenesis, we analyzed the changes in gene expression following treatment of primary myoblasts with BMP4 agonist or GREM1 antogonist.
Here we used microarrays and to clarify BMP4/GREM1 signaling and we identified several pathways and cellular processes affected.

overall_design: We cultured satellite cells-derived primary myoblasts in proliferating conditions (20% FBS), transfered them in 2% Horse Serum and stimulated the cells with recombinant BMP4 or GREM1 proteins. Cells were processed for RNA extraction after 24hours.

first: Alice

last: Parisi


title: Genome-wide Profiling of Long Noncoding RNA Expression Patterns in Thoracic Aorta from Spontaneously Hypertensive Rats.

summary: We used lncRNA-mRNA micro-array to analyze the transcriptome in the thoracic aorta tissue of 24 wees-old WKY and spontaneously hypertensive rats (SHRs).

overall_design: Tail blood pressure of WKY and SHRs was measured to confirm the hypertension. The thoracic aortae (1.5-2.0cm-long) of WKY and SHRs were quickly removed, cleaned of adhering fat, and connective tissue, then snap-frozen and stored in liquid nitrogen. Total RNA was extracted using Trizol reagent according to the instructions provided by the manufacturer. The Affymetrix GeneChip® Rat Gene 2.0 ST Array was used to analyze the expression profile of lncRNAs and mRNAs in thoracic aortae from adult WKY and SHRs based on the manufacturer’s standard protocols.

first: Chunyu

last: Zeng


title: Identification of novel activation marker and regulator of human basophils via transcriptomic analysis of IL-3-stimulated basophils

city: Xuzhou

first: Hui

last: Wang

address: 209 Tongshan Rd

institute: Xuzhou Medical University

summary: Human basophils regulate allergic immune responses by releasing histamine and effector cytokines such as interleukin 4 (IL-4) and IL-13. IL-3/IL-3R signaling axis plays key roles in the maturation, survival and activation of basophils. We and others have shown that IL-3-induced surface receptors e.g. ST2 and IL-17RB regulate the biology of basophils. We in this study aim to identify new basophil activation maker and regulator by transcriptomic analysis of IL-3-stimulated basophils.

overall_design: Human basophils were pre-enriched from PBMCs from buffy coat by Magnetic-activated cell sorting (MACS) positive sorting using rat anti-human CRTH2 microbeads. Next, basophils were further purified by FACS sorting of FSClowSSClowCD4-CRTH2high populations.Purified basophils at a density of 2×105 cells/well in a 96-well plate were cultured either with or without human IL-3 (50 ng/mL) (n = 3) for 24 hours. Gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8×60K V2 microarray according to the manufacturer’s instruction.


title: Suppression of poised oncogenes by ZMYND8 promotes chemo-sensitization

city: kolkata

first: Chandrima

last: Das

state: West Bengal

address: 1/AF Bidhan nagar, Sector-III, Salt Lake

department: Biophysics & Structural Genomics

country: India

institute: Saha Institute of Nuclear Physics

summary: In this study,  we have shown how ZMYND8, a putative chromatin reader, chemosensitizes, chemo-resistant breast cancer cells, by modulating poised oncogenes.

overall_design: Epigenetic therapy to treat chemo-resistant breast cancer

first: Shravanti

last: Mukherjee

first: Santanu

last: Adhikary


title: Temporal activation of WNT/ β-catenin signaling is sufficient to inhibit SOX10 expression and block melanoma growth

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: Despite advances in the systemic treatment of patients with metastatic melanoma using immune checkpoint and tyrosine kinase inhibitors (TKI), the majority of stage IV melanoma patients eventually succumb to the disease. We have previously identified the transcription factor Sox10 as a crucial player in melanoma, yet the underlying molecular mechanisms mediating Sox10-dependent tumorigenesis remain largely uncharacterized. Here, we show that MEK and RAF inhibitors do not suppress SOX10 expression in patient-derived cells in vitro, as well as in melanoma patients in vivo. In a search for pharmacological inhibitors of SOX10, we performed a mass spectrometry-based screen in human melanoma cells. Subsequent analysis revealed that SOX10 directly interacts with b-catenin, which is a key mediator of canonical Wnt/b-catenin signaling. We demonstrate that inhibitors of glycogen synthase kinase 3 alpha/beta (GSK3α/b) efficiently abrogate SOX10 expression in human melanoma cells in vitro and in melanoma mouse models in vivo. The mechanism of action of GSK3-mediated SOX10 suppression is transcription-independent and relies on the presence of a proteasome degradable form of b-catenin. Taken together, we provide evidence that activation of canonical Wnt signaling has a profound effect on melanoma growth and is able to counteract Sox10-dependent melanoma maintenance both in vitro and in vivo

overall_design: RNA Seq of human patient derived melanoma cell lines (resistant or sensitive to TKI inhibitors) treated vs not treated with GSK3a/b inhibitor

first: Rexhep

last: Uka

first: Olga

last: Shakhova


title: CD14+ monocytes repress gamma globin expression before the committed erythroblast stage

city: Amsterdam

first: Emile

last: van den Akker

address: Plesman 166

department: Hematopoiesis

country: Netherlands

institute: Sanquin Research

summary: This dataset provides transcriptome profiles for erythroid cells in terminal differentiation sorted on the type of hemoglobin expression; Beta- and Beta/gamma globin respectively

overall_design: RNA sequencing  for two populations sorted for hemoglobin type at 48h erythroid differentiation (3 donors each).

first: E

first: M

last: von Lindern


title: The Myc-Associated Zinc Finger Protein (MAZ) Works Both Independently and Together with CTCF to Control Cohesin Positioning and Genome Organization

first: Tiaojiang

last: XIao

address: rockville Pike

institute: NIDDK, NIH

summary:
Purpose: The objectives of this study are to evaluate the roles of MAZ in cellular processes using the NGS-deriveed ChIP-seq, RNA-seq and Hi-C profiles in K562 wild type and siRNA MAZ knockdown cells
Methods: ChIP-Seq and Hi-C profiles of K562 wild-type (WT) and  siRNA MAZ knockdown cells were generated by deep sequencing in duplicate or triplicate using Illumina GAIIx. The ChIP-seq sequence reads were analyzed with Burrows–Wheeler Aligner (BWA) followed by MACS software; The Hi-C sequence reads were analyzed with Juicer and HiC-Pro software.
Results: Comparative analysis of the ChIP-seq, RNA-seq and Hi-C data between K562 wild type and siRNA MAZ knockdown cells indicates that  1.MAZ colocalizes with CTCF in the genome, and helps stabilize CTCF binding; 2. MAZ is able to arrest the cohesin complex independently of CTCF and contributes additively to cohesin localization when it is associated with CTCF; 3. MAZ, similarly to CTCF, acts as an insulator protein to block interaction between promoter and enhancer ; 4. MAZ can pause the elongating form of RNA Pol II; and 5. MAZ helps control local chromatin organization and some aspects of TAD structure.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: K562 wild type and siRNA MAZ knocking down cells were used to generate ChIP-Seq and Hi-C libraries. The libraries were deep sequenced using Illumina GAIIx.

last: Xiao

first: Xin

last: Li

first: Gary

last: Felsenfeld


title: microRNA-252 and FoxO repress inflammaging by a dual inhibitory mechanism on Dawdle mediated TGF-β pathway in Drosophila muscle

city: shanghai

first: jing

last: zhao

address: Qiuyue Road

institute: IRCBC

summary: The abstract for the manuscript Inflammaging refers to low-grade, chronically activated innate immunity that negatively impacts adult survival. However, little is known about the intrinsic signaling pathway that upregulates innate immune genes during aging. Here using Drosophila melanogaster, we profile the microRNA targetomes in young and aged animals, and reveal Dawdle (Daw), an activin-like ligand of the TGF-beta pathway, as a physiological target of microRNA-252 (miR-252). We show that miR-252 cooperates with the transcriptional regulation of Daw by Forkhead box O (FoxO), a conserved transcriptional factor implicated in aging, at the post-transcriptional levels. Unopposed Daw triggers hyper activation of innate immune genes coupled with a catastrophic decline in organismal survival. Single-cell sequencing analysis describes a non-cell autonomous regulation between Daw and the induction of innate immune genes in the muscle. We further determine the downstream cascade by which Daw signaling leads to increased Kenny  /IKKgamma protein, which in turn activates Relish/NF-kappaB protein and consequentially upregulation of innate immune genes. Finally, while aging leads to a decline in FoxO activity, transgenic increase of miR-252 and FoxO pathway factors in wild-type Drosophila extends lifespan and mitigates the induction of innate immune genes in aging. Together, we propose that miR-252 and FoxO repress inflammaging by cooperative inhibition of Daw mediated TGF-beta pathway.

overall_design: The WT represented w1118(FlyBase Genotype), FBst0005905(FlyBase ID).And the double-mutant represented mir-252c328 foxoc431 double mutants. Both of them were dissection from fly chest to assessing transcriptome from single nuclei (sNuc-seq).

first: Xiaofen

last: Wu

first: Jing

last: Zhao

first: Xiaofan

last: Liu


title: Effect of Network-Correcting Molecules

first: Christina

last: Theodoris

address: 1650 Owens Street

institute: Gladstone Institutes, University of California, San Francisco

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

overall_design: Refer to individual Series


title: Effect of XCT790 on Human Aortic Valve (AV) Endothelial Cells (ECs) from Patients with Healthy Tricuspid, Calcified Tricuspid, or Calcified Bicuspid Avs

summary: RNA-seq on human primary AV ECs from patients with healthy tricuspid, calcified tricuspid, or calcified bicuspid AVs

first: Yu

last: Zhang

first: Tomohiro

last: Nishino

first: Casey

last: Gifford

first: Deepak

last: Srivastava


title: Genome wide SOX4 specific binding sites in BT549 human TNBC cells

city: Boston

first: Archis

last: Bagati

state: MASSACHUSETTS

address: 450 brookline ave.

institute: Dana-Farber Cancer Institute

summary: We identified the SOX4 transcription factor and integrin alpha V encoded by the ITGAV gene as important resistance mechanisms to T cell-mediated cytotoxicity of TNBC cells. Here, we performed RNA seq. analysis of SOX4 and ITGAV deficient (CRISPR knockout) BT549 human and 4T1 murine TNBC cells as compared to control edited counterparts. Additionally, we performed SOX4 specific ChIP-seq studies in BT549 human TNBC cells. The objective of the study was to identify the molecular regulators and signaling pathways that mediate resistance to T cell mediated immunity. GSEA analysis of RNA-seq data showed that the 'interferon response' represented one of the top pathways for genes upregulated in SOX4 or ITGAV edited compared to control TNBC cells.  In contrast, gene sets associated with TGF beta and TNF alpha/NF kappa b were negatively enriched in both Sox4 and Itgav edited TNBC cells. Further analysis of RNA-seq data showed that SOX4 or ITGAV edited TNBC cells contained higher mRNA levels of many interferon-stimulated genes (ISGs), including genes associated with important innate immune pathways such as RIG-I/MDA-5, cGAS - STING and the AIM2 inflammasome

overall_design: Chromatin from 10x10^6 cells was used for each ChIP. Nuclei/cells were fixed with 2 mM DSG (Pierce) for 45 min at RT (shaking) prior to formaldehyde fixation for 10min at RT. The reaction was quenched with glycine (0.125M). Nuclei/cells were then washed twice with ice-cold PBS, lysed in ChIP sonication buffer (50mM HEPES pH7.9, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS) supplemented with protease inhibitors, and were subjected to sonication to obtain DNA fragments of 300-800 bp. Immunoprecipitation was done using 5 ul of antibody and 40 ug of chromatin. The soluble chromatin (40 µg) was immunoprecipitated with 10 μg of SOX4 antibody (ab86809 Abcam). Chromatin immunoprecipitation (ChIP) experiments in human BT549 TNBC cells with a SOX4 specific antibody identified SOX4 specific peaks in the regulatory regions of innate immune genes (such as IFIH1, encoding MDA-5), interferon pathway genes (such as IRF7 and ISG15) and MHC-I pathway genes (including TAP1, TAP2, PSMB9, HLA-B and HLA-C).  These data are consistent with the hypothesis that SOX4 regulates the expression of multiple genes in the MHC-I and innate immunity pathways.

first: Kai

last: Wucherpfennig


title: Adrenergic-induced ERK3 pathway drives lipolysis and suppresses energy dissipation

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

summary: Beta-adrenergic stimulation stabilizes ERK3, resulting in the formation of a complex with MK5 and thereby driving lipolysis. A downstream target of the complex is FOXO1, which controls expression of the lipolytic enzyme ATGL. Deletion of ERK3 in mouse adipocytes inhibits lipolysis, but elevates energy dissipation.

overall_design: Global gene expression changes in differentiated adipocytes of mice after knockdown of ERK3.

first: Rabih

last: El-Merahbi

first: Jonathan

last: Trujillo Viera

first: Angel

last: Loza Valdes

first: Mona

middle: C

last: Löffler

first: Saskia

last: Reuter

first: Till

last: Karwen

first: Alexander

last: Mayer

first: Manuela

last: Erk

first: Martin

last: Eilers

first: Grzegorz

last: Sumara


title: RNA-seq analysis of murine Sox4+/+ versus Sox4-/- 4T1 TNBC cells

overall_design:
Total RNA was extracted from control, SOX4 or ITGAV edited human BT549 and murine 4T1 cells cultured in complete RPMI media in biological triplicates.  RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen # 74134) following the manufacturer’s protocol. Total RNA was quality-checked using an Agilent BioAnalyzer 2000 instrument.  RNA with an integrity number of greater than 9.5 was used for subsequent analyses. Total RNA was submitted to GeneWiz for RNA-seq analysis. Libraries were prepared with TruSeq RNA Sample Prep Kit v2 (Illumina). Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for single-end 75bp sequencing using an Illumina NextSeq 500 instrument. Statistics for differentially expressed genes were calculated using DESeq2 (version 3.5) (47) and Cufflinks (48).  Differential gene expression was analyzed using the DESeq2 (1.8.1) package in R using default settings (47). Principal component analyses were generated using the prcomp function in R and plotted with ggplot2. Human and mouse gene homologues were matched using the Mouse Genome Informatics annotation. Heatmaps were generated using the heatmap.2 function in R    GSEA analysis of RNA-seq data showed that the ‘interferon response’ represented one of the top pathway for genes upregulated in SOX4 or ITGAV-edited compared to control murine 4T1 TNBC cells .  Further analysis of RNA-seq data showed that Sox4 or Itgav edited 4T1 TNBC cells contained higher mRNA levels for of a large number ofmany interferon-stimulated genes (ISGs), including multiple genes associated with important innate immune pathways such as RIG-I/MDA-5, cGAS – STING and the AIM2 inflammasome
Idenfication of DEG in Sox4 knockout 4T1 murine TNBC cells versus control cell counterparts
Please note that each processed data file was generated from both replicates and is linked to the corresponding rep1 (*UT-1) sample records.


title: RNA-seq and ChIP-seq studies identify multiple pathways relevant for T cell-mediated tumor immunity regulated by SOX4.


title: Copy number alteration profiling of myxofibrosarcoma and undifferentiated pleomorphic sarcoma

first: Nicholas

last: Socci

state: NY

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

type: Genome variation profiling by genome tiling array

summary: We used array-based comparative genomic hybridization to identify copy number alterations in the TP53 and RB1 tumor suppressor genes in 64 myxofibrosarcoma and 30 undifferentiated pleomorphic sarcoma primary untreated tumor samples, and found that 68% of tumor samples had shallow or deep deletions in one or both genes.

overall_design: Comparative genomic hybridization arrays were used to analyze primary untreated myxofibrosarcom (n=64) and undifferentiated pleomorphic sarcoma (n=30) patient tumor samples

first: George

middle: Z

last: Li

first: Tomoyo

last: Okada

first: Young-Mi

last: Kim

first: Narasimhan

last: Agaram

first: Francisco

last: Sanchez-Vega

first: Yawei

last: Shen

first: Norifumi

last: Tsubokawa

first: Jordan

last: Rios

first: Axel

last: Martin

first: Li-Xuan

last: Qin

first: Samuel

last: Singer


title: Genome-wide binding of CrebA in the Drosophila salivary gland

city: Duluth

first: Matthew

last: Slattery

state: MINNESOTA

address: 1035 University Drive, SMed 219

institute: University of Minnesota Medical School

summary: Salivary gland-specific binding assays reveal that CrebA, a bZIP transcription factor, directly binds the vast majority of genes encoding the secretory machinery, including proteins of the signal recognition particle and receptor, proteins involved in co-translational import of cargo into the ER, proteins involved in vesicular transport between the ER and Golgi, as well as the structural proteins and enzymes of these organelles. CrebA does not bind salivary gland-specific cargo genes. Instead, it binds and boosts expression of Sage, which encodes a bHLH transcription factor that upregulates cargo expression. CrebA also directly binds and upregulates Xbp1, which encodes a key factor in the unfolded protein response, and Tudor-SN, which encodes a protein that in other systems increases secretory cargo mRNA levels.

overall_design: CrebA is expressed in multiple Drosophila embryonic tissues, including the salivary gland (SG), proventriculus, trachea, and epidermis. Thus, we employed the Gal4/UAS system to express C-terminal GFP-tagged CrebA (CrebA-GFP) for ChIP-Seq to identify SG-specific in vivo CrebA binding sites using a well-characterized GFP antibody that has been used extensively for ChIP-Seq studies of Drosophila TFs. Two Gal4 drivers were used, fkh-Gal4 and sage-Gal4; both drive UAS-transgene expression in multiple tissues, but have only SG expression in common. Whole embryo ChIP using CrebA antiserum was also performed on wild-type animals (Oregon R).

first: Dorothy

last: Johnson

first: Deborah

last: Andrew


title: Transcriptional Profiling of Target CD4+ T-cells that Survive Cytotoxic T Cell Co-culture

first: Richard

middle: Brad

last: Jones

department: Division of Infectious Diseases

summary: To identify candidate mechanisms that may confer CTL resistance to HIV reservoir harboring cells, we studied differential intrinsic sensitivity to CTL killing in primary CD4+ T-cells. Human CD4+ T cells were divided into either a “real” condition, where half of the cells were labeled with CFSE and pulsed with the HIV-Env peptide RLRDLLLIVTR (RR11), while the other half received no peptide and were labeled with CTFR, or a “mock” condition where cells were similarly labeled but received no peptide. Both conditions were then co-cultured with the corresponding HIV-specific CTL clone. Our result showed that the comparison between the ‘real survivors’ to the ‘real bystanders’ identified 1,061 differentially expressed genes (DEGs) by setting a threshold as FDR<0.05: 743 upregulated and 318 downregulated. Among these genes, we observed expression profiles that were consistent with specific selection of over-expression of BCL2, and under-expression of caspase-2 and PARP in the ‘real survivor’ cells that resisted elimination by CTL.

overall_design: Transcriptional profiling for CTL-resistant HIV-peptide-pulsed human CD4+ T cells (real survivors), comparing to HIV-peptide not pulsed bystanders

first: R.

middle: B

first: Yanqin

last: Ren

first: Dughan

last: Ahimovic


title: Next-generation RNA sequencing of murine bladder cancer cells isolated from P53/PTEN KO tumors at different stages of the disease.

city: Epalinges

first: Grégory

last: Verdeil

address: Ch. des Boveresses 155

department: Department of Oncology

institute: University of Lausanne

summary: Cancer cells from P53/PTEN KO bladder tumors collected at 5, 9, and 13 weeks after adenoviral vector injection.

overall_design: Induction of tumor in P53 Fl/Fl PTEN Fl/Fl mice with an adenoviral vector that expresses the Cre-recombinase, isolation of tumor cells by a percoll gradient, in vitro selection of tumor cells, RNA isolation and sequencing.

first: Sina

last: Nassiri

first: Marine

last: Leblond

first: Daniel

last: Speiser


title: Expression data from human lung cancer cell line NCI-H292

city: Suzhou

first: Gaochuan

last: Zhang

address: 199 Ren-Ai Road

institute: Soochow university

summary:
CT45 family  is abnormally overexpressed in various types of cancer. However, the molecular mechanisms of the oncogenic CT45 to trigger carcinogenesis and tumor malignant progression are largely enigmatic. We previously reported that CT45A1 functions as a proto-oncogene to promote the transcription  in the human breast cancer cells, thereby escalating tumorigenesis and cancer metastasis, However, the mechanism of CT45A1-mediated concurrent overexpression of the multiple oncogenic genes in cancer is unclear.
We used microarrays to study the role and mechanism of CT45A1 in gene transcriptional regulation in human lung cancer.

overall_design: Three replicates of NCI-H292_CT45A1-overexpression VS three replicates of NCI-H292_CT45A1-negative

first: Mei

last: Meng


title: Genome-wide H2A.X deposition in mouse ESC orchestrated by environmental cue-induced demethylation

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

summary: Epigenetic landscape in pluripotent stem cells undergoes dynamically changes in response to environmental cues. For example, recent studies suggest that long-term culture of mouse embryonic stem cells (ESCs) in the presence of Mek1/2 and Gsk3β inhibitors (2i culture) leads to the irreversible loss of 5mC and its oxidative derivatives (5hmC, 5fC, and 5caC) as well as genomic redistribution of the histone variant H2A.X, which underlie the impaired developmental potential. However, it remains unclear whether such epigenetic changes are mechanistically connected or merely coincidental.  In this study, we demonstrate that the accumulation of oxidative derivatives of 5mC, i.e. 5fC/5caC, serve as potent upstream signals for recruiting H2A.X in ESCs. Furthermore, our data suggest that global H2A.X redistribution in 2i cultured ESCs is due to the loss of 5fc/5caC.  We show that the 2i condition also diminishes a recently discovered DNA modification, N6-mA. Moreover, we find that alternative culture conditions, which maintain normal developmental potential, can preserve 5mC and its derivatives, N6-mA and H2A.X deposition in ESCs. Taken together, our results revealed that rare DNA epigenetic modifications and histone variant serve as genome sensors for environmental cues in ESCs and early development.

overall_design: H2A.X ChIP-seq in mouse ESCs

first: Kaixuan

last: Lin

first: Tao

last: Wu


title: MicroRNA-21-5p participate in IgA nephropathy by driving T helper cell polarization

city: Beijing

first: Boyang

last: Xu

address: No.8 Xi Shi Ku Street, Xi Cheng District

institute: Peking University First Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: Previous studies revealed the abnormal lymphocytes subsets in IgA nephropathy (IgAN). Recently, emerging studies indicate that microRNA could influence the balance of T helper differentiation and function. Here we explore the underlying mechanism regarding how miRNA regulated lymphocytes subsets in IgAN, focused on T helper cell polarization.

overall_design: miRNA and mRNA profiles in peripheral blood mononuclear lymphocytes (PBMC) from 5 biopsy proven IgAN patients and 4 healthy controls were determined by next-generation sequencing and gene expression array. The differentially expressed miRNA and mRNA were conbined analyzed later.

first: Bo-yang

first: Si-jun

first: Li

last: Zhu

first: Su-fang

last: Shi

first: Li-jun

last: Liu

first: Ji-cheng

last: Lv

first: Hong


title: Effect of Network-Correcting Molecules on NOTCH1 (N1)-Haploinsufficient Human Induced Pluripotent Stem Cell (iPSC)-Derived Endothelial Cells (ECs)

city: San Francisco

first: Christina

last: Theodoris

summary: Discovery of small molecules that correct gene networks dysregulated in human disease may allow identification of therapies that treat disease at its fundamental basis by leveraging mechanism-based data.  Here, we report the first broad gene network-based drug screen, which led to discovery of a drug candidate that effectively treats aortic valve disease in an animal model. We previously reported haploinsufficiency of NOTCH1 (N1) as a genetic cause of human aortic valve thickening and calcification, the third most common form of heart disease, and described the resulting gene network dysregulation in human induced pluripotent stem cell (iPSC)-derived endothelial cells (ECs). We exposed isogenic N1+/+ or N1+/– iPSC-derived ECs to each of 1595 small molecules or control and developed a machine learning approach that accurately distinguished WT or N1-haploinsufficient cells based on expression of 119 genes assayed by targeted RNA-sequencing. 9 small molecules corrected the gene network of N1+/– ECs sufficiently to be classified as WT. Among hits tested in vivo, the estrogen receptor-related alpha inverse agonist XCT790 significantly reduced aortic valve thickening, calcification, and stenosis in N1-haploinsufficient mice with shortened telomeres, which model the range of age-dependent cardiac disease observed in humans. This strategy, made feasible by human iPSC technology, next generation sequencing approaches, and machine learning, may represent a more effective path for drug discovery compared to conventional screening approaches.

overall_design: RNA-seq on WT vs N1-haploinsufficient iPSC-derived ECs exposed to DMSO or one of 9 network-correcting small molecules (Fmoc-leu, RO4929097, Cytochalasin, GSK837149A, CB1954, Biperiden, TG003, Putrescine, XCT790)

first: Deepak

last: Srivastava


title: The microarrays from human gastric cancer SGC-7901 cells

city: Nanchang

first: Suhong

last: Di

state: China

address: Medicalcollege of Nanchang University

institute: Nanchang University

summary:
NUAK1 was highly expressed in tumors, and promoted their invasion and metastasis..
The study is to explore the downstream of NUAK1 in human gastric cancer SGC-7901 cells

overall_design: The gastric cancer cells SGC-7901 were interfered by NUAK1-specific siRNA and profiled using AffymetrixPrimeView Human Gene Expression Array.

first: Zhuoqi


title: Aberrant stabilized ETV4 expression cooperates with loss of p53 to promote invasive prostate carcinoma

city: New York City

first: Dan

last: Li

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

summary: Chromosomal translocations or upregulations involving ETS transcription factor are frequent events in prostate cancer pathogenesis and significantly co-occurrence with p53 or PTEN loss. Caused by the low stabilities of ETS proteins in cytosol, mouse models with aberrant expression of wild type ETS transcription factors had subtle phenotypes and only drive prostate cancer progression in the setting of Pten loss. Here we show that prostate specific aberrant expression of mutated ETV4 (V70P71D72-AAA, ETV4-AAA), which is resistence to COP1 mediated protein degradation, results in more stabilized ETV4 protein in mouse prostate. We found that ETV4-AAA mice develop marked prostatic intraepithelial neoplasia (mPin) and p53-dependent cell senescence within 2 weeks, but without tumor development when aged. Interestingly, ETV4-AAA positive cells reduce dramatically in a PTEN loss background, which means that there is no cooperation between ETV4-AAA and PTEN loss. Aberrant ETV4-AAA expression promotes progression of mPin to prostatic adenocarcinoma in a Tp53 deficiency or haploinsufficiency background. In contrast to PTEN loss induced mouse prostate cancers which loss NKX3.1 expression and resistant to castration therapy, these ETV4-AAA tumor cells well maintain AR and NKX3.1 expression and are sensitive to castration therapy.

overall_design: Assay for transposase-accessible chromatin and transcriptome profiling in EYFP, ETV4WT and ETV4AAA mouse prostate cells.

first: Yu

last: Chen


title: Hoxb1 GoF RNA-seq

city: MARSEILLE

first: Sonia

last: Stefanovic

address: 27 BD JEAN MOULIN

institute: INSERM U1251

summary: Transcriptomic profiling of second heart field progenitor cells expressing Hoxb1 ectopically in mouse embryos.

overall_design: Microdissection of the second heart field region in E9.5 embryos.

first: Jean-Pierre

last: Devignes

first: Stéphane

last: Zaffran


title: Tissue resident and bone marrow derived macrophages in murine lung tumors

city: La Jolla

first: Judy

last: Varner

address: 3855 Health Sciences DR

department: Pathology

institute: Moores UCSD Cancer Center

summary: We isolated macrophages from murine lung tumors and their in vitro derived progenitors for RNA sequencing

overall_design: Lewis lung carcinoma tumors grown in mice were used to isolate tissue resident CD45+CD11b+Gr1-F4/80hi and bone marrow derived CD45+CD11b+Gr1+F4/80lo macrophages for RNA sequencing. These cells were also used to generate macrophage progenitors by culture in methycellulose + stem cell growth factors. Resulting Colony cells were then sorted for Kit expression and sequenced.


title: Treatment with ginseng flower buds extract prevents hepatic steatosis by ameliorating hepatic inflammation and insulin resistance

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

institute: Dongguk Uvi.

summary: Background: Ginseng flower bud (GFB) is a part of ginseng with high content of ginsenosides, the known active components of ginseng. While the scientific data for the pharmacological activity of ginseng roots are accumulating, the therapeutic potential of GFB have been neglected. The current study aimed to examine the therapeutic effect of GFB on hepatic steatosis and to elucidate the underlying mechanisms.  Methods: HepG2 cells treated with free fatty acids mixture and hepatocytes isolated from rats after 3 weeks of HFD feeding were used as in vitro models of hepatic steatosis for evaluation of anti-steatotic effect of GFB. The effect of GFB was further investigated in pathological conditions of hepatic steatosis induced by 12 weeks of HFD feeding in C57BL/6J mice. We performed systematical analyses on hepatic gene expression profiles in GFB treated mice. The effect of GFB on the expression profile of selected genes was validated by quantitative PCR.  Results: GFB treatment markedly reduced oil red O stained lipid droplets and intracellular triglyceride levels in HepG2 cells and rat hepatocytes. In HFD-fed mice, GFB (500 mg/kg) treatment markedly reduced histological signs of hepatic steatosis and decreased hepatic triglyceride content by 34.1% compared to those of HFD. These changes by GFB treatment were accompanied by improved insulin signaling. Global gene expression analysis revealed that hepatic gene expression in the steatotic liver was reversed by GFB treatment, and the GFB-regulated genes are involved in immune process, insulin response and lipid storage.   Conclusion: These findings provide a substantial evidence for the medicinal use of GFB in prevention or treatment of NAFLD through suppression of hepatic inflammation and fatty acid uptake while sensitizing hepatic insulin signaling

overall_design: Mice were orally administered with either vehicle or GFB once a day for 12 weeks. Liver tissue was dissected from the mice after an overnight fast, snap-frozen in liquid nitrogen, then stored at -75°C until analysis.

first: Go

last: Kim

first: Wonhee

last: Jang

first: Sung

last: Chung


title: Campylobacter jejuni butyrate resopnse

city: Athens

first: Matthew

last: Powers

state: GA

address: 501 DW Brooks Dr

institute: University of Georgia

summary: Growth of Campylobacter jejuni in butyrate, including deletions of a TCS involved in sensing this response

overall_design: Campylobacter jejuni WT and mutants were grown in the presence or absence of butyrate to assess the transcriptomic responses.

first: Dave

last: Hendrixson

first: Stephen

last: Trent

first: Kyle

last: Goodman


title: Genome-wide RNA-seq from PARP1 and PRC2 double-depleted MDA-MB-231 cell lines

city: DaeJeon

first: Mi Young

address: Biological science

institute: KAIST

summary:
Purpose: To identify downstream signaling pathways mediated by PARP1 and PRC2 in breast cancer
Methods: RNAs isolated from MDA-MB-231 cells depleting PARP1 and EZH2 (PARP1 KO shEZH2) and PARP1 and SUZ12 (PARP1 KO shSUZ12) were analyzed by using an Illumina Nextseq500
Conclusions: Our study represents the first transcriptomic profiles of effects of PARP1 and PRC2 double deficiency in breast cancer

overall_design: mRNAs prepared from wild type, PARP1-EZH2 double-depleted and PARP1-SUZ12 double-depleted MDA-MB-231 cells were analyzed in duplicaters by Illumina Nextseq500.

first: A-Yeong

last: Yang

first: Mi-Young

first: Seon


title: Transcriptome changes in pea leaves with sulfur deficency/sufficiency during reproductive phase

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

institute: IPS2_Institute of Plant Sciences Paris-Saclay

summary:
transcriptome changes in pea leaves with sulfur deficency/sufficiency during reproductive phase.-Characterization of transcriptome changes in leaves of wild-type and PsSultr4 mutant lines (for a sulfur transporter) subjected or not to sulfur deficiency during the reproductive phase

4plex_pea_2014_01 - transcriptome changes in pea leaves with sulfur deficency/sufficiency during reproductive phase. - Role of sulfur and of the sulfate store in leaf metabolism. - Comparison of: 1- The leaf transcriptome of pea subjected or not to sulfur deficiency during the reproductive phase (S+ versus S –) 2- The leaf transcriptome of wild-type and mutant lines for a sulfur transporter (two TILLING alleles) grown under sulfur sufficient conditions : WT1/Mut1 S+ et WT2/Mut2 S+ 3- The leaf transcriptome of wild-type and mutant lines for a sulfur transporter (two TILLING alleles) grown under sulfur deficient conditions : WT1/Mut1 S+ et WT2/Mut2 S+

overall_design:
20 dye-swap - gene knock out,genotype comparaison,treated vs untreated comparison

WT alleles: 4693 and 2684. Allele ID is included in sample title and source name.
Mutant alleles are also named 4693 and 2684. Allele ID is included in sample title and source name.
A supplementary file is included below with sample and corresponding allele numbers.

first: Karine

last: Gallardo

first: Sandrine

last: Balzergue

first: Marie-Laure

last: Martin-Magniette


title: Microglia-specific loss of PU.1 function rescues neurodegenerative phenotypes in a mouse model of Alzheimer’s disease

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

summary: Alzheimer’s disease (AD) is an age-related neurodegenerative disorder characterized by progressive decline of cognitive ability.  An important component of AD, and other chronic neurodegenerative diseases, is generation of an innate inflammatory response within the CNS, characterized by activation of microglia, the resident immune cells of the brain.  Transcription factor PU.1 has been known to play an important role in myeloid and lymphoid cell development, however its function in microglia and how it contributes to disease pathology is not well understood.  Using transcriptional and chromatin state profiles during  AD-like pathology in the CK-p25 mouse model of neurodegeneration, we showed that PU.1 specifically targets noncoding regions which regulate expression changes of immune response genes during AD, suggesting it may act as master regulator of microglia activation.  Here, we examine the role of PU.1 in neurodegeneration by using a conditional knockout (cKO) cassette (Cx3cr1CreER+/-) to inducibly deplete PU.1 from microglia in the CK-p25 mouse model of neurodegeneration.  We found that knocking out PU.1 rescues multiple neurodegenerative phenotypes.  Specifically, PU.1 inhibition reduces neurodegeneration-specific increase in microglia cell number, improves neuronal survival and reverses functional synaptic plasticity deficits in the hippocampus of the CK-p25 mouse.

overall_design: Profiling genome-wide  changes in PU.1 binding by ChIP-seq in the hippocampus of a mouse model of neurodegeneration and PU.1-dependent changes in gene expression by RNA-Seq in mouse hippocampal FAC-sorted microglia

first: Elizabeth

last: Gjoneska

first: Fan

last: Gao


title: Characterization of microRNA signature in CD4+ T cells from mouse models of myocarditis (EAM) and myocardial infarction (LAD)

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

summary: In order to evaluate the differential expression of miRNAs by T cells from mice with autoimmune-inflammatory versus ischemic cardiomyopathy, we isolated CD4+ T cells from draining-lymph nodes (dLNs) of acute EAM and LAD mice, 3 and 6 days after the onset of disease. Out of 1881 miRNAs described by the array, 704 were detected as differentially expressed (with Benjamini-Hochberg adjusted p-value < 0.1). 367 were upregulated in CD4EAM relative to CD4LAD, and 337 were detected as downregulated.

overall_design: CD4+ T cells were isolated from draining-lymph nodes (dLNs) of acute EAM (n=4) and LAD mice (n=3), 3 and 6 days after induction, respectively.

first: Rafael

last: Blanco-Dominguez

first: Beatriz

last: Linillos-Pradillo

first: Raquel

last: Sánchez-Díaz

first: Pilar

last: Martín


title: Expression data in sera from patients with anti-tuberculosis drug-induced liver injury

city: Zhuzhou

first: Long

last: Yunzhu

address: Tian Yuan Qu Chang Jiang Nan Lu

institute: The affiliated Zhuzhou hospital Xiangya medical college, Central South University

summary:
The pathogenesis of liver damage induced by anti-tuberculosis drugs is not fully understood, andcurrently, there is  no clinically useful biomarker for early diagnosis and treatment.By comparing the differences in the expression of global gene transcripts in the serum of patients with and without anti-tuberculosis drugs induced liver injury, dysregulation genes not only provides a basis for studying  pathogenesis, but also provides important information to find new targets for diagnosis and treatment of disease.
We used microarrays to detail the global programme of gene expression in sera underlying anti-tuberculosis drug-induced liver injury and identified distinct classes of transcript during this process.

overall_design: sera from patients with anti-tuberculosis drug-induced liver injury were selected for RNA extraction and hybridization on Affymetrix microarrays. We examined blood samples from 4 patients, in order to reduce the age , gender and the interference of the treatment with the drugs, we matched the blood samples of 4 patients with comparable TB treatment as controls. To that end, diagnostic criteria was in keeping with the Guidelines for the diagnosis and treatment of anti-tuberculosis drug-induced liver injury by the Chinese Medical Association Tuberculosis Branch (2019 edition). The laboratory test indicators used are serum biochemical results: Alanine aminotransferase (ALT) ≥3 times Upper limit of normal value (ULN) and/or total bilirubin≥2 times ULN; or Aspartate aminotransferase (AST), alkaline phosphatase (ALP) and total Bilirubin are elevated at the same time, in addition at least one item is ≥2 times ULN.

first: Zhou

last: Juan


title: Differentially expressed microRNAs in antigen-specific Th17 cell cultures from WT and CD69KO mice

summary: To explore miRNA signature in T cells during moderate (wild type BALB/c) and severe (cd69-/- in BALB/c background) EAM development, we performed microarray experiments with OVA-specific Th17 (Th17 Ag-sp) cell skewed cultures. The comparison of miRNA profiles from Th17 Ag-sp subsets of cd69-/- and wild type mice, with severe and mild EAM respectively, revealed a number of deregulated miRNAs.

overall_design: Naïve CD4+ T cells from spleen and mesenteric lymph nodes from WT or cd69-/- OTII mice were skewed for Th17 in the presence of OVA (Th17agWT / Th17agKO).

first: Adela

last: Matesanz-Marin


title: The transcription factor PBX1 drives natural killer cells to promote fetal development

city: Hefei

last: Yonggang

state: Anhui

address: 443 HuangShan Road

department: School of Life Science and Medical Center

institute: University of Science and Technology of China

summary: Perfect fetal development is a solid foundation for successful fertility, in which the abundant natural killer (NK) cells in the decidua tissue at the maternal-fetal interface play an important role during the first trimester. The functional subsets and transcriptional regulation mechanisms of decidual NK (dNK) cells remain poorly understood. Here, we identified CD49a+PBX1+ dNK cells as a unique subset of NK cells that promote fetal development in both human and mice. PBX1 drove the transcription of key functional molecules pleiotrophin and osteoglycin that promote fetal development through direct promoter binding. In patients with unexplained recurrent spontaneous abortion (URSA), decreased expression of PBX1 and PBX1(G21S) mutation correlated with fetal growth restriction and pregnancy failure. Inactivation of Pbx1 in mouse NK cells caused impaired fetal development due to a decrease in growth promoting factors. Our observations reveal the molecular regulation mechanism of CD49a+PBX1+ dNK cells promoting fetal development, and indicate that impaired PBX1 in dNK cells may serve as pathogenesis and biomarker of URSA.

overall_design: We performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) assay by anti-PBX1 antibody in purified NK cells from normal human decidua; assay by anti-IgG was used as control.

first: Yonggang

last: Zhou

first: Binqing

last: Fu

first: Xiuxiu

last: Xu

first: Jinghe

last: Zhang

first: Haiming

last: Wei


title: MicroRNA-21-5p participate in IgA nephropathy by driving T helper cell polarization [array]

first: Boyang

first: Bo-yang

first: Si-jun

last: Meng

first: Li

last: Zhu

first: Su-fang

last: Shi

first: Li-jun

last: Liu

first: Ji-cheng

last: Lv

first: Hong


title: Inhibition of H3K9me3 induces cytoplasmic localization of histone H3 coupled with autophagy

city: Wuhan

first: gao

last: chuan

state: Hubei province

address: bayi road

department: College of life science

institute: Wuhan university

summary: Nucleophagy, or nuclear autophagy, is termed to describe the cellular process of selective autophagic degradation of nuclear components. It was first discovered in yeast; however, the key regulatory gene is not conserved in mammals . Recently a pioneer work linked nucleophagy with senescence in mammalian cells, and the following studies showed that telomere damage is associated with nucleophagy . However, it is largely unknown whether other signals can activate nucleophagy and how the process is controlled in nuclear. Here, we show that inhibition of H3K9me3 by small chemicals induced cytoplasmic localization of histone H3.1 and degradation by autophagy. BIX-01294 treatment also induced cytosolic DNA and activated the cGAS/TBK1 dependent innate immunity pathway, expression of inflammatory genes and autophagic cell death. the deficiency of ATG5/7 enhanced the activation of cGAS pathway. Our study discovered a novel autophagic process selectively degrading nuclear materials in mammalian cells, which is induced by epigenetic dysregulation and coupled with activation of innate immunity pathway and autophagic cell death.

overall_design:
ChIP-Seq of BIX-treated, SETDB1.KO Cell Lines.
RNA-Seq of BIX-treated, ATG5 KD, cGAS KO and SETDB1 KO cell lines.

first: Wang

last: zhen


title: Gene expression analysis of vastus medialis cells after tourniquet-induced ischemia during Total Knee Arthroplasty: A randomized clinical trial

city: Mannheim

first: Ahmed

last: Jawhar

state: Badenwürttemberg

address: Theodor-Kutzer-Ufer 1-3

institute: Universitätsmedizin Mannheim

summary: Purpose The effects of the commonly utilized intraoperative tourniquet on gene expression within the skeletal muscle cells are barely examined. Our group already showed that tourniquet application results in higher proteolytic activity within vastus medialis cells (KSSTA 2016), without influence on the amount and function of mitochondria (EJOT 2016).  The purpose of the present study was to examine the gene expression within the skeletal muscle cells after tourniquet-induced ischemia and to identify differential expressed genes (DEGs).  Methods As part of a randomized, controlled, monocentric trial (Clinical-Trials.gov NCT02475603) we included 20 patients scheduled to undergo primary total knee arthroplasty (TKA). The patients received a written consent and were randomly assigned to Group A (TKA with tourniquet) (n=10) and Group B (TKA without tourniquet) (n=10). Muscle biopsies of (5×5×5 mm) were obtained from the vastus medialis immediately after performing the surgical approach and exactly 60 min later.  After preparation of a muscle homogenate, RNA extraction was performed (RNeasy Plus Universal Mini Kit Qiagen) and RNA integrity (RIN) was determined (Agilent 2100 Bioanalyzer,RNA 6000 Pico Kit). Gene expression profiling was performed methodological validated (GeneChip™ Human Transcriptome Array 2.0;Affymetrix).  Statistical analysis include the number of significant DEGs with p-value < 0,05, number of DEGs with relative difference >25% and pathway analysis (SPSS-Version 24; SAS JMP10 Genomics, Version 6).  The power analysis considered an effect size of 0,4 and a statistical power > 0,8, sample size n=10 for each group.  The protocol was approved by our Institutional Ethics Committee (File reference 2012-334N-MA).  Results and conclusion Numerous genes were differencially expressed during tourniquet induced ischemia. Further investigations and statistical analysis are ongoning.

overall_design: included 20  patients scheduled to undergo primary total knee arthroplasty (TKA). Group A tourniquet n=10, Group B non tourniquet (control) n=10

first: Desiree

last: Brenner

first: Carolina

last: Delatorre

first: Norbert

last: Ponelies

first: Udo

last: Obertacke


title: The role microglia in electroconvulsive threapy (ECT) in depressed-like mice

city: Jerusalem

first: Raz

last: Yirmiya

address: Mount Scopus

country: Israel

institute: Hebrew University of Jerusalem

summary: Recent studies implicate microglia alterations in the pathogenesis and pathophysiology of depression. For example, chronic unpredictable stress (CUS) in mice can cause degeneration of microglia and depressive-like symptoms, which can be reversed by microglia stimulating drugs. To further test the causal role of microglia in CUS-induced depression and its reversal by an anti-depressive procedure, we examined the effects of microglia depletion with the CSF-1 antagonist PLX5622 or pharmacological blockade of microglial activation with minocycline on normal mood-related behavior, CUS-induced depressive-like symptoms, and the amelioration of these symptoms by electroconvulsive treatment (ECT). We report that microglia-depleted mice showed no depression, anxiety or spatial memory disturbances. Microglia depletion had no effect on the development of CUS-induced depressive-like symptoms and suppressed neurogenesis, but it completely abrogated the beneficial effects of ECT on depression and neurogenesis, as well as on the all ECT-induced transcriptomic changes. ECT induced several morphological changes in microglia, suggestive of increased activation status, and blockade of this activation by minocycline attenuated the anti-depressive and pro-neurogenesis effect of ECT and reduced the number of contacts between microglia and neurogenic cells. The immune checkpoint gene Lag3, whose expression by microglia was increased following CUS, was the only microglial transcript significantly reduced by ECT. Furthermore, treatment of depressed-like mice with a LAG3 monoclonal antibody was further tested.

overall_design: 2*2  Chornic unpredictable stress exposed mice treated with ECT/SHAM* Control Diet/PLX Diet. There is an extra control non-stressed group.

first: Neta

last: Rimmerman


title: Gene expression profiling of elderly newly diagnosed multiple myeloma patients included in the HOVON87/NMSG-18 clinical trial

city: Rotterdam

first: P

last: Sonneveld

address: Wytemaweg 80

department: Department of Hematology

institute: ErasmusMC cancer institute

summary: This gene expression set contains data from 180 patients included in the HOVON-87/NMSG-18 clinical trial. Using this data the SKY92 classifier was validated in the elderly newly diagnosed multiple myeloma patients (median age = 72).  Additional to its proven value in younger patients, the MMprofiler?s SKY92 classifier was found to be a robust marker of high risk patients in the elderly MM population.

overall_design: Bone marrow aspirates were processed by CD138 based magnetic bead sorting (Stem Cell Technologies) to a purity of >80% plasma cells. Purified cells are prepared for RNA isolation using Qiagen RLTplus buffer (Qiagen). Samples were collected and processed by the central labs in The Netherlands, Denmark, Norway and Sweden (as part of the HOVON-NMSG collaboration).  RNA sample workup was performed according to the instructions for use of the MMprofilers at the SkylineDx reference lab (SkylineDx, Rotterdam, The Netherlands) . Samples were hybridized to Affymetrix HG-U133 plus2 chips, using Affymetrix Inc. (Santa Clara, CA) GPR reagent for samples obtained in 2014 or earlier (n = 87), and Affymetrix 3' IVT PLUS reagents for samples obtained after 2014 (n = 93). All samples passed wet lab and data QC acceptance criteria. Gene expressions were MAS5.0 normalized (values below 30 were truncated) with a target value of 1500. The MMprofiler CE IVD assay was used to obtain SKY92 scores, classifying a patient as high risk or standard risk.

first: Pieter

first: Rowan

last: Kuiper

first: Mark

last: van Duin

first: Martin

last: van Vliet

first: Erik

last: van Beers

first: Belinda

last: Dumee

first: Sonja

last: Zweegman


title: Characterization of gene expression noise modulated by microRNA

status: Public on Dec 31 2020

city: Beijing

first: Xiaowo

last: Wang

address: Qinghuayuan, Haidian

institute: Tsinghua University

summary: We measured the mRNA and microRNA profiles of HeLa cells to quantify the amount of microRNAs and their competing RNAs to investigate the relationship between microRNAs, competing RNAs and gene expression noise.

overall_design: HeLa cells were harvested and then total RNAs of the cells were extracted for NGS.

first: Lei

last: Wei

first: Shuailin

last: Li


title: Comparative leaf transcriptome analysis of Lancaster vs. Non-Lancaster maize inbred lines revealing genetic background associated cold-responsive genes

city: Beograd

first: Dragana

last: Dudić

address: Cara Dušana 62-64

country: Serbia

institute: Union Nikola Tesla University

summary: Sequencing of 46 maize leaf whole transcriptome revealed 77 differentially expressed genes (DEGs) between Lancaster and Non-Lancaster maize genetic resources under optimal growing conditions. Cold test of the subset of four Lancaster and four Non-Lancaster lines showed that the first were cold sensitive and the later cold tolerant, with the majority of identified DEGs showing FPKM values above the plate mean in Lancaster, but below the plate mean in Non-Lancaster subset. Cold induced expression analysis for revealed that, among seven tested DEGs, ATP-sulfurylase and photosystem II I encoding genes showed responsiveness to low temperatures in a genetic-background-dependent manner, likely contributing to different cold response/adaptability of Lancaster and Non-Lancaster lines.

overall_design: Comparative leaf whole transcriptome analysis between Lancaster and Non-Lancaster maize genetic sources for 46 maize inbred lines grown in the greenhouse under the optimal conditions in order to determine main gene expression differences in their genetic background

first: B

last: Banovic Djeri

first: D

last: Dudic

first: A

last: Nikolic

first: J

last: Vancetovic

last: Micic

first: N

last: Delic


title: Nucleome Dynamics during Retinal Development [scRNA-seq/scATAC-seq_Mm]

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

summary: Single cell RNA-sequencing shows cell type specific expression of genes in the retina. Single cell ATAC-sequencing of the wild type retina revealed that chromatin in the Vsx2 CRC SE, a stage- and cell type-specific core regulatory circuit super-enhancer (CRC-SE) upstream of the Vsx2 gene, was only open in bipolar cells. Deletion of the Vsx2 CRC-SE in mice led to the loss of bipolar neurons in the retina, which was confirmed by scRNA-sequencing of Vsx2SEKO mice.

overall_design:
Single cell RNA sequencing from adult WT and VSX2SE KO mouse retina and single cell ATAC-sequencing from WT mouse retina.
Please note that the scRNA-seq processed data was generated from multiple samples as indicated in the corresponding sample description field and thus, is linked to the Series records.

first: Jackie

last: Norrie


title: Crosstalk between histological alterations, oxidative stress and immune aberrations of the emerging PFOS alternative OBS in developing zebrafish

city: Nanchang

first: Wenqing

last: Tu

address: Changdong Road No.7777

institute: Jiangxi Academy of Science

summary: Sodium p-perfluorous nonenoxybenzene sulfonate (OBS) has been widely applied as a novel PFOS alternative in many industrial fields. However, our knowledge about its toxic effects is limited. In this study, we reported the RNA-seq data for zebrafish exposed with perfluoroalkyl substance PFOS and its alternative OBS. It was used for evaluating the PFOS and OBS induced toxic effects at RNA level to zebrafish. The transcriptome analysis showed that the expression of most immune-related genes was upregulated in both PFOS and OBS treatment groups, but the latter was to a lesser extent. Simultaneously, PFOS exposure blocked the translational process represented by a significant decrease in the expression of eukaryotic translation elongation factor eef1, while the expression of other translation elongation factors did not increase to compensate. This study provides the toxic effects at transcription level when zebrafish exposed with PFOS and OBS.

overall_design: 4 dpf zebrafish larvae RNA of untreated group, 20 mg/L PFOS treated group, 20 mg/L and 30 mg/L OBS treated groups was sequenced. There were 4 treatment groups in total, and each treatment contains 3 replicates.

first: Jing

last: Huang

first: Qiyu

first: Shuai

last: Liu

first: Miao

last: Zhang

first: Yu

first: Yongming

last: Wu


title: Characterization of microRNA signature in activated CD4+ T, polyclonal Th17 (Th17 poly), OVA-specific Th17 (Th17 Ag-sp) cell skewed cultures

first: Manuel

last: Gomez

summary: To determine specific miRNAs for Th17 cells, we performed comparative miRNA screening of activated CD4+ T, polyclonal Th17 (Th17 poly) and OVA-specific Th17 (Th17 Ag-sp) cell skewed cultures or Th17 Ag-sp sorted cells. The expression of miRNAs analyzed by microarray revealed 27 miRNAs exclusively expressed in culture or sorted Th17 Ag-sp cell subset.

overall_design:
Naïve CD4+ T cells from spleen and mesenteric lymph nodes from WT BALB/c mice were cultured in polarizing conditions (TGFbeta/IL-6) for Th17 cells (Th17poly). Cells from OTII mice were skewed for Th17 in the presence of OVA (Th17ag ). Activated CD4+ T cells with anti-CD3/anti-CD28 were used as control.

Please note that there are two types of raw data files with two different Grid_Name values 019119_D_20081121 and 019119_D_F_20091030;
Raw data files with Grid_Name = 019119_D_20081121 were generated with FeatureExtractor_Version = 10.1.1.1.
Raw data files with Grid_Name = 019119_D_F_20091030 were generated with FeatureExtractor_Version = 10.7.3.1.

first: Adela

last: Matesanz-Marin

first: Pilar

last: Martín


title: Genomic and epigenomic adaptation in SP-R210 (Myo18A) isoform-deficient macrophages

city: Hershey

first: Zissis

last: Chroneos

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State College of Medicine

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

overall_design: Refer to individual Series


title: microRNA signature of murine CD4+ T cell subpopulations under different skewing conditions


title: In vivo transcriptome profiling of control and GANAB-KD UMUC3 bladder carcinoma cells

city: Shen Zhen

first: GuoYu

last: Peng

address: 47 Youyi Road, Luohu District

institute: Shenzhen Luohu Hospital Group


title: scRNA-seq analysis of dendritic cells in skin draining lymph nodes of CLEC4C-DTR mice treated with FITC hapten

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Skin draining lymph node dendritic cell populations are known to be diverse and distinguishable via their migratory or resident properties as well as by lineage.  We analyzed these populations at steady state and during the sensitization phase of the Th2-driven FITC-hapten contact hypersensitivity (CHS) model.  We also analyzed the dendritic cells populations of CLEC4C-DTR+ mice treated with diptheria toxin, which demonstrate exacerbated pathology in the FITC-CHS model.  We demonstrate the diversity of dendritic cell populations at steady state and during type 2 inflammation, and surprisingly, reveal a skewing of the DC populations in DT treated CLEC4C-DTR+ mice, with an enrichment of DC2 migratory populations and depletion of CD326+ migratory cells in addition to pDC.

overall_design:
Isolated mouse dendritic cells were subjected to droplet-based 3’ end massively parallel single-cell RNA sequencing using Chromium Single Cell 3’ Reagent Kits as per manufacturer’s instructions (10x Genomics). The libraries were sequenced using Illumina HiSeq4000 sequencers.
CD11c+ MHCII+, Siglec H+ CD11c+ from the inguinal and axillary skin draing lymph nodes of DT-treated CLEC4C-DTR+ and CLEC4C-DTR- mice treated with epicutaneous FITC hapten were isolated after 48h of treatment.  SiglecH+GFP–, SiglecH+GFPlow/int and SiglecH–GFPhigh cells from inguinal and axillary skin DLN of untreated Zbtb46GFP x CLEC4C-DTR+ were also isolated for comparison.  Cells were submited for scRNAseq via the 10x Genomics platform.

first: Hannah

last: Miller

first: Prabhakar

middle: S

last: Andhey

first: Melissa

last: Swiecki

first: Bruce

last: Rosa

first: Konstantin

last: Zaitsev

first: Alexandra

last: Chloe-Villiani

first: Makedonka

last: Mitreva

middle: N

first: Susan

last: Gillfilan

first: Marina

last: Cella

first: Marco

last: Colonna


title: Expression data from WT mouse amd 9-month-old APP/PS1 mouse

first: Jinze

last: Li

address: 2A Nanwei Road

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

summary:
To identify the differentially expressed genes in the brain of WT mice in comparison with 9-month-old APP/PS1 mice, we examined the microarray gene expression profile of the groups above.
Neuroinflammation is well implicated in the progression of Alzheimer’s Disease (AD) now. What’ more, neuroinflammation is supposed to be one of the essential trigger to induce neurodegeneration. In this study, we examined the differentially expressed genes (including coding transcripts and lncRNA) between the wild type (WT) mouse and a AD model, the APP/PS1 mouse. We found that, among all these P2XR family genes, P2X7R is not only the most abundant expressed, but also identified as the highest upregulated gene. The elevated P2X7R expression promotes neuroinflammation through activation of NLRP3 inflammsome, and further mediate one kind of inflammatory cell death, pyroptosis. Blockade of P2X7R could not only inhibit pyroptosis, but also could mildly alleviate cognitive deficits in APP/PS1 mice. Our study provides new insight into an alternative strategy for the development of AD therapy.

overall_design: Total RNA from WT mouse brain and 9-month-old APP/PS1 mouse brain were obtained.  Biological replicates: 3 WT replicates, 3 9-month-old APP/PS1 replicates.

first: Tiantai

last: Zhang