title: Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality [HSCP]

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Tissue-specific stem cells persist for a lifetime and can differentiate to maintain homeostasis or transform to initiate cancer. Despite their importance, there are no described quality assurance mechanisms for newly formed stem cells. We observed intimate and specific interactions between macrophages and blood stem cells in zebrafish embryos. Stressed stem cells were marked by surface Calreticulin, which stimulates macrophage interaction as an “eat me” signal. Macrophage-stem cell interactions either lead to removal of cytoplasmic material and stem cell proliferation or resulted in complete stem cell engulfment. Using cellular barcoding, we found that calreticulin knock-down or embryonic macrophage depletion substantially reduced the number of stem cell clones into adulthood. Our work supports a model in which embryonic macrophages determine hematopoietic clonality by monitoring stem cell quality.

overall_design: Single-cell RNA-seq of FACS purified runx1+23:mCherry HSPCs from 3 dpf irf8 morpholino or standard morpholino injected embryos.

first: Sam

last: Wattrus

first: Song

last: Yang


title: Disrupted development and altered hormone signaling in male Padi2/Padi4 double knockout mice

status: Public on Oct 19 2022

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

country: USA

institute: Cornell University

type: Expression profiling by high throughput sequencing

summary: Peptidylarginine deiminase enzymes (PADs) convert arginine residues to citrulline in a process called citrullination or deimination. Recently, two PADs, PAD2 and PAD4, have been linked to hormone signaling in vitro and the goal of this study was to test for links between PAD2/PAD4 and hormone signaling in vivo. Preliminary analysis of Padi2 and Padi4 single knockout (SKO) mice did not find any overt reproductive defects and we predicted that this was likely due to genetic compensation. To test this hypothesis, we created a Padi2/Padi4 double knockout (DKO) mouse model and tested these mice for a range of reproductive defects. Results from controlled breeding trials found that DKO breeding pairs appeared to take longer to have their first litter than WT controls and that DKO male weanlings weighed significantly less than their WT counterparts. Additionally, DKO males took significantly longer than WT males to reach puberty and also had lower serum testosterone levels. Furthermore, DKO males had smaller testes than WT males and also had increased rates of germ cell apoptosis. The DKO mouse model provides a new tool for investigating PAD function and outcomes from our studies provide the first in vivo evidence linking PADs with hormone signaling.

overall_design: The RNAseq study consisted of 3 different genotypes (WT, Padi2 single knockout and Padi2/4 double knockout) each with 2 biological replicates.

first: Scott

middle: A

last: Coonrod

first: Chinatsu

last: Mukai

first: Kelly

middle: L

last: Sams

first: Ann

middle: E

last: Tate

first: Faraz

last: Ahmed


title: Effect of Fnip2 genetic variant in mouse tissues

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

summary: We have modeled the Fnip2 rs2291007 genetic variant in the mouse genome. In this study we aimed to investigate the effect of this genetic variant in the transcriptome of two metabolically relevant tissues: liver and white adipose tissue (WAT)

overall_design: Comparative gene expression profiling analysis of RNA Seq data for Fnip2T/T and Fnip2C/C livers and WAT. We have included 5 and 5 biological replicates for livers and 5 and 4 replicates for WAT.

first: Nerea

last: Deleyto-Seldas

last: Graña-Castro

first: Alejo

last: Efeyan


title: RNA-Sequencing of COPD ferret lung reveals uniquely expressed gene common to human COPD.

city: Birmingham

first: Dr Steven

middle: M.

last: Rowe

state: AL

address: 1720 2nd Avenue South, MCLM 804

department: Professor and Director, Cystic Fibrosis Research Center

institute: University of Alabama at Birmingham

summary: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease typified by not fully reversible and often progressive airflow obstruction, along with persistent respiratory symptoms. This gap is due to lack of animal models that more closely mimic human COPD are needed to bridge translational gaps. Commonly used mice model produces primarily emphysematous disease and do not develop features pathognomonic for chronic bronchitis. Suggesting the potential for additional molecular insights to be obtained from animal models that exhibit COPD with features of chronic bronchitis and emphysema, as in humans. We sought to identify whether our ferret model of COPD captures unique genetic signatures in comparison to mouse models that can help improve understanding of the molecular pathogenesis of COPD and promote the development of new and effective therapies.

overall_design: Age and sex-matched ferrets (Mustela putorious furo) were procured from Marshall BioResources and exposed to room air or cigarette smoke generated by an automated cigarette smoke generator (TSE Systems, Chesterfield, MO). Smoke exposure consisted of 1 hour of smoke from 1R6F research cigarettes, twice daily for at least 6 months. At the end of study, We conducted RNA-Sequencing on tissue samples isolated from ferret lung parenchyma of the six COPD ferrets and six air control ferrets. All animal experiments were approved by the Institutional Biosafety Committee of the University of Alabama at Birmingham (IACUC 20232).

first: Shah

middle: S

last: Hussain

first: Yvonne

middle: J

last: Edwards

first: Steven

middle: M


title: The protease DDI2 regulates NRF1-metallothionein pathway in response to Cadmium toxicity in the liver

city: Epalinges

first: Fabio

last: Martinon

address: 155 Ch. des Boveresses

department: Dept. of Biochemistry

country: Switzerland

institute: University of Lausanne

summary: DNA-damage inducible 1 homolog 2 (DDI2) is an aspartic protease that cleaves and activates the transcription factor NRF1. Cellular models have shown that this pathway contributes to cell-stress adaption, for example, upon proteasome inhibition. However, DDI2 physiological function is unknown. Ddi2 Knock-out (KO) mice are embryonic lethal. However, we found that liver-specific Ddi2-KO animals are viable. We used comprehensive genetic analysis to identify the molecular pathways regulated by DDI2. We show that DDI2 mediates metallothionein (MT) expression in mouse and human hepatocytes in response to cadmium (Cd). Cd exposure inhibits the proteasome activity, resulting in NRF1 accumulation in the cytoplasm, followed by cleavage by DDI2 and translocation to the nucleus to activate MTs. Depleting DDI2 or NRF1 by CRISPR/Cas9 impaired MTs activation and sensitized the cells to Cd or cisplatin toxicity. This study identifies a new function for DDI2 that links proteasome homeostasis to heavy metal mediated toxicity.

overall_design: liver RNA prolifes of adult wild-type and DDI2-KO mice

first: Sérgio

middle: T

last: Ribeiro


title: Transcriptome profiling of lung immune responses potentially related to acute respiratory distress syndrome in forest musk deer

city: Xi'an

first: Yan

last: Wang

address: 85 Xingqing Road, Beilin District

country: China

institute: Shaanxi Institute of Zoology

summary: ARDS-mediated lung transcriptome alterations were identified in forest musk deer. Moreover, multiple transcripts/genes involved in lung development and lung defense responses to bacteria/viruses/fungi in ARDS were filtered out in forest musk deer.

overall_design: High-throughput RNA sequencing (RNA-seq) technology was used to explore the lung transcriptome changes triggered by ARDS in forest musk deer.

first: Jie

last: Tang

first: Chao

first: Lijuan

last: Suo

first: Feiran

last: Li

first: Kun

last: Bian


title: The Mediator Kinase Complex Cooperates with Swi/Snf to Regulate Lineage-Resolved Enhancers and Differentiation [RNA-Seq]

city: Clayton

first: Ron

last: Firestein

state: VIC

address: 21 Wright street

department: CCR

country: Australia

institute: Hudson Institute of Medical Research

summary: To identify novel functions of Mediator kinases CDK8 and CDK19 in the intestinal epithelium, we generated novel genetic mouse model enabling the individual and compound deletion of CDK8 and CDK19. RNA-sequencing was performed on primary intestinal epithelial cells and murine small intestinal organoids at different time points after CDK8/19 deletion.

overall_design: 1) RNA samples from some control and CDK8/19-deficient IECs; 2) RNA samples from triplicates of organoids with the indicated genotypes, treatements collected at the indicated time points.

first: Marius

last: Dannappel

first: Danxi

last: Zhu

first: Claire

middle: X

last: Sun


title: Evaluation of gene expression changes in Candida albicans biofilms for wild-type SC5314 and stp2Δ at three time points (8 h, 24 h, 48 h) under normoxia and hypoxia.

city: Jena

first: Bettina

last: Böttcher

address: Albert Einstein Str. 10

department: Septomics Research Center

country: Germany

institute: Friedrich Schiller University

summary: The regulatory mechanisms during biofilm aging were determined using RNA-seq of C. albicans biofilms from three time points. The role of oxygen was investigated by comparing normoxic and hypoxic grown biofilms. Since nutrient uptake is important during biofilm maturation, the transcriptome of a stp2Δ strain lacking proper amino acid uptake was compared to the wild-type parent strain.

overall_design: Biofilms of C. albicans wild type and stp2Δ mutant were cultivated under normoxia and hypoxia in RPMI medium. Samples were after 8 h , 24 h, and 48 h.

first: Dominik

last: Driesch

first: Thomas

last: Krüger

first: Enrico

last: Garbe

first: Franziska

last: Gerwien

first: Olaf

last: Kniemeyer

first: Axel

last: Brakhage

first: Slavena

last: Vylkova


title: The Mediator Kinase Complex Cooperates with Swi/Snf to Regulate Lineage-Resolved Enhancers and Differentiation

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: The transcriptome of Magnetospirillum gryphiswaldense during magnetosome biomineralization

city: Bayreuth

first: Cornelius

middle: Nicolas

last: Riese

address: Universitätsstraße 30

department: Microbiology

institute: University of Bayreuth

summary: One of the most complex prokaryotic organelles are magnetosomes, which are formed by magnetotactic bacteria as sensors for navigation in the Earth’s magnetic field. In the alphaproteobacterium Magnetospirillum gryphiswaldense magnetosomes consist of chains of magnetite crystals (Fe3O4) that under suboxic conditions are biomineralized within membrane vesicles. To form such an intricate structure, the transcription of >30 specific structural genes clustered within the genomic magnetosome island (MAI) has to be coordinated with the expression of an as-yet unknown number of auxiliary genes encoding several generic metabolic functions. However, their global regulation and transcriptional organization in response to anoxic conditions most favorable for magnetite biomineralization are still unclear. Here, we compared transcriptional profiles of anaerobically grown magnetosome forming cells with those in which magnetosome biosynthesis has been suppressed by aerobic condition. Using whole transcriptome shotgun sequencing, we found that transcription of about 300 of the >4300 genes was significantly enhanced during magnetosome formation. The about 40 top upregulated genes are directly or indirectly linked to aerobic and anaerobic respiration (denitrification) or unknown functions. mam and mms gene clusters specifically controlling magnetosome biosynthesis were highly transcribed, but constitutively expressed irrespective of the growth condition. By Cappable-sequencing, we show that the transcriptional complexity of both the MAI and the entire genome decreased under anaerobic conditions optimal for magnetosome formation. In addition, predominant promoter structures were highly similar to sigma factor σ70 dependent promoters in other Alphaproteobacteria.  Our transcriptome-wide analysis revealed that magnetite biomineralization relies on a complex interplay between generic metabolic processes such as aerobic and anaerobic respiration, cellular redox control, and the biosynthesis of specific magnetosome structures. In addition, we provide insights into global regulatory features that have remained uncharacterized in the widely studied model organism M. gryphiswaldense, including a comprehensive dataset of newly annotated transcription start sites and genome-wide operon detection as a community resource.

overall_design: RNA-Seq of primary transcripts, whole transcriptome and 3'-ends of wild type cells

middle: N

first: Manuel

last: Wittchen

first: Valérie

last: Jérôme

first: Ruth

last: Freitag

first: Tobias

last: Busche

first: Jörn

last: Kalinowsky

first: Dirk

last: Schüler


title: The Mediator Kinase Complex Cooperates with Swi/Snf to Regulate Lineage-Resolved Enhancers and Differentiation [ChIP-Seq]

first: Ron

last: Firestein

summary: Depletion of CDK8 and its paralogue CDK19 in intestinal organoids resulted in the downregulation of genes associated with intestinal secretory cells. To determine the consequence of loss of CDK8/19 in re-defining enhancers we performed ChIP sequencing for MED1, MED12, H3K27Ac and ARID1A. We identified that loss of MED1 and MED12 at super enhancers regulating key intestinal transcription factors and loss of ARID1A binding across intestinal (super-)enhancers.

overall_design: Examine the binding of RNA pol II, MED1, MED12, H3K27Ac and ARID1A in the genome in control and CDK8/19 KO organoids

first: Marius

last: Dannappel

first: Danxi

last: Zhu


title: Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality

first: Leonard

last: Zon


title: Quality assurance of hematopoietic stem cells by macrophages determines stem cell clonality [macrophages]

overall_design: Single-cell RNA-seq of FACS purified embryonic mpeg1:EGFP macrophages on the basis of uptake of fluorescence from runx1+23:mCherry HSPCs.

first: Sam

last: Wattrus

first: Song

last: Yang


title: Gene expression profileing of DDR1 overexpression and control T24 human bladder cancer cell line

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

summary: We performed RNA-seq analysis on xenograft mouse model generated by T24 human bladder cancer cell line with enforced expression of DDR1 or controls.

overall_design: mRNA profiles of xenograft mouse model generated by T24 human bladder cancer cell line with enforced expression of DDR1 or controls.

first: Sungyong

last: You

first: Dan

last: Theodorescu

first: Keith

last: Chan


title: Gene expression profiling of shDDR2 or scrambled shRNA treated NA13, a recently described murine tumor cell line with high DDR2 expression

summary: We performed RNA-seq analysis on xenograft mouse model generated by NA13 bladder cancer cell lines treated with shDDR2 or scrambled shControl to identify gene signatures representing the changes of DDR2 status.

overall_design: mRNA profiles of xenograft mouse model generated by NA13 mouse bladder cancer cell line treated with shControl or shDdr2.


title: A super enhancer-controlled BRD4/ERα-RET-ERα positive feedback loop promotes ERα-positive breast cancer [GRO-seq]

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

summary: Dysregulated estrogen and estrogen receptor (ER)-induced gene transcription is tightly associated with estrogen receptor alpha (ERα)-positive breast carcinogenesis. ERα-occupied enhancers, particularly super enhancers, have been suggested to play a vital role in such transcriptional events. However, the landscape of ERα-occupied super enhancers (ERSEs) as well as key super enhancer-associated genes remain to be fully characterized.  Here, we defined the landscape of ERSEs in MCF7, a ERα-positive breast cancer cell line, and demonstrated that bromodomain protein BRD4 is a master regulator of the transcriptional activation of ERSE and cognate ERα-target genes.  Furthermore, RET, a member of the tyrosine protein kinase family of proteins, was identified to be a key target gene of BRD4-regulated ERSEs, which is vital for estrogen/ ERα-induced gene transcriptional activation and malignant phenotypes through activating the Ras-Raf-MEK-ERK-p90RSK-ERα phosphorylation cascade. Accordingly, combination therapy with BRD4 and RET inhibitors exhibited synergistic effects on suppressing ERα-positive breast cancer both in vitro and in vivo. Taken together, our data uncovered the critical role of a super enhancer-associated BRD4/ERα-RET-ERα positive feedback loop in ERα-positive breast cancer, and targeting components in this loop will provide new therapeutic avenue for treating ERα-positive breast cancer in the clinic.

overall_design: 4 GRO-seq

first: Zao-zao

last: Zheng

first: Lin

last: Xia

first: Guo-sheng

first: Jun-yi

last: Liu

first: Ya-hong

first: Yu-jie

last: Chen

first: Wen-juan

last: Zhang

first: Wen


title: A super enhancer-controlled BRD4/ERα-RET-ERα positive feedback loop promotes ERα-positive breast cancer [RNA-seq]

overall_design: 2 RNA-seq


title: A super enhancer-controlled BRD4/ERα-RET-ERα positive feedback loop promotes ERα-positive breast cancer [ChIP-seq]

overall_design: 2 ChIP-seq


title: Continuous sensing of IFNα by hepatic endothelial cells shapes a vascular antimetastatic barrier

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

summary: Hepatic metastases are a distinctive negative prognostic hallmark of colorectal cancer (CRC), thus there is an urgent need to develop new strategies aimed at reducing the risk of liver CRC colonization. Herein we demonstrate that adjuvant steady interferon-alpha (IFNα) administration, intravascularly control invading CRC cells through its direct action on liver sinusoidal endothelial cells (LSECs). Mechanistically, steady IFNα promotes the development of a vascular anti-metastatic niche, characterized by LSEC defenestration, extracellular matrix remodeling and glycocalyx deposition that reinforce the liver vascular barrier impairing CRC transendothelial migration. Furthermore, IFNα promotes LSEC-mediated innate and adaptive immunity, including antigen processing and presentation, that along with the early intravascular reduction of tumor burden, promote anti-tumor CD8+ T cell cross-priming and the generation of a protective long-term anti-tumor-memory response.

overall_design: We analyzed total RNA from CD31+ sorted LSECs from WT and Cdh5(PAC)-CreERT2-Ifnar1-fl/fl mice seven days after IFNα treatment.

first: Lorena

last: Ferreira

first: Blanca

last: Alvarez-Moya

first: Eugenia

last: Bezzecchi

first: Giovanni

last: Sitia


title: A flavonoid-attracted Aeromonas spp enhances plant Na_H1 resistance without cry-for-help [Bacteria_RNA-seq]

city: Shanghai

first: Huiming

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant Na_H1 resistance.

overall_design: Examination of 2 different samples of Aeromonas spp H1 with and without Naringenin treatment, each of samples contains 3 biological replicates. They are named as mock and Na-H1.

first: Danxia

last: He

first: Li

last: Peng


title: A super enhancer-controlled BRD4/ERα-RET-ERα positive feedback loop promotes ERα-positive breast cancer

first: Guosheng


title: A flavonoid-attracted Aeromonas spp enhances plant drought resistance without cry-for-help [Plant_RNA-seq]

summary: Flavonoids are stress-inducible metabolites important for plant-microbe interactions. In contrast to their well-known function in initiating rhizobia nodulation in legumes, it is unclear whether and how flavonoids may contribute to plant stress resistance through affecting non-nodulating bacteria in the root microbiome. Here we show how flavonoids preferentially attracts Aeromonadaceae in Arabidopsis thaliana root microbiome and how flavonoid-dependent recruitment of an Aeromona spp. results in enhanced plant drought resistance.

overall_design: Examination of 4 different samples of Col-0, each of samples contains 3 biological replicates. They are named as mock, drought, H1 and H1+drought, respectively..


title: Transcriptome profile of NON CF (normal) bronchial epithelial cells treated with TNFalpha, IL17 and TNFalpha+IL17

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary: To analyse gene expression differences between differentiated bronchial epithelial cells kept under control conditions or treated for 72 hours with cytokines (TNFalpha10 ng/ml; IL17 20ng/ml)

overall_design: Total RNA was extracted from n=4

first: R


title: Transcriptome profile of NON CF (normal) and CF bronchial epithelial cells treated with IL-4 or TNFalpha+IL17


title: Transcriptome profile of CF (cystic fibrosis) bronchial epithelial cells treated with TNFalpha+IL17

summary: To analyse gene expression differences between differentiated bronchial epithelial cells kept under control conditions or treated for 72 hours with TNFalpha+IL-17 (10 ng/ml and 20ng/ml respectively)

overall_design: Total RNA was extracted from n=3


title: Gene expression programs between genetically matched PEF and porcine iPSCs

city: Nanjing

first: Aiwen

last: Jiang

state: Jiangsu

address: Weigang

institute: Nanjing Agricultural University

summary: Somatic cells gain pluripotency after transfection of Oct4, Sox2, Klf4, and cMyc (OSKM), and chromatin remodeling has been proved to be involved in this process. To date, chromatin accessibility in porcine induced pluripotency stem cells (piPSCs) was less researched. Here, we explore the connection of chromatin accessibility and transcriptome between genetically matched PEF and piPSCs with high throughput sequencing (ATAC-seq and RNA-seq) approach. In addition, we acquire parent-of-origin chromatin loci and genes after blasting ATAC-seq and RNA-seq data with polymorphic SNP loci which derive from two parental genomes. As a result, we find 4,373 differentially expressed genes (DEGs), and 10,883 differential chromatin locus. Compared with PEF, the closed chromatin loci in piPSCs are tightly connected with the down-expressed genes, while the opened chromatin plays a limited role in the up-regulation of genes. Potential mechanisms of transcription factors (TF) in piPSCs reprogramming have been identified. Moreover, we find 77 parent-of-origin genes and 7 parent-of-origin chromatin loci commonly existed in PEF and piPSC; parent-of-origin chromatin accessibility is not related to the bias expression of RNA. These data reveal regulatory association between global or parent-of-origin chromatin accessibility and transcriptome, which provides new sight to research porcine iPSC reprogramming and genome imprinting.

overall_design: RNA-seq were applied on PEF and piPScs,three replicates were performed for each group.

first: Xue

first: Honglin

first: Yangyang

last: Ma


title: Transcriptome profile of NON CF (normal) bronchial epithelial cells treated with IL-4

summary: To analyse gene expression differences between differentiated bronchial epithelial cells kept under control conditions or treated for 72 hours with IL-4 (10 ng/ml)

overall_design: Total RNA was extracted from n=4 cell preparations


title: Chromatin structure programs between genetically matched PEF and porcine iPSCs

overall_design: ATAC-seq were applied on PEF and piPScs,three replicates were performed for each group.


title: Gene regulation by PCGF1 in hematopoietic progenitor cells

city: Yokohama-shi

first: Junichiro

last: Takano

state: Kanagawa-kwn

department: IMS

country: Japan

institute: RIKEN

summary: Polycomb group proteins (PcG), namely polycomb repressive complexes 1 and 2 (PRC1 and 2), repress lineage inappropriate genes during development to maintain proper cellular identities. It has been recognized that PRC1 localizes at replication fork, however, the precise functions of PRC1 during DNA replication are elusive. In this study, to elucidate the role of PCGF1 in the fork we’ve examined nucleosome occupancy at the fork by iPOND-MNase seq. In addition we’ve examined the biological relevancy by performing single cell RNA-seq derived Pcgf1 deficient hematopoietic progenitor cells to describe how cellular fate is affected by the impact of PCGF1 on nascent nucleosome configuration.

overall_design: MNaseSeq, single cell RNA seq

first: J

first: T

last: Ikawa

first: H

last: Koseki


title: Chromatin structure and gene expression programs between genetically matched PEF and porcine iPSCs

overall_design: Refer to individual Series


title: A fine-tuned regulation of Bmp2 by Nodal/TGFβ signalling induced lncRNA-Smad7

city: Beijing

first: kong

last: xiaohui

state: Beijing

address: Zheng Yutong medical building

department: school of life science

summary: The transforming growth factor beta (TGF-β) superfamily proteins are potent regulators of cellular development and differentiation. Long non-coding RNAs (lncRNAs) play widespread roles in spatial-temporal regulation of early development. However, the roles of lncRNAs regulated by nodal/TGF-β signaling is still elusive. Here, we showed a nodal-driven Smad induced lncRNA in mouse embryonic stem cells (mESCs), lncRNA-Smad7, which is divergently transcribed to Smad7, regulates cell fate determination through repressing Bmp2. Depletion of lncRNA-Smad7 dramatically impairs cardiomyocyte differentiation in mESCs. Moreover, LncRNA-Smad7 represses Bmp2 expression and binds at the promoter region of Bmp2. Importantly, knock-down Bmp2 rescues the defect of cardiomyocyte differentiation. Hence, we showed that lncRNA-Smad7 is antagonistic to BMP signaling in mESCs. Furthermore, lncRNA-Smad7 regulates cell fate determination between osteocytes and myocytes formation in C2C12 cells by repressing Bmp2. Thus, we provide new insights regarding the antagonistic effects between nodal/TGF-β and BMP signaling via lncRNA-Smad7.

overall_design: Identifiy Nodal/TGF-β regulated  lncRNA, dissect function and molecular mechanism of alncRNA in early development

first: Xiaohui

last: Kong

first: Kun

last: Yan

first: Qiaoran

last: Xi


title: 16S V3-V4 -based microbial profiling of  duodenal mucosa samples obtained by esophagogastroduodenoscopy  from patients affected by potential celiac disease and celiac disease

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: Potential celiac diseasase (PCD) is characterized by a positive celiac disease (CD)  serology and a normal small intestinal mucosa. This particular condition is usually considered a clinical challenge because, although its diagnostic criteria are clear, many questions are still unsettled. Therefore, given that PCD is a valuable biological model of the pathway leading to small intestinal mucosal damage in genetically predisposed individuals, the aim of our study is to evaluate whether immunological, microbial and lipid signatures could better characterize the PCD from the CD condition.

overall_design: Total DNA was extracted from duodenal mucosa samples of 17 patients affected CD and 10 patients with PCD and amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene were sequenced in paired end (2x300 cycle) on MiSeq Illumina platform.

first: M

first: A

last: Amedei


title: The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase [RNA-seq]

city: Eugene

first: Elizabeth

middle: Toomey

last: Wiles

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

summary: The recurrent mutation of histone variant H3.3 at glycine-34 (H3.3G34) defines a type of pediatric glioma. Characteristic changes to the epigenome associated with the disease are thought to be the consequence of altered methylation of the adjacent lysine-36 (K36) residue, but the complexity of this regulatory pathway in humans, combined with a multi-component disease etiology, has limited our understanding of how H3.3G34 mutations contribute to oncogenesis. Here we use Neurospora crassa to show that the most common mutation associated with this tumor, glycine to arginine (G34R), drives aberrant heterochromatin formation and abnormal growth by inhibiting the H3K36 methyltransferase ASH1. Inactivation of ASH1, either directly or with H3G34R, drives spurious intergenic DNA methylation, redistribution of H3K27 methylation, and derepression of silent genes. We provide evidence that these defects are largely due to aberrant activity of RNA polymerase II (RNAPII)-associated SET-2, and propose targeted SET-2 inhibition as a therapeutic strategy for H3.3G34R gliomas.

overall_design: We analyzed gene expression changes in Neurospora crassa by poly-A+ mRNA-sequencing performed in duplicate. Five strains representing three genetic backgrounds (N5247, N5248 (H3G34R), N6777 (H3G34R; delta set-2), and N6266, N6267 (ash1(Y888F); delta set-2)) serve as test strains here. Wild-type controls used as reference and related, previously described, mutants are deposited at GSE82222 and GSE118495.

first: Vincent

last: Bicocca

first: Michael

middle: R

last: Rountree

first: Tereza

last: Ormsby

first: Eric

middle: U

last: Selker


title: Understanding the functional role of cyanidin-3-O-glucoside in mouse osteoblastic cell line MC3T3-E1 by RNA-seq analysis

city: Shenyang

first: Lin

last: Chen

state: Liaoning

address: 146 North Huanghe St

department: School of Public Health

institute: Shenyang Medical College

summary: Cyanidin-3-O-glucoside (C3G) is one of the most widely distributed anthocyanins and has the effect of reducing the risks of osteoporosis. However, the molecular mechanism by which C3G promotes bone formation remains incompletely understood. Our aim was to investigate the effect of C3G on gene expression profiles, during the proliferation and differentiation in MC3T3-E1, a kind of osteoblast cell line from mice, by RNA sequencing. The results identified 34 up-regulated and 17 down-regulated genes. We further performed Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes analyses (KEGG), and other bioinformatics methods to do further analysis of differentially expressed genes (DEGs). Analysis of sequencing data showed that these genes were highly enriched in functions related to Lysosomal and Glycolipid biosynthetic. Lastly, we used RT-qPCR to validate the differentially expressed mRNAs. The results showed that C3G increased the expression levels of Ly6a (Lymphocyte antigen 6 family member A), Atp6v0c (ATPase H+ transporting v0 subunit c), and decreased the expression levels of Cx3cl1 (C-X3-C motif chemokine ligand 1). This study suggested that C3G activated osteoblast via Glycosylphosphatidylinositol(GPI)-anchor biosynthesis and the Cx3cl1/Cx3cr1 signaling pathway.

overall_design: MC3T3-E1 cells were divided into 2 groups, including the control group and C3G group. The mRNA profiles of each group were generated by RNA-seq.

first: Bosen

last: Hu

first: Xiaohong

last: Wang

first: Yong

first: Bo

last: Zhou


title: Gene regulation by PCGF1 in hematopoietic progenitor cells [ChIP, MNaseSeq]

first: Junichiro

last: Takano

summary: Polycomb proteins are epigenetic regulators important for cell fate decision and maintenance. Here we show that PCGF1, one of components of Polycomb repressive complex (PRC) 1 is important for the differentiation of hematopoietic stem/progenitor cells (HSPCs) towards lymphoid lineage. The deletion of Pcgf1 in HSPCs lead to severe defects in B cell development with an expansion of myeloid progenitors. The blockade of B cell differentiation occurred at the lymphoid-primed multipotent progenitor (LMPP) stage. Chromatin immunoprecipitation followed by DNA sequencing analysis of normal LMPP-like cells demonstrated that PCGF1 colocalized with RING1A/B and PRC2. Upon deletion of Pcgf1, we found dramatic decline of H3K27me3 levels, resulting in de-repression of target genes. Strikingly, the occupancy of RING1A/B, PRC2 and monoubiquitination of histone H2A at lysin 119 on the target loci was not affected. These results demonstrate that the PCGF1 safeguards the immune system development by directly regulating the PRC2-mediated H3K27me3 levels.

overall_design: ChIP, MNaseSeq

first: J

first: T

last: Ikawa

first: H


title: The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase

type: Methylation profiling by high throughput sequencing

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


title: Transcriptional profiling of cortex from 6-month-old wildtype C57BL/6 mice

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

summary: As part of collaboration between the X. William Yang Lab at UCLA and CHDI, a transcriptomic study of normal murine cortex was carried out. Cortex was dissected from 6-month-old wildtype (WT) control mice. Transcriptomic analysis (RNASeq) was performed.

overall_design: RNASeq analysis was performed on samples from cortex of 6-month-old WT control mice. N = 8 per line (4M/4F).

first: X

middle: W

last: Yang

first: Jim

last: Rosinski


title: Ambient RNA analysis reveals misinterpreted and masked cell types in brain single-nuclei  datasets

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

summary: Ambient RNA contamination in single-cell RNA sequencing (RNA-seq) is a significant problem, but its consequences are poorly understood. Here, we show that ambient RNAs in brain single-nuclei RNA-seq can have a nuclear or extra-nuclear origin, and each origin results in a distinct gene set signature. Both ambient RNA signatures are predominantly neuronal and we find that some previously annotated neuronal cell types are distinguished by ambient RNA. Strikingly, we also detect pervasive neuronal ambient RNA contamination in all glial cell types unless glia and neurons are physically separated prior to sequencing. We demonstrate that this contamination can be removed in silico using existing tools. We also show that previous annotations of immature oligodendrocytes are likely glial cells contaminated with ambient RNAs. After ambient RNA removal, we can detect extremely rare committed oligodendrocyte progenitor cells, which were infrequently annotated in previously published adult human brain datasets. Together, these results provide an in-depth analysis of ambient RNA contamination in brain single-cell datasets.

sample_organism:
Homo sapiens
Mus musculus

overall_design:
Data were reanalzyzed from raw fastq files with or without CellBender. Cells were annotated based on their cell type and glial cells were additionally annotated for ambient RNA contamination based on ambient RNA marker gene enrichment. Oligodendrocyte progenitor cells were additionally clustered and annotated.
---------------------------------------
Reanalyzed data includes PRJNA434002 (SRR9262927-SRR9262957), GSE192773, GSE97930, and GSE198640)

first: Emre

last: Caglayan

first: Yuxiang

last: Liu


title: Transcriptommic profiling of hematopoietic progenitor cells following PCGF1 loss

overall_design: RNA-seq analysis  in Pcgf1 -/- and control hematopoietic progenitor cells

last: Koseki


title: Hematopoietic progenitor cells


title: Transcriptional profiling of striatum from 6-month-old mice heterozygous knockout for 52 genes and corresponding wildtype control mice

summary: As part of collaboration between the X. William Yang Lab at UCLA and CHDI, a list of 52 genes that were implicated in Huntington’s disease (HD) through various computational modeling efforts was compiled, and murine lines with heterozygous knockout of these genes were obtained from public repositories or newly created. Striatum was dissected from 6-month-old mice that were either heterozygous KO for one of 52 genes or the corresponding wildtype (WT) controls. Transcriptomic analysis (RNASeq) was performed.

overall_design: RNASeq analysis was performed on samples from striatum of 6-month-old mice with heterozygous KO of one of 52 genes and corresponding WT controls. N = 2x8 per line (KO gene).


title: The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase [ATAC-seq]

first: Elizabeth

last: Wiles

overall_design: We analyzed the distribution of DNA methylation in Neurospora crassa strains (wild-type and four mutants) by Whole Genome Bisulfite-Seq. Biological replicates are included for wild-type and ash1(Y888F) backgrounds.

first: Vincent

last: Bicocca

first: Michael

first: Tereza


title: Exploring the molecular mechanism of artesunate intervening in glioma based on DNA methylation sequencing technology

status: Public on Oct 18 2022

city: beijing

first: xiangying

last: yan

address: Dongzhimen Jiedao

institute: Institute of Chinese Medicine

type: Methylation profiling by genome tiling array

summary: Whole gene methylation profiles of U87 and U251 glioma cells before and after artesunate treatment, Infinium MethylationEPIC BeadChip, samples including 3 U87 cell normal group, 3 U251 cell normal group, 3 artesunate treated U87 cell group,  U251 cell group was treated with 3 artesunate.

overall_design: 500 ng of DNA from each sample was bisulfite converted and the converted product was sequenced in 850K BeadChips according to the manufacturer's (Illumina) guidelines and protocols

first: YAN

last: Xiang-ying

first: LI

last: Tao


title: The histone H3G34R mutation disrupts the epigenome via catalytic inactivation of the ASH1 H3K36 methyltransferase [ChIP-seq]

overall_design: We analyzed the distribution of histone H3 lysine 27 methylation (H3K27me2/3), H3K36me2/3, and H3K9me3 in Neurospora crassa by chromatin immunoprecipitation. Strains were grown, crosslinked, lysed, modified nucleosomes were immunopurified, and associated DNA was sequenced. A total of five genetic backgrounds are included here. Each background and each mark was done in replicate. Data sets with wild-type strains and related mutant backgrounds are deposited in GEO submision GSE118495.

last: Rountree

last: Ormsby

first: Eric

last: Selker


title: Analysis of physiological and miRNA-mRNA responses in the liver of crucian carp reveals its tolerance to hypoxia stress

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

type: Non-coding RNA profiling by high throughput sequencing

summary: Hypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. In this study, we detected the changes of biochemical parameters after hypoxia stress (3 h (H3h), H12h, and H24h) and reoxygenation (reoxygenation for 3 h after hypoxia 24 h (R3h)), mRNA and miRNA expression profiles under H12h compared to the control, and key hypoxia-related genes expression patterns in the liver of crucian carp through biochemical methods, RNA-seq, and qRT-PCR. Compared with the control, increased T-SOD, CAT, GSH-Px, T-AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress, and LDH activity increased only in the H12h and H24h groups. Based on RNA-seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif-1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrc3, nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre-miR-125c-3p/novel_173, dre-miR-181b-5p, and dre-miR-338-5p/dre-miR-128-3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, NOD−like receptor signaling pathway, and cytokine-cytokine receptor interaction. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp, which are of great significance for genetics and breeding of other fishes tolerant to hypoxia.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: Effect of Urolithin A on T cell differentiation and gene expression

city: Frankfurt am Main

first: Dominic

middle: Pascal

last: Denk

address: Theodor-Stern-Kai 7

department: Medizinische Klinik 1

institute: Universitätsklinikum Frankfurt

summary: To investigate the effect of Uroltihin A on T cell differentiation and gene expression, we treated purified CD3+ cells with DMSO or Urolithin A

first: Valentina

last: Petrocelli

first: Florian

last: Greten


title: Assessing Cellular and Transcriptional diversity of IIeal Mucosa amongst Treatment Naïve and Treated Crohn’s disease

city: Atlanta

first: Suresh

last: Venkateswaran

state: Georgia

address: 1760 Haygood Drive, HSRB, Room No: E-250

department: Pediatrics

institute: Emory University

summary: Crohn’s disease (CD) is a  chronic inflammatory disease of the gastrointestinal tract. We used single cell RNA sequencing (scRNAseq) to define the cellular and transcriptional activity of the mucosa at different stages of disease progression  in CD.

overall_design: Terminal ileal mucosal derived single cells was processed and analyzed using scRNAseq

first: Maddipatla

last: Chowdary

first: Vasantha

last: Kolachala

first: Ann

middle: F

last: Dodd

first: Pelia

last: Ranjit Singh

first: Geem

last: Duke

first: Yin

last: Hong

first: Yutong

last: Sun

first: Congmin

last: Xu

first: Angela

last: Mo

first: Junkai

last: Yang

first: Astrid

last: Kosters

first: Jason

last: Matthews

first: Eliver

last: Ghosn


title: Generation of human kidney organoids from urine cells (RNA-seq)

city: guangzhou

first: huan

last: chen

address: Huangpu District

institute: Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)

summary: Kidney organoids are ideal models to study the complex process of human kidney development. Here we report the generation of functional kidney organoids by reprogramming human urine epithelial cells (hUCs). RNA-seq and ATAC-seq revealed the  three-stage process of the 2D U-iRO induction. Single cell RNA-seq further reveals the cell types in 2D and 3D organoids, 2D U-iRO dominated with mesenchyme and 3D U-iRO with tubule.

overall_design: We analyzed the transcriptome expression profiles (RNA-seq)  during U-iRO induction

first: H

last: Chen

first: Y

last: Yuan

first: B

last: Cai


title: Generation of human kidney organoids from urine cells

summary: Kidney organoids are ideal models to study the complex process of human kidney development. Here we report the generation of functional kidney organoids by reprogramming human urine epithelial cells (hUCs). RNA-seq and ATAC-seq revealed the three-stage process of the 2D U-iRO induction. Single cell RNA-seq further reveals the cell types in 2D and 3D organoids, 2D U-iRO dominated with mesenchyme and 3D U-iRO with tubule.

overall_design: We analyzed the transcriptome expression profiles (RNA-seq) and chromation accessibility (ATAC-seq) during 2D U-iRO induction. 10X Chromium were used to profile 2D and 3D U-iRO


title: Generation of human kidney organoids from urine cells (ATAC-seq)

overall_design: We analyzed the chromation accessibility (ATAC-seq)  during U-iRO induction


title: In Vitro Propagation of XXY Human Klinefelter Spermatogonia Stem Cells; a step towards new fertility opportunities

city: TORRANCE

first: Yanhe

last: Lue

address: 1124 W. Carson St

department: Medicine

institute: The Lundquist Institute

summary: Human testicular cells of XY and XXY were isolated from cryopreserved tissue in an experimental testicular tissue banking program and propagated in long-term culture for 110 days.

overall_design: Cultured testicular cells were used for cell capture and 10X single cell 3' gene expression sequence library preparation were performed. The resultant library was sequenced using a NovaSeq 6000 SP (100 Cycles).

first: Guillermo

last: Galdon

first: Nicolas

middle: A

last: Deebel

first: Nima

last: Pourhabibi Zarandi

first: Darren

last: Teramoto

first: YanHe

first: Christina

last: Wang

first: Ronald

last: Swerdloff

first: Mark

last: Pettenati

first: William

last: Kearns

first: Stuart

last: Howards

first: Stanley

last: Kogan

first: Anthony

last: Atala

first: Hooman

last: Sadri-Ardekani


title: N-myc mediated translation control is a therapeutic vulnerability in medulloblastoma

city: San Francisco

first: Duygu

last: Kuzuoglu Ozturk

state: California

address: 1450 3rd Street, Helen Diller Cancer Building

institute: UCSF

summary: Deregulation of N-myc is a leading cause of malignant brain tumors in children. To target N-myc-driven medulloblastoma, most research has focused on identifying genomic alterations or on the analysis of the medulloblastoma transcriptome. Here, we have broadly characterized the translatome of medulloblastoma and shown that N-myc unexpectedly drives selective translation of transcripts that promote protein homeostasis. Cancer cells are constantly exposed to proteotoxic stress associated with alterations in protein production or folding. It remains poorly understood how cancers cope with proteotoxic stress to promote their growth. Here, our data unexpectedly revealed that N-myc regulates the expression of specific components (~5%) of the protein folding machinery at the translational level through the major cap binding protein, eukaryotic initiation factor eIF4E.  Reducing eIF4E levels in mouse models of medulloblastoma blocked tumorigenesis. Importantly, targeting Hsp70, a protein folding chaperone translationally regulated by N-myc, suppressed tumor growth in mouse and human medulloblastoma xenograft models. These findings reveal a previously hidden molecular program that promotes medulloblastoma formation and identify new therapies that may have impact in the clinic.

overall_design: Cells were originated from our germline genetically engineered mouse model (GEMM) for MYCN-driven medulloblastoma  (GLT1-TRE-MYCN/Luciferase-GTML), in which a human MYCN transgene was targeted to murine hindbrain neural progenitor cells (Swartling et al., 2010). Medulloblastoma cells were treated for three hours with the ATP-site inhibitor Rapalink-1, which blocks the two translation arms, ribosomal protein S6 kinase (S6K) and eIF4E cap-binding protein downstream of mTORC1; or rapamycin, an allosteric inhibitor that blocks S6K but not eIF4E signaling. Three replicates were used for each condition. Genome-wide ribosome profiling was performed.

last: Kuzuoglu-Ozturk

first: Ozlem

last: Aksoy

first: Davide

last: Ruggero

last: Weiss


title: Generation of human kidney organoids from urine cells (scRNA-Seq)

first: huan

last: chen

overall_design: 10X Chromium were used to profile 2D and 3D U-iRO

first: H

last: Chen

first: Y

last: Yuan

first: B

last: Cai


title: PI3Kδ inhibition potentiates glucocorticoids in B-ALL by decreased receptor phosphorylation and enhanced gene regulation

city: Iowa City

first: Miles

last: Pufall

state: IA

address: 51 Newton Rd., BSB Rm 4-430

department: Biochemistry

institute: University of Iowa

summary: Glucocorticoids, including dexamethasone and prednisone, are key components of therapy for B-lymphoblastic leukemia (B-ALL) that work through the glucocorticoid receptor (GR). However, glucocorticoids are not effective for all patients, leading to poor outcomes, and the high doses used in chemotherapy cause many toxicities. We have shown that inhibition of the leukocyte restricted PIK3δ is a promising way to specifically enhance glucocorticoids in B-ALL, with the potential to improve outcomes without increasing toxicities. Here, we show that the PI3Kδ inhibitor idelalisib potentiates both prednisolone and dexamethasone in both B-ALL cell lines and primary patient specimens, particularly at sub-saturating doses. Potentiation is partially explained by a widespread enhancement of glucocorticoid gene regulation, including effector genes that drive B-ALL cell death. Idelalisib causes a reduction in direct phosphorylation of GR at S203 and S226. Ablation of these phospho-acceptor sites enhances glucocorticoid potency. Phosphorylation of S226 inhibits GR DNA binding, indicating that PI3Kδ mediated phosphorylation directly inhibits GR function in part though reduction of DNA binding affinity. Thus, PI3Kδ inhibition improves glucocorticoid efficacy in B-ALL in part by decreasing GR phosphorylation and enhancing DNA binding and downstream gene regulation. Identification of this and other contributing mechanisms will help identify patients who can most benefit clinically from this combination therapy.

overall_design: We performed RNA-seq (poly A selected) on a BCP-ALL cell line model, NALM-6.  Cells were trerated with glucocoroticoids and/or idelalisib for 24 hours. There were five treatment groups: vehicle, idelalisib only (250 nM), low dexamathasone (5 nM), high dexamethasone (50 nM),  both low dexamethasone and idelalisib, and both high dexamethasone and idelalisib.

first: M

first: Jessica

last: Zimmerman


title: lncExACT1 and DCHS2 Regulate Physiological and Pathological Cardiac Growth

city: Boston

first: Haobo

last: Li

state: MA

address: MEDR410 / Lunder Bldg Dock, 255 Charles St

department: Department of Anesthesia, Critical Care, and Pain Medicine

institute: Massachusetts General Hospital and Harvard Medical School

summary: The heart grows in response to pathological and physiological stimuli, while the former often precedes cardiomyocyte loss and heart failure, the latter paradoxically protects the heart and enhances cardiomyogenesis. Long noncoding RNAs (lncRNAs) are important in cardiac development and disease, less is known about their roles in physiological hypertrophy or cardiomyogenesis. The purpose of this study was to compare transcriptome profilings in exercise-induced physiological cardiac growth and stress-induced pathological cardiac growth. We identified a set of lncRNAs called long noncoding exercise associated cardiac transcripts (lncExACT). One of them, lncExACT1, whose cardiac expression was downregulated after exercise but upregulated after transverse aortic constriction. Inhibition of lncExACT1 induced physiolgoical cardiac growth while overexpression of lncExACT1 induced pathological hypertrophy and heart failure.

overall_design: RNA profiles of hearts from mice receiving eight weeks exercise, or two or eight weeks after transverse aortic constriction

last: Rosenzweig


title: Gene expression profiling of MYC inducible murine tumor models

city: Stanford

first: Dean

last: Felsher

address: 269 Campus Drive

institute: Stanford University

overall_design: Refer to individual Series


title: Gene expression profiling of MYC inducible murine tumor models (tissues) [microarray]

summary: The transcription factor, c-MYC, is a proto-oncogene that is activated in many types of cancer. To study how MYC promotes and maintains the neoplastic phenotype, we use tetracycline-regulated systems in transgenic mice whereby we can conditionally activate MYC. We profile the changes in gene expression when MYC is activated versus inactivated in order to identify a gene signature that is associated with the ability of MYC to promote tumorigenesis.

overall_design: Total RNA was obtained from mouse tumors, driven by the activation of MYC (or another oncogene), as well as from the tissue of control FVB/N mice.

first: Delaney

middle: K

last: Sullivan


title: ETV6 dependency in Ewing sarcoma by antagonism of EWS-FLI1-mediated enhancer activation

city: Cold Spring Harbor

first: Xiaoli

middle: Sky

last: Wu

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: we report a synthetic lethality of ETV6 and EWS-FLI1 in ewing sarcome that is imposed by ETV6 antagonize EWS-FLI1 from particular GGAA microsatellite sites

overall_design: RNA-Seq and ChIP-Seq of different manipulation of ETV6 and EWS-FLI1 in ewing sarcoma cell lines

first: Yuan

last: Gao

first: Christopher

last: Vakoc


title: Gene expression profiling of MYC inducible murine tumor models (cell lines) [microarray]

overall_design: Total RNA was obtained from cell lines derived from the tumors of transgenic mice with tetracycline-regulated MYC expression.


title: Using single cell RNA-seq to assess heterogeneous subpopulations and optimize therapeutic strategy in triple-negative breast cancer cells

city: PORTLAND

first: Hongmei

last: Zhang

address: 2730 SW Moody Ave

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

summary:
Purpose: Triple Negative Breast Cancer (TNBC) is a particularly aggressive form of breast cancer with high intertumoral and intratumoral heterogeneity. Our overall goal in this study is to investigate the heterogeneity of TNBC, and develop effective combination therapy.
Methods: We applied HCC1143 cell line as a representative of aggressive TNBC and performed single cell RNA-seq with 10x genomics platform for cells before and after paclitaxel treatment. Different cell subpopulations were identified with Seurat, and the relationship between different subpoulations were investigated with scEpath.
Results: Different subpopulations were detected in TNBC cell populations. Targetable genes were identified and some of them were validated with drug.

overall_design: Whole transcriptome profiles of HCC1143 cell populations for vehicle control and treated samples at 24h and 72h.

first: Laura

last: Heiser

first: Zhi

last: Hu


title: Effects of 14 days of confinement on blood gene expression profiles in men

city: Tsukuba

first: Masaya

last: Seki

state: Ibaraki

address: Sengen 2-1-1

department: JEM Utilization Center

institute: Japan Aerospace Exploration agency

summary:
The effects of short-term confinement on gene expression profiles in blood were evaluated. Fourteen days confinement study was conducted 2 times. In each experiment, 8 male subjects were stayed in an isolation and confinement facility at Japan Aerospace Exploration Agency. DNA microarray of extracted RNA from whole blood samples revealed that the expression levels of 3,659 genes were significantly altered by the 14-day confinement. The changes in gene expression profiles were not exactly the same as those in response to the other stress conditions, such as chronic psychological stress and spaceflight. In particular, 7 genes, LIN9, AK125040.1, MGC45922, C9orf173-AS1, OR1P1P, KRTAP10-12, and ARFRP1, responded to the confinement prominently.
Therefore, the analysis of expression levels of these genes might be useful to assess the stress responses of human body to the confinement. In addition, biological interpretation of the alteration of gene expression profiles with Ingenuity Pathway Analysis indicated that 14-day confinement stimulated various signaling related to proinflammation and leukocyte extravasation but suppressed apoptosis signaling. In agreement with the interpretation, the decrease of white blood cells in blood was confirmed during the confinement. On the other hand, red blood cells and platelets did not decrease. These results suggest that 14-day confinement is likely to induce shift of white blood cells from “the circulating pool” to “the marginated pool”.

overall_design: Short-term confinement induced gene expression profiles in blood were evaluated. Fourteen days confinement study was conducted 2 times. In each experiment, 8 male subjects were stayed in an isolation and confinement facility.

first: Takashi

last: Ohira

first: Ken-ichi

last: Iwasaki

first: Go

last: Suzuki

first: Satoshi

last: Furukawa


title: Differential Gene expression after peroxiredoxin2 downregulation in human extravillous cytotrophoblast-derived cell line HTR8

status: Public on Oct 17 2022

city: Shanghai

first: Fan

address: 910 Hengshan Rd

institute: International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine

summary: The study was designed to expolre the differential gene expression after peroxiredoxin2 (Prdx2) downregulation by siRNAs transfection in human trophoblast cell line HTR8 compared with negative control.

overall_design: siRNA targeting the human Prdx2 or negative control siRNA were transfected into HTR8 cells. Cells were cultured for 48 h after transfection before they were harvested. Three independent experiments were performed for each sample. The Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray was used to detect gene expression.

first: Yi

last: Lin


title: Identification of the regulation of circMAN1A2-miRNA in esophageal squamous cell carcinoma.

city: Shijiazhuang

first: Lie

last: Liu

address: Jiankang Road No.12

institute: The Fourth Affiliated Hospital of Hebei Medical University

summary: ESCC (Esophageal squamous cell carcinoma) is a common malignant tumor with high morbidity and mortality. CircRNAs (Circular RNAs) play important roles in various cancers including ESCC, the role of circMAN1A2(CircRNA mannosidase alpha class 1A member 2) in ESCC has not been sufficiently elucidated. The purpose of this study is to explore the biological function and potential mechanism of circMAN1A2 in ESCC, so as to provide a solid theoretical basis for circRNAs as a new target for diagnosis and treatment of ESCC.

overall_design: Six samples (including three NC groups and three si-MAN1A2 groups) were used to detect the differential gene expression.The sample labeling, microarray hybridization , washing and data analysis were performed based on the manufacturer's standard protocols.Feature Extraction software was used to analyze array images to get raw data.

first: Baoen

last: Shan

first: Meixiang

last: Sang


title: Expression of LncRNA in oral squamous carcinoma

first: WEI

last: Cao

address: Zhizaoju Road 639

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao  Tong University School of Medicine

summary: To elucidate the biological functions of lncRNA DUXAP9 in the process of oral squamous carcinogenesis and progression, and to evaluate its potential as a clinical predictive biomarker and therapeutic target,and toinvestigate the mechanism on how lncRNA DUXAP9 regulates EZH2,we screened lncRNAs differentially expressed in OSCC

overall_design: To study the differentially expressed lncrnas in oral squamous cell carcinoma, we selected oral cancer tissues and adjacent tissues.

first: Wei


title: Single-cell RNA sequencing of immune landscape in hepatocellular carcinoma treated with sintilimab and sorafenib

city: Guangzhou

first: Feiye

address: No.13, Shiguagang Road, Haizhu District, Guangzhou

institute: Department of Oncology, Southern Medical University Hospital of Integrative Medicine

summary: Checkpoint inhibitors combined with sorafenib for hepatocellular carcinoma (HCC) treatment have achieved satisfactory results in many clinical trials. Understanding the mechanism underlying this modality may provide better strategies to eradicate HCC. In the present study, peripheral blood mononuclear cells (PBMCs) from patients who received combination sintilimab and sorafenib treatment were analyzed by single-cell RNA sequencing (scRNA-seq).

overall_design: Three HCC patients who were confirmed by the computed tomography (CT) and biopsy at Southern Medical University Affiliated Traditional Chinese Medical Hospital were enrolled in the study from 1 Jan 2019 to 1 May 2022.

first: Baoguo

last: Xie

first: Jinzhang

last: Chen

first: Fengsheng


title: Single-cell Transcriptome Atlas of Testis Aging

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

summary: Unhealthy aging of testis seriously affects fertility and life quality of older men, while its interventions depend on in-depth knowledge of the molecular and functional changes of various testicular cell types. Here, we profile human testicular single-cell transcriptomes from young adult, healthy old men and late-onset hypogonadism (LOH) patients, and identified the somatic cells underwent a greater change than germ cells.

overall_design: All donors signed their consent after being fully informed of the goal and characteristics of our study. Aged testis samples (> 55-year-old) were obtained from 4 old male donors who underwent surgical castration for the purpose of prostate cancer treatment. Factors that might affect normal testicular function, such as a history of antiandrogen medications, diabetes mellitus, metastatic testicular malignancy, and abnormal BMI, were excluded. The two LOH patients were denoised according to the presence of at least three sexual symptoms associated with a total testosterone level of less than 3.2 ng/ml and a free testosterone level of less than 64 pg/ml

first: Zhi

last: Zhou

first: Zheng

last: Li


title: Mutation in LBX1/Lbx1 precludes transcription factor cooperativity and causes congenital hypoventilation in humans and mice [RNA-seq]

city: Berlin

first: Daniel

middle: Murad

last: Ibrahim

state: Berlin

address: Augustenburger Platz 1

department: Center for Regenerative Therapies

institute: Berlin Institute of Health

summary: The respiratory rhythm is generated by the preBötzinger complex in the medulla oblongata, and is modulated by neurons in the retrotrapezoid nucleus (RTN), which are essential for accelerating respiration in response to high CO2. Here we identify a LBX1 frameshift (LBX1FS) mutation in patients with congenital central hypoventilation. The mutation alters the C-terminal but not the DNA-binding domain of LBX1. Mice with the analogous mutation recapitulate the breathing deficits found in humans. Furthermore, the mutation only interferes with a small subset of Lbx1 functions, and in particular with development of RTN neurons that coexpress Lbx1 and Phox2b. Genome-wide analyses in a cell culture model show that Lbx1FS and wild-type Lbx1 proteins are mostly bound to similar sites, but that Lbx1FS is unable to cooperate with Phox2b. Thus, our analyses on Lbx1FS (dys)function reveals an unusual pathomechanism; that is, a mutation that selectively interferes with the ability of Lbx1 to cooperate with Phox2b, and thus impairs the development of a small subpopulation of neurons essential for respiratory control.

overall_design: RNA-seq of retinoic acid induced P19 cells expressing virally expressed Phox2b alone or with either Lbx1wt or Lbx1-frameshift constructs

first: Luis

last: Hernandez-Miranda

first: Carmen

last: Birchmeier


title: Soil exposure modulates the immune response to an influenza challenge in a mouse model

city: Chapel Hill

first: Alex

last: McCumber

state: NC

address: 426 Hickory Drive

institute: Duke University

summary: This study began with 72 male 4-week-old BALB/c mice. The mice were split evenly into one of four cohorts: Control, River, Pine, and Road. The control mice were raised with standard corn cob bedding whereas the remaining mice were raised with clean bedding amended with 300 mL of one of three different types of soil. The soil exposure continued throughout the experiment, with 300 mL of new soil added with bi-weekly cage changes. The soils used to amend the cage bedding were previously characterized as having high (Pine), medium (River), and low (Road) diversity. The River and Pine soil were collected from Duke Forest and the Road soil was collected adjacent to Highway 15-501 in Chapel Hill, North Carolina. All mice were given a standard diet and the cages were distributed reverse osmosis treated water through a centralized Lixit® system that was fed to each cage in parallel. After 32 days of standard rearing with amended soils, the mice were exposed via oropharyngeal aspiration to either live influenza A (PR8) virus or heat inactivated (HI) virus.

first: Alexander

first: Yeon

middle: J

last: Kim

first: Joshua

last: Granek

first: Robert

last: Tighe

first: Claudia

last: Gunsch


title: Microarray of Sirt1 KO and control astrocytes after cocktail stimulation

city: Philadelphia

first: Guang-Xian

last: Zhang

state: PA

address: 900 walnut street

institute: Thomas Jefferson University

summary:
The affection of Sirt1 on astrocyte is not well understanded. Here we studied the change of RNA expression profile after Sirt1 knockout in primary astrocyte after stimulating with A1 astrocyte inducing cocktails.
To analyze the change of RNA expression profile after Sirt1 knockout in astrocytes, we built Sirt1 knockout and control astrocytes using crispr technique, and analyzed RNA expression profiles of Sirt1 KO and control astrocytes after treating with cocktail (C1q, IL-1α, TNF-α) by using microarray.

overall_design: Primary astrocytes isolated from p2-3 pups were treated with lentivirus carrying sgScramble (control) or sgSirt1, and selected with puromycin for 3 days. 5×10^5 sgSirt1 or sgScramble treated astrocytes were seeded in a 6-well plate in astrocyte serum-free medium. The following day, cells were treated with cytokine cocktail (C1q, IL-1α, TNF-α) for 24 h. The cells  were collected immediately after cocktail stimulation.  RNA was extracted by using Qiagen RNeasy Plus Kits and used for microarray.

first: Weifeng

first: Dan

last: Xiao

first: Guang-xian


title: Selective Regulation of Tuft Cell-Like Small Cell Lung Cancer by Novel Transcriptional Co-activators C11orf53 and COLCA2

city: Oxford

first: Yang

last: Shi

address: Old Road Campus Research Building, Roosevelt Drive

country: United Kingdom

institute: Ludwig Institute for Cancer Research, University of Oxford

summary: The DepMap project has generated a huge resource for investigating selectively essential genes, which represent potential cancer therapeutic targets. However, manually sorting out which of the hundreds of selectively essential genes is understudied and warrants investigations is time-consuming and probably not practical. To efficiently identify uncharacterized, selectively essential genes, we collected and ranked the 347 selectively essential genes from the DepMap dataset by their PubMed publication counts, based on the assumption that genes with low publication counts are un-studied or under-studied. We successfully validated two of the top candidates in our ranking system, C11orf53 and COLCA2, as new vulnerabilities that are selectively essential in the class II POU domain transcription factor POU2F3-dependent tuft cell-like small cell lung cancer (SCLC) cell lines. Importantly, we found that the sequence motif, which mediates physical interactions of the transcriptional co-activator POU2AF1 with two of the class II POU domain-containing family of transcription factors (POU2F1 and POU2F2), is also present in the N-terminal regions of C11orf53 and COLCA2. We further confirmed that 1) COLCA2 physically interacts with POU2F3 through this conserved sequence motif; 2) this interaction is important for COLCA2 to regulate tuft cell-like SCLC cell growth, and 3) both C11orf53 and COLCA2 contain transcriptional co-activator domains. Consistently, we find similar transcriptomic changes in response to the loss of COLCA2 or POU2F3 in SCLC cells. In summary, our analysis pipeline enables identification and prioritization of understudied but important, selectively essential genes, leading to the identification of two new transcriptional co-activators for the class II POU domain transcription factors. Disruption of this important physical interaction is predicted to be a potential therapeutic strategy to selectively inhibit tuft cell-like SCLCs.

overall_design: We performed RNA-sequencing for NCI-H1048 cells treated with COLCA2 gRNA (2 samples were treated with different COLCA2 gRNAs), POU2F3 gRNA or non-targeting gRNA.

first: Chen


title: RNA-seq of Ideonella sakaiensis 201-F6 when grown on PET, TPA·2Na, and EG

city: Ikoma

first: Shosuke

last: Yoshida

state: Nara

address: 8916-5 Takayama-cho

institute: Nara Institute of Science and Technology

summary: Poly(ethylene terephthalate) (PET)-degrading bacterium Ideonella sakaiensis produces hydrolytic enzymes that convert PET, via mono(2-hydroxyethyl) terephthalate (MHET), into the monomeric compounds, terephthalic acid (TPA) and ethylene glycol (EG). Understanding PET metabolism is critical if this bacterium is to be engineered for bioremediation and biorecycling. TPA uptake and catabolism in I. sakaiensis have previously been studied, but EG metabolism remains largely unexplored despite its importance. First, we identified two alcohol dehydrogenases (IsPedE and IsPedH) and one aldehyde dehydrogenase (IsPedI) in I. sakaiensis as the homologs of EG metabolic enzymes in Pseudomonas putida KT2440. IsPedE and IsPedH exhibited EG dehydrogenase activities with Ca2+ and a rare earth element (REE) Pr3+, respectively. We further found an upregulated dehydrogenase gene when the bacterium was grown on EG, whose gene product (IsXoxF) displays a minor EG dehydrogenase activity with Pr3+. IsPedE displayed a similar level of activity toward various alcohols. In contrast, IsPedH was more active toward small alcohols, whereas IsXoxF was the opposite. Structural analysis with homology models revealed that IsXoxF had a larger catalytic pocket than IsPedE and IsPedH, which could accommodate relatively bulkier substrates. Pr3+ regulated the protein expression of IsPedE negatively; IsPedH and IsXoxF were positively regulated. Taken together, these results indicated that the combination of IsPedH and IsXoxF complements the function of IsPedE in the presence of REEs. IsPedI exhibited dehydrogenase activity toward various aldehydes with the highest activity toward glycolaldehyde (GAD). This study demonstrated a unique alcohol oxidation pathway of I. sakaiensis, which could be efficient in EG utilization.

overall_design: I. sakaiensis cells were cultured in the minimal medium containing PET, TPA·2Na, and EG as a carbon source for 20 h. Cells were collected for total RNA extraction and subsequent RNA-seq. Differential expression of various conditions was analyzed.

first: Akiyo

last: Takayama


title: 3D Biocomposite Culture Enhances Differentiation of Dopamine-like Neurons from SH-SY5Y cells: A Model for Studying Parkinson’s Disease Phenotypes

city: Medford

first: Nicholas

middle: James

last: Fiore

address: 200 College Ave

department: Biomedical Engineering

institute: Tufts University

summary: Studies of underlying neurodegenerative processes in Parkinson’s Disease (PD) have traditionally utilized cell cultures grown on two-dimensional (2D) surfaces. Biomimetic three-dimensional (3D) cell culture platforms have been developed to better emulate features of the brain’s natural microenvironment. We here use our bioengineered brain-like tissue model, composed of a silk-hydrogel composite, to study the 3D microenvironment’s contributions on the development and performance of dopaminergic-like neurons (DLNs). Compared with 2D culture, SH-SY5Y cells differentiated in 3D microenvironments were enriched for DLNs concomitant with a reduction in proliferative capacity during the neurodevelopmental process. Additionally, the 3D DLN cultures were more sensitive to oxidative stresses elicited by the PD-related neurotoxin 1-methyl-4-phenylpyridinium (MPP). MPP induced transcriptomic profile changes specific to 3D-differentiated DLN cultures, replicating the dysfunction of neuronal signaling pathways and mitochondrial dynamics implicated in PD. Overall, this physiologically-relevant 3D platform resembles a useful tool for studying dopamine neuron biology and interrogating molecular mechanisms underlying neurodegeneration in PD.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SH-SY5Y cells differentiated into dopamine-like neuron (DLN) cultures for 15 days using traditional 2D culture dishes and our bioengineered 3D silk-collagen platform. On day 13, 2D- and 3D-differentiated DLN cultures were treated with 1mM 1-methyl-4-phenylpyridinium (MPP) for 48 hours to investigate the effects of culture microenvironment on replicated features of PD.

first: Jackson

middle: D

last: Tamer-Mahoney

first: Afshin

last: Beheshti

first: Thomas

last: Nieland

first: David

middle: L

last: Kaplan


title: A Small Molecule Activator of the TET2 Tumor Suppressor

city: HOUSTON

first: Bin

last: Guo

state: TX

address: 4849 Calhoun Rd

institute: University of Houston

summary: TET2 protein is a dioxygenase that oxidizes 5-methylcytosine and is responsible for DNA demethylation. We found that a small molecule drug (3FM-dC) activates the enzyme activity of TET2. The sequencing data suggest that 3FM-dC induced global changes in DNA hydroxymethylation and gene expression.

overall_design: To determine the effects of 3FM-dC on global gene expression, we performed RNA-seq on control and 3FM-dC treated K-562 cells.


title: Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation

city: Mainz

first: Annabelle

last: Dold

address: Ackermannweg 4

institute: Institute of Molecular Biology, IMB

summary: Makorins are evolutionary conserved proteins that contain C3H-type zinc finger modules and a RING E3 ubiquitin ligase domain. In Drosophila maternal Makorin 1 (Mkrn1) has been linked to embryonic patterning but the mechanism remained unsolved. Here, we show that Mkrn1 is essential for axis specification and pole plasm assembly by translational activation of oskar. We demonstrate that Mkrn1 interacts with poly(A) binding protein (pAbp) and binds specifically to osk 3’ UTR in regions overlapping Bruno1 (Bru1) responsive elements (BREs), which regulate osk translation. We observe increased association of the translational repressor Bru1 with osk mRNA upon depletion of Mkrn1, indicating that both proteins compete for osk binding. Consistently, reducing Bru1 dosage partially rescues viability and Osk protein level in ovaries from Mkrn1 females. We conclude that Mkrn1 controls embryonic patterning and germ cell formation by specifically activating osk translation, most likely by competing with Bru1 to bind to osk 3’ UTR.

overall_design: iCLIP analysis of Mkrn1 in ovaries

first: Heike

last: Hänel

first: Anke

last: Busch

first: Mirko

last: Brüggemann

first: Kathi

last: Zarnack

first: Julian

last: König

first: Jean-Yves

last: Roignant


title: GCN2 enhances the growth and progression of prostate cancer by maintaining amino acid homeostasis [CHARGE-seq]

city: Indianapolis

first: Kirk

middle: Alan

last: Staschke

state: IN

address: 635 Barnhill Drive, MS4063

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

summary: Here we report genome wide tRNA charging analysis (CHARGE seq) on DMSO, GCN2iB and GCN2iB plus essential amino acid (EAA) treated WT LNCaP cells

overall_design: CHARGE Seq on DMSO, GCN2iB and GCN2iB plus essential amino acid (EAA) treated WT LNCaP cells

first: Ricardo

last: Cordova

first: Jagannath

last: Misra

first: Parth

middle: H

last: Amin

first: Angela

last: Klunk

first: Nur

middle: P

last: Damayanti

first: Kenneth

last: Carlson

first: Andrew

last: Elmendorf

first: Hyeong-Geug

last: Kim

first: Emily

middle: T

last: Mirek

first: Bennet

last: Elzey

first: Marcus

last: Miller

first: X Charlie

last: Dong

first: Liang

last: Cheng

first: Tracy

middle: G

last: Anthony

first: Roberto

last: Pili

first: Ronald

middle: C

last: Wek


title: DNase-seq from kidney (ENCSR291KQU)

status: Public on Oct 16 2022

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: RNA-Seq Transcriptomic analysis in tumor and non-tumor tissues of Atg7-/- and Atg7-/-/Hmgb1-/- livers

first: Xiao-Ming

last: Yin

address: 975 W Walnut St IB411/406

department: Pathology and Laboratory Medicine

institute: Indiana University

summary: HMGB1 is important for tumor development of autophagy-deficient liver. However, detailed molecular signals impacted by HMGB1 is unclear. RNA seq data will provide a comprehensive gene expression profile data that will help to dissect the signaling pathways affected by HMGB1 during tumorigenesis in autophagy deficient liver.

overall_design: 3 samples per group, total 12 samples, from 4 different groups of 15 month old mouse- Atg7-/- Tumor,Atg7-/- non-Tumor, Atg7-/-/Hmgb1-/- tumor, and Atg7-/-/Hmgb1-/- non-tumor

first: Bilon

last: Khambu


title: Tumor-Infiltrating Myeloid Cells Confer de novo Resistance to PD-L1 Blockade through EMT-stromal and Tgf-beta Dependent Mechanisms

city: New York

first: Haocheng

last: Yu

address: 1 Gustave L. Levy Place

department: Precision Immunology Institute

institute: Icahn School of Medicine at Mount Sinai

summary: Most bladder cancers are poorly responsive to immune checkpoint blockade (ICB) of PD-L1. Thus, there is a need to define mechanisms of de novo resistance including contributions from tumor infiltrating immune cells. In this study, we used single-cell transcriptional profiling to map and define infiltrating myeloid cells in 10 human bladder tumors. Human data sets were qualitatively compared with myeloid data sets from the carcinogen (BBN) induced mouse model of bladder cancer which we have demonstrated to be poorly responsive to PD-L1 blockade. We previously established a signature of acquired ICB resistance which we apply here to new human and murine tumor data sets that have not received prior ICB (or systemic treatment). In doing so, we reveal conservation in EMT-stromal core genes and TGF beta signaling between human and mouse myeloid cells consistent with signatures of de novo ICB resistance. Untreated BBN tumors were highly infiltrated with M0-M2 macrophages, low in T-NK infiltration and modeled a patient subpopulation with poor survival outcome. Concordantly, the combined targeting of TGFb + PD-L1 reverted immune cell exclusion and resulted in increased survival and delayed BBN mouse tumor progression. These data constitute the stromal and myeloid cell populations as providing a coordinate mechanism de novo resistance to PD-L1 blockade in a TGF-beta dependent manner.

overall_design: In this study, 10 human primary bladder cancer samples were obtained from patients who underwent either trans urethral resection bladder tumor (TURBT) or cystectomy under approval of the Mount Sinai School of Medicine IRB and written consent from all subjects. Resected tumor sample were examined by a genitourinary pathologist who confirmed the pathological staging and tumor content. Tumor tissues were then resected and dissociated to the single cell level in a solution of RPMI-10% FBS (Gibco) + 1% type 1 collagenase (Gibco). The dissociate is subject to mechanical dissociation through a 16G needle and syringe (5-10 passes) and then a 21.5G needle (5-10 passes). Single cell dissociates were then sorted into CD45 positive/negative cells using a BD Aria after cell staining using a BV510-CD45 antibody (Biolegend) and DAPI stain. Single cell suspensions of all sorted samples were then resuspended in BSA (0.2 % in PBS) at a concentration of 2x10^6 cells/ml followed by barcoding with a 10x Chromium Controller (10x Genomics). Sequencing was done on a Nextseq 500 platform.

first: John

last: Sfakianos

first: Matthew

last: Galsky

first: Nina

last: Bhardwaj

first: Jun

last: Zhu

first: Li

last: Wang


title: RNA Sequencing Reveals Sex Differences in Transcriptional Changes in Muscle Tissue in Response to Muscle Pain in Sedentary and Physically Active Mice

city: Iowa City

first: Michael

last: Chimenti

address: 431 Newton Road

department: Iowa Institute of Human Genetics

institute: University of Iowa

summary: The goal of this study was to use RNA sequencing to identify sex specific transcriptional changes in the development of muscle pain and uncover novel mechanisms through which physical activity prevents the onset of muscle pain. We performed bulk RNA sequencing of the gastrocnemius muscle which is where we induce muscle pain. We found distinct sex differences in the transcriptional alterations in the muscle following induction of muscle pain. We also identified several pathways in which exercise was able to prevent against the development of muscle pain.

overall_design: Comparative gene expression  analysis of RNA-seq data for gastrocnemius muscle tissue of C57/BL6 mice. Animals were grouped as pain free, sedentary with muscle pain, or physically active with muscle pain. Pain free animals served as control for both the sedentary and physically active mice. Male and female data sets were analyzed seperately and then differentially expressed genes were compared between the sexes.

first: Joseph

middle: B

last: Lesnak

first: Kazuhiro

last: Hayashi

first: Ashley

middle: N

last: Plumb

first: Adam

last: Janowski

middle: S

first: Kathleen

last: Sluka


title: Systemic LSD1 inhibition prevents aberrant remodeling of metabolism in obesity

city: La Jolla

last: Wortham

address: 2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102

institute: University of California, San Diego

summary: The transition from lean to obese states involves systemic metabolic remodeling that impacts insulin sensitivity, lipid partitioning, inflammation, and glycemic control. Here, we have taken a pharmacological approach to test the role of a nutrient-regulated chromatin modifier, lysine-specific demethylase (LSD1), in obesity-associated metabolic reprogramming. We show that systemic administration of an LSD1 inhibitor (GSK-LSD1) reduces food intake and body weight, ameliorates non-alcoholic fatty liver disease (NAFLD), and improves insulin sensitivity and glycemic control in mouse models of obesity. GSK-LSD1 has little effect on systemic metabolism of lean mice, suggesting LSD1 has a context-dependent role in promoting maladaptive changes in obesity. Analysis of insulin target tissues identified white adipose tissue as the major site of insulin sensitization by GSK-LSD1, where it reduces adipocyte inflammation and lipolysis. We demonstrate that GSK-LSD1 reverses NAFLD in a non-hepatocyte-autonomous manner, suggesting an indirect mechanism potentially via inhibition of adipocyte lipolysis and subsequent effects on lipid partitioning. Pair-feeding experiments further revealed that effects of GSK-LSD1 on hyperglycemia and NAFLD are not a consequence of reduced food intake and weight loss. These findings suggest that targeting LSD1 could be a strategy for treatment of obesity and its associated complications including type 2 diabetes and NAFLD.

overall_design: mRNA-seq was used to assess transcriptional changes in gWAT in db/db mice treated with the Lsd1 inhibitor GSK-LSD1 or vehicle for 6 weeks. db/+ mice treated with vehicle were used as a lean control.


title: Drug Delivery in Plants Using Silk Microneedles

city: Singapore

first: Sally

last: Koh

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: New systems for agrochemical delivery in plants will foster precise agricultural practices and provide new tools to study plants and design crop traits, as standard spray methods suffer from elevated loss and limited access to remote plant tissues. Silk-based microneedles can circumvent these limitations by deploying a known amount of payloads directly in plants’ deep tissues. However, plant response to microneedles’ application and microneedles’ efficacy in deploying physiologically relevant biomolecules are unknown. Here, we show that gene expression associated with Arabidopsis thaliana wounding response decreases within 24 hours post microneedles’ application. Additionally, microinjection of gibberellic acid (GA3) in A. thaliana mutant ft-10 provides a more effective and efficient mean than spray to activate GA3 pathways, accelerating bolting, and inhibiting flower formation. Microneedles’ efficacy in delivering GA3 is also observed in several monocot and dicot crop species, i.e., tomato (Solanum lycopersicum), lettuce (Lactuca sativa), spinach (Spinacia oleracea), rice (Oryza Sativa), maize (Zea mays), barley (Hordeum vulgare), and soybean (Glycine max). The wide range of plants that can be successfully targeted with microinjectors opens the doors to their use in plant science and agriculture.

overall_design: 30-day old ft-10 A. thaliana were injected with GA3-loaded or mock silk microneedles (the mass ratio of silk to GA3 = 60mg : 5.19mg), for a total duration of 0h (no injection), 3h (GA3 microneedle), 24h (GA3 or mock microneedle), and 168h (GA3 microneedle). There are 2-3 biological replicates per timepoint/treatment.

first: Daisuke

last: Urano


title: Identification of slow-cycling cells in Ewing sarcoma

city: Kobe

first: Shunsuke

last: Yahiro

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Orthopaedic Surgery

institute: Kobe University Graduate School of Medicine

summary: We identified slow-cycling cells (SCCs) in Ewing sarcoma using a label retention assay with CFSE. We labeled cells of SK-ES-1, an Ewing sarcoma cell line, with CFSE. After 5 days culture, we isolated cells retaining strong fluorescence (upper, ~10%) as SCCs and other cells (lower, ~90%) as non-slow-cycling cells (non-SCCs) using FACS AriaTM Ⅲ cell sorter.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SCCs and non-SCCs.

first: Teruya

last: Kawamoto

first: Shuichi

last: Fujiwara


title: CXCL12 defines lung endothelial heterogeneity and promotes distal vascular growth

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

summary: In adults, there is a growing amount of data uncovering the cellular diversity of the pulmonary circulation and mechanisms governing vascular repair after injury, however, molecular and cellular mechanisms contributing to the morphogenesis and growth of the pulmonary vasculature during embryonic development are less clear. Importantly, deficits in vascular development lead to a large number of lung diseases in children, indicating a need to uncover fetal programs that promote pulmonary vascular growth. To address this, we used a transgenic mouse reporter for expression of Cxcl12, an arterial hallmark gene, and performed single-cell RNA sequencing on isolated Cxcl12-DsRed+ endothelium to assess cellular heterogeneity within pulmonary endothelium. Combining cell annotation, gene ontology analysis, and spatial transcriptomics allowed us to segregate the developing artery into spatially and functionally distinct subpopulations.  In addition, expression of Cxcl12 suggests a morphogen gradient from arteries to capillaries, suggesting directed cell migration for pulmonary vascular development.  Disruption of this gradient led to abnormal branching and pulmonary vascular hypoplasia. These data provide evidence for arterial endothelial functional heterogeneity and reveal conserved signaling mechanisms essential for pulmonary vascular development.

overall_design: Single Cell RNAseq of dissociated mouse lungs at ages E13.5, E15.5, E18.5, and P8 then sorted for Cxcl12-DsRed+ cells (DsRed+/CD31+/EpCAM-/CD45-). Further, Cxcl12 homozygous null (Cxcl12DsRed/DsRed) embryos at E18.5 were also analyzed and compared to Cxcl12 heterozygous (Cxcl12DsRed/+) E18.5 controls.

first: Prashant

last: Chandrasekaran

first: Nicholas

middle: M

last: Negretti

first: Aravind

last: Sivakumar

first: Maureen

last: Peers de Nieuburgh

first: Joanna

first: Fatima

last: Chaudhry

first: Nigel

last: Michki

first: Hongbo

last: Wen

first: Sukhmani

last: Kaur

first: MinQi

last: Lu

first: Jarod

middle: A

last: Zepp

first: Lisa

middle: R

last: Young

first: David

last: Frank


title: DNase-seq from frontal cortex (ENCSR391LJN)

first: ENCODE

last: DCC


title: Stepwise Generation of Human Induced Pluripotent Stem Cell-Derived Cardiac Pericytes to Model Coronary Microvascular Dysfunction

city: palo alto

first: Chun

last: Liu

address: 1291 Welch Road BMI building, 3200-CVI Rm

institute: stanford

summary: Cardiac pericytes (PC), a major mural cell type maintaining homeostasis, integrity, and perfusion of the coronary microvasculature. Here, we report a stepwise, developmental trajectory-matched approach to generate first-of-its-kind cardiac PCs from human induced pluripotent stem cells (iPSCs), which were shown to transcriptionally and functionally resemble their primary counterparts.

overall_design: We performed gene expression profiling analysis using data obtained from RNA-seq of iPSC differentiated cardiac pericytes (PCs), PCs with sunitinib treatment, and PCs with sunitinib and thalidomide treatment.

first: Mengcheng

last: Shen


title: GCN2 enhances the growth and progression of prostate cancer by maintaining amino acid homeostasis [mRNA-seq]

first: Kirk

last: Staschke

summary: Here we report mRNA seq on DMSO and GCN2iB treated WT LNCaP cells

overall_design: mRNA Seq on DMSO and GCN2iB treated WT LNCaP cells.

first: Ricardo

last: Cordova

first: Jagannath

last: Misra

first: Parth

last: Amin

first: Angela

last: Klunk

first: Nur

last: Damayanti

first: Kenneth

last: Carlson

first: Andrew

last: Elmendorf

first: Hyeong-Geug

last: Kim

first: Emily

last: Mirek

first: Bennet

last: Elzey

first: Marcus

last: Miller

first: X Charlie

last: Dong

first: Liang

last: Cheng

first: Tracy

last: Anthony

first: Roberto

last: Pili

first: Ronald

last: Wek


title: DNase-seq from HCT116 (ENCSR799GSS)

first: ENCODE

last: DCC


title: DNase-seq from HCT116 (ENCSR795ZKB)


title: DNase-seq from natural killer cell (ENCSR794TLA)


title: DNase-seq from naive B cell (ENCSR796PIM)


title: DNase-seq from thymus (ENCSR794LIK)


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR794KUS)


title: DNase-seq from Calu3 (ENCSR366NBE)


title: DNase-seq from kidney (ENCSR788KLG)


title: DNase-seq from activated T-helper 2 cell (ENCSR780ABS)


title: DNase-seq from PC-9 (ENCSR781TYE)


title: ATAC-seq from heart left ventricle (ENCSR745CGG)

summary:
ATAC-seq on human heart left ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: WGBS from motor neuron (ENCSR778ACS)

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: Control PGP - iNPC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from layer of hippocampus (ENCSR385DQL)


title: DNase-seq from kidney (ENCSR373ZJT)


title: DNase-seq from ovary (ENCSR362ZRQ)


title: DNase-seq from right cerebral cortex (ENCSR740POH)


title: DNase-seq from left cerebral cortex (ENCSR386OBA)


title: DNase-seq from type B pancreatic cell (ENCSR362ZFC)


title: ATAC-seq from heart right ventricle (ENCSR374ZRW)

summary:
ATAC-seq on human heart right ventricle

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from memory B cell (ENCSR736VVP)


title: DNase-seq from urinary bladder (ENCSR759ZVU)


title: DNase-seq from spleen (ENCSR736DMJ)


title: ATAC-seq from heart left ventricle (ENCSR769DGC)


title: DNase-seq from left cerebral cortex (ENCSR357REQ)


title: DNase-seq from frontal cortex (ENCSR356UVK)


title: DNase-seq from lung (ENCSR756QHG)


title: DNase-seq from kidney (ENCSR352FCL)


title: DNase-seq from activated CD4-positive, alpha-beta T cell (ENCSR365CUB)


title: DNase-seq from right cerebral cortex (ENCSR751LYJ)


title: DNase-seq from cerebellum (ENCSR336MBU)


title: DNase-seq from frontal cortex (ENCSR338GYD)


title: DNase-seq from cerebellum (ENCSR335MHR)


title: DNase-seq from layer of hippocampus (ENCSR348NWY)


title: ATAC-seq from heart right ventricle (ENCSR327DCG)


title: DNase-seq from frontal cortex (ENCSR325RZJ)


title: DNase-seq from HCT116 (ENCSR595CME)


title: ATAC-seq from bile duct (ENCSR325NFE)

summary:
ATAC-seq on human bile duct

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: ATAC-seq from stimulated activated effector memory CD8-positive, alpha-beta T cell (ENCSR335XRZ)


title: DNase-seq from naive B cell (ENCSR326TID)


title: ATAC-seq from left cardiac atrium (ENCSR330WUK)

summary:
ATAC-seq on human left cardiac atrium

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from ovary (ENCSR591ILA)


title: ATAC-seq from heart left ventricle (ENCSR593YFB)


title: DNase-seq from layer of hippocampus (ENCSR315NES)


title: DNase-seq from spleen (ENCSR597QYA)


title: DNase-seq from layer of hippocampus (ENCSR581XCY)


title: DNase-seq from right cerebral cortex (ENCSR571UMX)


title: DNase-seq from inflammatory macrophage (ENCSR593WXK)


title: WGBS from motor neuron (ENCSR310GNQ)

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: ALS-29 - iPSC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from T-cell (ENCSR560MXA)


title: ATAC-seq from ovary (ENCSR571JFO)

summary:
ATAC-seq on human ovary

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from left cerebral cortex (ENCSR559CFZ)

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from right cerebral cortex (ENCSR551ZTT)


title: DNase-seq from spleen (ENCSR718NBH)


title: DNase-seq from adrenal gland (ENCSR551FWJ)


title: DNase-seq from layer of hippocampus (ENCSR544UYQ)


title: DNase-seq from urinary bladder (ENCSR193XFZ)


title: DNase-seq from naive B cell (ENCSR184TUE)


title: WGBS from motor neuron (ENCSR707MKB)

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: ALS-52 - iNPC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from left cerebral cortex (ENCSR538SKV)


title: DNase-seq from layer of hippocampus (ENCSR529QVB)


title: DNase-seq from frontal cortex (ENCSR193OYD)


title: DNase-seq from cerebellum (ENCSR181OOF)


title: DNase-seq from CD4-positive, alpha-beta memory T cell (ENCSR526TFD)


title: ATAC-seq from sciatic nerve (ENCSR533WFB)

summary:
ATAC-seq on human sciatic nerve

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from naive thymus-derived CD4-positive, alpha-beta T cell (ENCSR181OGW)


title: DNase-seq from HCT116 (ENCSR542UWN)


title: DNase-seq from CD4-positive, CD25-positive, alpha-beta regulatory T cell (ENCSR534RXN)


title: DNase-seq from heart (ENCSR541MWB)


title: ATAC-seq from mucosa of urinary bladder (ENCSR548SSP)

summary:
ATAC-seq on human mucosa of urinary bladder

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: DNase-seq from HCT116 (ENCSR980GWI)


title: WGBS from motor neuron (ENCSR519EKA)

summary:
Whole genome bisulfite-seq on human motor neuron cell lines derived from neural progenitor cells: ALS-28 - iPSC

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf