title: Proteomic and single-cell transcriptomic dissection of human plasmacytoid dendritic cell response to influenza virus

status: Public on Mar 10 2022

city: Mahasset

first: Andrew

last: Shih

address: 350 Community Dirive

institute: Feinstein Institute - Northwell Health

summary: Plasmacytoid dendritic cells (pDCs) represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons (IFN-I). This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in response to challenge with live influenza H1N1. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversification following stimulation. Our data reveal an abundance of protein species released by pDCs in addition to IFN-I, and evidence highly specialized roles within the pDC population ranging from dedicated cytokine super-producers to cells with APC-like functions. Moreover, dynamic expression of transcription factors and surface markers characterize activated pDC fates.

overall_design: pDCs were stimulated with flu virus and examined at 0, 6 and 24 hours to see their temporal response

first: Mustafa

middle: H

last: Ghanem

first: Houman

last: Khalili

first: Emily

last: Werth

first: Jayanta

middle: K

last: Chakrabarty

first: Lewis

last: Brown

first: Kim

middle: R

last: Simpfendorfer

first: Peter

last: Gregersen


title: Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression

status: Public on Mar 11 2022

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

country: USA

institute: The Wistar Institute

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
human gammaherpesvirus 4

platform_organism:
Homo sapiens
human gammaherpesvirus 4

overall_design: Refer to individual Series


title: Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate [ATAC-seq]

status: Public on Mar 08 2022

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

type: Genome binding/occupancy profiling by high throughput sequencing

summary: During cardiac development, cells from the precardiac mesoderm fuse to form the primordial heart tube, which then grows by addition of further progenitors to the venous and arterial poles. In the zebrafish, wilms tumor 1 transcription factor a (wt1a) and b (wt1b) are expressed in the pericardial mesoderm at the venous pole of the forming heart tube. The pericardial mesoderm forms a single layered mesothelial sheet that contributes to further the growth of the myocardium, and forms the proepicardium. Proepicardial cells are subsequently transferred to the myocardial surface and give rise to the epicardium, the outer layer covering the myocardium in the adult heart. wt1a/b expression is downregulated during the transition from pericardium to myocardium, but remains high in proepicardial cells. Here we show that sustained wt1 expression impaired cardiomyocyte maturation including sarcomere assembly, ultimately affecting heart morphology and cardiac function. ATAC-seq data analysis of cardiomyocytes overexpressing wt1 revealed that chromatin regions associated with myocardial differentiation genes remain closed upon wt1b overexpression in cardiomyocytes, suggesting that wt1 represses a myocardial differentiation program. Indeed, a subset of wt1a/b-expressing cardiomyocytes changed their cell adhesion properties, delaminated from the myocardial epithelium, and upregulated the expression of epicardial genes, as confirmed by in vivo imaging. Thus, we conclude that wt1 acts as a break for cardiomyocyte differentiation by repressing chromatin opening at specific genomic loci and that sustained ectopic expression of wt1 in cardiomyocytes can lead to their transformation into epicardial cells.

overall_design: In this study we compared genome accessibility between two zebrafish transgenic lines: Tg(eGFP:5xUAS:RFP; gcryst:cerulean)cn15/Tg(myl7:Gal4)cbg2Tg, which served as the control group and Tg(eGFP:5xUAS:wt1b; gcryst:cerulean)cn15/Tg(myl7:Gal4)cbg2Tg, representing the experimental group. For each group (control and experimental) 3 replicates were analyzed

first: Ines

last: Marques

first: Alexaner

last: Ernst

first: Prateek

last: Arora

first: Andrej

last: Vianin

first: Tanja

last: Hetke

first: Andrés

last: Sanz-Morejón

first: Uta

last: Naumann

first: Adolfo

last: Odriozola

first: Xavier

last: Langa

first: Laura

last: Andrés-Delgado

first: David

last: Haberthür

first: Benoît

last: Zuber

first: Carlos

last: Torroja

first: Ruslan

last: Hlushchuk

first: Marco

last: Osterwalder

first: Filipa

last: Simões

first: Christoph

last: Englert


title: Dietary Inclusion of Hydrolyzed Debaryomyces hansenii Yeasts Modulates Physiological Responses in Plasma and Immune Organs of Atlantic Salmon (Salmo salar) Parr Exposed to Acute Hypoxia Stress

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

summary: The present work studies the effect of  Debaryomyces hansenii yeast-based products on physiological responses in Atlantic salmon exposed to a short-term stress. For this, a control fishmeal-based diet (CD) and experimental diets containing 0.1% of Debaryomyces hansenii were fed to fish for 8 weeks in fresh water. At the end of the feeding experiment, fish were exposed to 1-minute hypoxia stress and samples were collected post-stress

overall_design: Gill mRNA profiles from Atlantic salmon after a short-term stress

first: Margareth

last: Øverland


title: ACTL6a knockout peripheral nerve RNA seq at postnatal day 3

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Cells need to integrate chemical and physical signals into transcriptional programs. In the peripheral nerves, axonal caliber selection by specialized Schwann cells, is critical for developmental myelination. However, only mechanisms through which Schwann cells sense chemical signals are well characterized. We identify ACtin-Like protein 6a (ACTL6a), a component of the SWI/SNF chromatin remodeling complex, as critical for axonal caliber recognition and developmental myelination. ACTL6a is expressed in the developing nerve and, when activated by contact with axons or nanofibers of specific caliber, it promotes the eviction of repressive histone marks thereby enhancing the transcriptional program of myelination. Mutant mice with Schwann cells lacking ACTL6a display aberrant recognition of axonal caliber, resulting in defective radial sorting and lower levels of transcripts regulating myelination of developing nerves. We suggest that developing peripheral nerves require an ACTL6a-dependent integration of physical and chemical signals in Schwann cells to release of repressive histone modifications and promote myelination.

overall_design: compare RNA seq results from the postnatal day 3 sciatic nerve of wild type and  CnpcreActl6a mouse mutant

first: Eric

last: Tsai

first: Dennis

last: Huang


title: Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate

first: Nadia

last: Mercader


title: Single-cell transcriptomic analysis of blood T cells from healthy controls, MS patients and COVID-19 patients by 10X genomics

city: Stanford

first: Mark

last: Davis

state: CA

address: Stanford University

institute: Institute for Immunity, Transplantation and Infection

summary: In order to better understand the functional properties of this type of cells under different circumstances, we integrated the single-cell RNA-seq data of peripheral blood CD8+ T cells from healthy subjects, MS patients and COVID-19 patients generated from the 10X Genomics platform using the Seurat package. KIR+CD8+ T cells from different conditions (healthy, MS, and COVID-19) formed a distinct cluster with high expression of effector genes (GZMB and PRF1) as well as KIR transcripts. These findings reveal the commonality of KIR+CD8+ T cells across physiological and diseased status as well as their uniqueness relative to other CD8+ T cells.

overall_design: Pan T cells were isolated from the blood of healthy subjects (N=4) and MS patients (N=6) and then subjected to scRNA-seq analysis by 10X genomics. 10X scRNA-seq data of blood CD8 T cells from COVID-19 patients (N=25) were acquired  from ArrayExpress: E-MTAB-9357.

first: Jing

last: Li

first: Naresha

last: Saligrama

first: Joy

last: Pai

first: Maxim

last: Zaslavsky


title: Single cell RNASeq analysis of memory TH2 cell response to an intestianl nematode

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

country: Germany

institute: BIH at Charité

summary: Intestinal parasitic nematodes, affecting a quarter of the world’s population, typically elicit prominent effector Th2-driven host immune responses. However, a more detailed understanding of nematode-induced memory Th2 responses remains scarce. We investigated the activation of peritoneal memory Th2 cells and the mechanisms driving early recall responses to the enteric nematode Heligmosomoides polygyrus in mice. We show memory Th2 cells with distinct transcriptional profiles to persist systemically in lymphoid and non-lymphoid tissues following cure of infection. Moreover, peritoneal memory Th2 cells display strong cytokine production, upregulate costimulatory marker Ox40 (CD134) and IL-5 production in a parasite-specific manner as early as 3 days following challenge infection. This effect is paralleled by an influx of Ox40L+ dendritic cells (DC) and eosinophils, both appearing exclusively in the peritoneum of reinfected mice. Finally, we show that peritoneal mesothelial cells (PeM) significantly downregulate their expression of VCAM-1 and ICAM-1 in response to a secondary infection, pointing towards an involvement in immune cell efflux. Thus, our data indicate a pivotal role of the peritoneum for memory Th2 responses and a role for PeM cells in immune cell recruitment, activation and efflux during recall responses to a strictly intestinal pathogen.

overall_design: RNA from single TH2 cells derived from different tissues of two mice cured after nematode infection

first: Birgit

last: Sawitzki

first: Ulrike

last: Krüger

first: Marten

last: Jäger

first: Ivet

last: Yordanova


title: Sperm heterogeneity and DNMT/TET activities do not account for sperm DNA methylation changes observed in the epididymis

city: BREST

first: Delphine

last: Bernard

address: 22 avenue Camille Desmoulins

department: Faculté de Médecine

country: France

institute: UMR1078 - Université de Bretagne Occidentale

type: Methylation profiling by high throughput sequencing

summary: Following their production in the testis, spermatozoa enter the epididymis to gain their motility and fertilizing abilities. This post-testicular maturation coincides with sperm epigenetic profile changes that influence the progeny outcome. While recent studies underscored the dynamics of small non-coding RNAs in the maturing spermatozoa, little is known regarding sperm methylation changes and their impact at the post-fertilization level. To map out the sperm methylome dynamics, we purified spermatozoa by FACS from the testis and the different epididymal segments (i.e. caput, corpus and cauda) of CAG/su9-DsRed2; Acr3-EGFP transgenic mice. Reduced-Representation Bisulfite Sequencing (RRBS-Seq) performed on DNA from these respective sperm populations indicated that high methylation changes were observed between spermatozoa from the caput vs. testis with 5546 entries meeting our threshold values (q value < 0.01, methylation difference above 25 %). Most of these changes were transitory during epididymal sperm maturation according to the low number of entries identified between spermatozoa from cauda vs. testis.

overall_design: DNA methylation profile of isolated sperm from testis, caput, corpus, and cauda

first: Hong

last: Chen

first: Marie-Pier

last: Scott-Boyer

first: Arnaud

last: Droit

first: Claude

last: Robert

first: Clémence

last: Belleannée


title: Zeb1 regulates mammary basal epithelial fate and proliferation dynamics through modulating EMT gene expression and Wnt signaling

city: Irvine

first: Lupe

last: Gutierrez

address: 825 Health Sciences Rd D288

institute: University of California, Irvine


title: Transcriptome analysis in placenta, fetal duodenum and jejunum

status: Public on Mar 07 2022

city: Nanjing

first: HD

last: Guo

address: Weigang NO.1

country: China

institute: Nanjing Agricultural University

summary: We aimed to investigate the effects of maternal heat stress on the expression of  differentilally expressed genes in th placenta, fetal duodenum and jejunum

overall_design: Placenta, fetal  duodenum and jejunum mRNA profiles in the IUTN and IUHS groups (There are 18 samples in the study and three biological replicates per group  in each tissue)

first: Huiduo


title: Single cell RNA-seq of adult mouse mammary epithelium from control and  Zeb1 MSKO mice

summary: Molecular/cellular events that associate with epithelial-to-mesenchymal transition (EMT) are linked to acquisition of cancer stem cell traits, but whether EMT mechanisms regulate tissue epithelial cell fate and stem cell activity in vivo remains ambiguous. Using single-cell RNA sequencing, we detect heterogeneous EMT gene expression in stem cell-containing mammary basal/myoepithelial cells that normally possess both epithelial and smooth muscle characteristics. We show that EMT-inducing transcription factor Zeb1 is required within the mammary epithelium for ductal branching morphogenesis and regeneration, and that it promotes basal cell fate and regulates stem cell proliferation dynamics. We provide genetic and molecular evidence for EMT-dependent and -independent mechanisms of Zeb1 function, and show that Zeb1 cooperates with YAP to directly activate targets that inhibit Wnt signaling or control cell cycle. Together, our findings underscore Zeb1-mediated EMT control in governing mammary basal cell fate and proliferative activity, but with an interesting turn that involves mechanisms beyond EMT.

overall_design: Droplet-based single cell RNA-seq experiments were performed to identify transcriptomic heterogeneity between control and Zeb1 MSKO cells in the mammary gland.

first: Xing

last: Dai

first: Yingying

last: Han

first: Alvaro

last: Villareal-Ponce

first: Guadalupe


title: Highly efficient prime editing by introducing same-sense mutations in pegRNA or stabilizing its structure.

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Prime editors (PEs) can mediate versatile genome editing but their efficiency remains low. Here, we developed spegRNA by introducing same-sense mutations at proper positions in the reverse-transcription template of pegRNA to increase PE’s single-base editing efficiency or apegRNA by altering the pegRNA secondary structure to increase PE’s indel-editing efficiency . When used in PE3 and PE5, the efficiencies of sPE3, aPE3, sPE5 and aPE5 were all enhanced significantly.

overall_design: Development of spegRNA and apegRNA to improve PE editing efficiency

first: Jia

first: Xiaodong

last: Sun

first: Xiaosa

last: Li

first: Lina

last: Zhou

first: Bao-Qing

last: Gao

first: Guangye

first: Xiao

last: Wang

first: Ying

last: Wei

first: Wenyan

first: Zixian

first: Jifang

first: Runze

first: Junjie

last: Zhu

first: Wenchao

last: Xu

first: Jing

last: Wu

first: Bei


title: Single cell RNA seq of adult mouse mammary gland using Fluidigm C1 platform.

first: Lupe

overall_design: Microfluidics enabled single cell RNA-seq experiment was performed on single cells from mouse mammary gland

first: Xing

first: Yingying

first: Alvaro

first: Guadalupe


title: Downregulation of WT1 transcription factor gene expression is required to promote myocardial fate [RNA-seq]

first: Nadia

last: Mercader

overall_design: Dorsal pericardium, proepicardium and heart-tube were manually dissected, with tungsten needles, from 60 hpf epi:eGFP;myl7:mRFP zebrafish larvae. A minimum of 10 of each tissue/organ were collected and pooled for each sample. For pericardium, two samples were analysed. For the proepicardium 3 samples were analysed. For heart tube 3 samples were analysed.

first: Ines

last: Marques

first: Alexaner

last: Ernst

first: Prateek

last: Arora

first: Andrej

last: Vianin

first: Tanja

last: Hetke

first: Andrés

last: Sanz-Morejón

first: Uta

last: Naumann

first: Adolfo

last: Odriozola

first: Xavier

last: Langa

first: Laura

last: Andrés-Delgado

first: David

last: Haberthür

first: Benoît

last: Zuber

first: Carlos

last: Torroja

first: Ruslan

last: Hlushchuk

first: Marco

last: Osterwalder

first: Filipa

last: Simões

first: Christoph

last: Englert


title: Transcriptional profiling of human KIR+ and KIR- CD8 T cells by bulk RNA-seq

first: Mark

last: Davis

summary: Previous reports show that Ly49+CD8+ T cells can suppress autoimmunity in mouse models of autoimmune diseases. Here we find a markedly increased frequency of CD8+ T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalents of the Ly49 family, in the blood and inflamed tissues of various human autoimmune diseases. Moreover, KIR+CD8+ T cells can efficiently eliminate pathogenic gliadin-specific CD4+ T cells from Celiac disease (CeD) patients’ leukocytes in vitro. Furthermore, we observe elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 and influenza-infected patients, and correlate with disease severity and vasculitis in COVID-19. Expanded KIR+CD8+ T cells from these different diseases display shared phenotypes and similar T cell receptor sequences. These results characterize a regulatory CD8+ T cell subset in humans, broadly active in both autoimmune and infectious diseases, which we hypothesize functions to control self-reactive or otherwise pathogenic T cells.

overall_design: KIR+ and KIR- CD8 T cells (CD3+CD56-CD8+) were sorted from healthy subjects (N=5), MS (N=3), SLE (N=4) or CeD (N=1) patients and then subjected to RNA-seq analysis. CD8 T cells with high or low  expression of KIR2DL3 or KIR3DL1 were sorted from the blood of healthy subjects (N=3) and subjected to RNA-seq analysis.

first: Jing

last: Li

first: Michael

last: Sikora


title: The noncanonical cGAS-STING-PERK pathway enables a selective translation program and underlies organ fibrosis [STING2]

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Innate DNA sensing via the cGAS-STING pathway surveys both microbial invasion and cellular damage, constituting a ubiquitous mechanism for host defense and tissue homeostasis. However, very little is known about the signaling mechanism(s) and physiological impacts downstream of cGAS-STING signaling and independent of the classical TBK1-IRF3-IFN cascade. Here, we identified an unrecognized STING-PERK-eIF2α signaling axis that was specific and controlled cap-dependent translation, a fundamental cellular process. STING, upon activation by 2'3'-cyclic GMP-AMP (cGAMP), robustly bound and directly activated the endoplasmic reticulum (ER)-located kinase PERK, and this process was upstream of IRF3 activation and independent of the unfolded protein response (UPR) and TBK1/IKKε. Innate DNA sensing suppressed global translation programs but selectively ensured the activation of some pathways by PERK-mediated eIF2α phosphorylation and the rapid regulation of protein synthesis, enabling translational modulation of immune responses. Notably, the STING-PERK-eIF2α axis is an evolutionarily primitive component of STING-TBKI-IRF3-IFN signaling and is physiologically critical in pulmonary and renal fibrosis as well as in the regulation of cellular senescence. Therefore, these findings establish the first noncanonical pathway of the cGAS-STING mechanism and demonstrate the physiological importance of this STING-triggered selective translation, which we propose as a promising therapeutic target for fibrotic diseases.

overall_design: HEK293 cells transfected with Vector/STING for two replicates are performed Polysome sequencing.

first: Dan

last: Zhang

first: Yezhang

last: Zhu

first: Pinglong

last: Xu


title: Transcriptomic analysis of Pv11 cells derived from Polypedilum vanderplanki

city: Tsukuba

first: Yuki

last: Yoshida

state: Ibaraki

address: 1-2 Owashi

department: NIAS

country: Japan

institute: NARO

summary: RNA-Seq of Pv11 cells derived from the anhydrobiotic organism Polypedilum vanderplank, exposed to various stresses.

overall_design: Pv11 cells were submitted to various stresses and transcriptome sequences were conducted in triplicates.

first: Takahiro

last: Kikawada

first: Oleg

last: Gusev


title: aCGH Trypanosoma cruzi G vs D11.

status: Public on Mar 06 2022

city: São Paulo

first: José

middle: Franco

last: Da Silveira

state: São Paulo

address: Rua Botucatu, 862

department: Departamento de Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de São Paulo

summary: Comparative genomic analysis of Trypanosoma cruzi G with Trypanosoma cruzi D11.

overall_design: The 8x60K array was designed and produced by Agilent (Agilent Technologies, Santa Clara, CA,US) based on the T. cruzi clone CLB genome, release 9, available in TriTrypDB. Two groups of probes totaling 48,787 probes covering all the in silico chromosomes were selected. The first group of probes covered all the chromosomes, including coding and non-coding regions, with an average of one probe every 1.2 kb to give a total of 44,860 probes. To design the second group, we selected 422 specific chromosome markers (i.e., single copy genes present only in the homologous chromosomes). In order to obtain a higher coverage with these markers, probe density was increased to one probe every 120 bp.

first: Danielle

last: Cortez

first: Marjorie

middle: M

last: Marini

first: Fabio

last: Lima

first: João

last: Luís Reis-Cunha

first: Daniella

last: Castanheira Bartholomeu

first: Rolando

middle: A

last: Rios Villacis

first: Silvia

last: Rogatto

first: André

middle: G

last: Costa-Martins

first: Fernanda

middle: S

last: Marchiano

first: Rafaela

last: do Carmo

first: Jose

middle: F

last: da Silveira


title: Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation

city: Los Angeles

first: Montgomery

last: Blencowe

address: 610 Charles E Young Drive East

institute: UCLA

summary: We systemetically distinguished the effects of each class of sex-biasing factors on transcriptome regulation in liver and adipose tissues with the Four Core Genotype (FCG) mouse model. The results offers a tissue-specific account of the individual contribution of major sex-biasing factors to gene regulation.

overall_design: We utilized the Four Core Genotype (FCG) mouse model with or without hormone replacement to distinguish the effects of each class of sex-biasing factors on transcriptome regulation (e.g., gene expression, molecular pathways, gene network organizations, etc.) in liver and adipose tissue.

first: Xuqi

last: Chen

first: Yutian

last: Zhao

first: Yuichiro

last: Itoh

first: Caden

middle: N

last: McQuillen

first: Yanjie

last: Han

first: Benjamin

last: Shou

first: Rebecca

last: McClusky

first: Karen

last: Reue

first: Arthur

middle: P

last: Arnold

first: Xia

last: Yang


title: Comparison of microRNA expression profiling in porcine brain among three time points after infection with Chinese I genotype strain of Toxoplasma gondii

city: Yangzhou

first: Hou

last: Zhaofeng

state: Jiangsu

address: No. 12, Wenhui East Road

institute: Yangzhou University

type: Non-coding RNA profiling by high throughput sequencing

summary: The objectives of the present study were to analyze the changes on miRNA expression profile in porcine brain using next-generation sequencing (NGS) technology and bioinformatic analysis at 10, 25 and 50 days post inoculation (DPI) with Chinese I genotype strain of T. gondii. Compared to control group,  87, 68, and 135 differentially expressed miRNAs (DEMs) were found in the brains of infected pigs at 10, 25, and 50 DPI, respectively.  The results not only showed that the miRNA expression of the host can be changed by the invasion of T. gondii, but also revealed the differences on the regulation of the key biological processes or pathways involved in host responses between the acute and chronic T. gondii infection.

overall_design: Differential expression of porcine microRNAs at three time points after infection with Chinese I genotype strain of Toxoplasma gondii were analyzed by deep sequencing

first: Zhaofeng

last: Hou

first: Jianping

last: Tao


title: Transcriptional profiling of human KIR+ CD8 T cells

first: Mark

last: Davis

overall_design: Refer to individual Series


title: The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates with Stimulation of the Host Endoplasmic Reticulum Stress Pathway

city: Liverpool

first: William

middle: Anderson

last: Paxton

state: England

address: 8 West Derby Street, Ronald Ross Building

department: IVES

country: United Kingdom

institute: University of Liverpool

summary: Comparison of cells expressing or not expressing the HCV envelope glycoprotein, E1E2, reveals upregulation of host endoplasmic reticulum stress pathways, including genes such as HSPA5 and ATF3

overall_design: Transcritome profiles of HEK293T cells transfected with control plasmid compared with those expressing E1E2 using Oxford Nanopore cDNA sequencing method.

first: Georgios

last: Pollakis

first: Lindsay

last: McKay

first: Jordan

last: Thomas


title: A coordinated regulatory network of ApiAP2 transcription factors involved in heterochromatic gene expression during Plasmodium falciparum blood-stage development [RNA-Seq]

first: Mei

last: Jiang

state: Shanghai

address: 1239 Siping Road

institute: Tongji University

summary: Effects of PfApiAP2 knockouts on gene expression in the intraerythrocytic cycle

overall_design: at least 2 biological RNA-seq replicates for wild type and PfApiAP2 knockout parasite lines at the ring (10-15 hpi), trophozoite (25-30 hpi), and schizont (40-45 hpi) stages, respectively

first: Xiaomin

last: Shang

first: Qingfeng

last: Zhang


title: A coordinated regulatory network of ApiAP2 transcription factors involved in heterochromatic gene expression during Plasmodium falciparum blood-stage development [ChIP-Seq]

summary: Genome-wide occupancy of sixteen PfApiAP2 transcription factors and PfHP1 throughout the intraerythrocytic cycle

overall_design: 2 biological ChIP-seq replicates using an antibody against either GFP or PfHP1, and input DNA


title: Single-cell RNA-seq analysis of human KIR+ CD8 T cells by Smart-seq2

summary: KIR+ CD8 T cells (Live CD3+CD56-TCRab+CD8+KIR+ cells) were sorted from the blood of healthy subjects (N=10) and patients with MS (N=2), SLE (N=6), or CeD (N=5) and subjected to single-cell RNA-seq analysis by Smart-seq2. In parallel, we also analyzed their T-cell receptor (TCR) α and β sequences. Unsupervised clustering of these KIR+CD8+ T cells by Seurat identified six clusters, with Clusters 1 to 3 mostly containing expanded KIR+CD8+ T cells (≥2 cells expressing same TCR) and Clusters 5 and 6 consisting of unexpanded cells expressing unique TCRs. There are common features shared by KIR+CD8+ T cells from healthy subjects and different diseases, yet there is also heterogeneity (i.e., upregulated type I IFN signaling and glycolysis in Clusters 2 and 3) associated with different diseases or treatments.

overall_design: KIR+ CD8 T cells were sorted from healthy subjects (N=10) and patients with MS (N=2), SLE (N=6), or CeD (N=5) and subjected to single-cell RNA-seq analysis by Smart-seq2.

first: Jing

last: Li


title: Integrative analysis of DNA methylation and gene expression identified follicular thyroid cancer-specific diagnostic biomarkers [Expression]

status: Public on Mar 05 2022

first: Lisong

last: Teng

address: Yuhangtang Road

institute: Zhejiang University

summary: The diagnosis of follicular thyroid carcinoma (FTC) prior surgical resection remains a challenge, as routine screening methods, such as ultrasound or even FNAB, could not diagnose FTC preoperatively. Here, we performed an integrative analysis of DNA methylation and RNA assays data from our own cohort (14 Follicular thyroid carcinoma vs 16 Benign thyroid lesion) to identify thyroid cancer-specific DNA methylation markers. We first identified differentially methylated and expressed genes and examined their correlations. Candidate DNA methylation sites were selected and further verified in validation set. Among all candidate methylation sites, cg06928209 was the most promising site as a molecular marker for early diagnosis, with a sensitivity of 90%, a specificity of 80% and an AUC of 0.77. Overall, our study demonstrates the potential use of methylation markers in FTC diagnosis and may boost the development of new epigenetic therapies.

overall_design: Here, we performed an integrative analysis of DNA methylation and RNA-seq data from our own cohort (14 Follicular thyroid carcinoma vs 16 Benign thyroid lesion) to identify thyroid cancer-specific DNA methylation markers. We first identified differentially methylated and expressed genes and examined their correlations. Candidate DNA methylation sites were selected and further verified in validation set.

first: Li

first: Wang

last: Weibin

first: Lou

last: Xiaoming


title: FSCN1 promotes esophageal carcinoma progression through downregulating PTK6 via its RNA-binding protein effect

city: jilin

first: Hongfei

last: cai

address: No.1 Xinmin Street, Chaoyang District, Changchun City, Jilin Province

department: Ddepartment of Thoracic Surgery

institute: The First Hospital of Jilin University

summary: To explore the downstream molecules of FSCN1, shRNA targeting FSCN1 was designed and transfected into the ESCC cell line, ECA-109. Whole-genome expression profiling was performed to screen for related molecules.  To investigate the RNA binding property of FSCN1 in ESCC, RNA immunoprecipitation (RIP) was performed using an FSCN1 monoclonal antibody in ECA-109 cell lysate, and the associated RNA was analyzed by RNA-seq.

last: Cai


title: Functional primordial germ cell-like cells from pluripotent stem cells in rats

city: Kashihara

first: Hisato

last: Kobayashi

state: Nara

address: 840 Shijo-Cho

department: Department of Embryology

institute: Nara Medical University

summary: In vitro generation of germ cells from pluripotent stem cells (PSCs) can crucially impact future reproductive medicine and animal breeding. A decade ago, in vitro gametogenesis was established in the mouse. However, induction of primordial germ cell-like cells (PGCLCs) to produce fertile gametes has not been achieved in any other species. Here, we demonstrate the induction of functional PGCLCs from rat PSCs. We show that epiblast-like cells in floating aggregates form rat PGCLCs. The gonadal somatic cells support maturation and epigenetic reprogramming of the PGCLCs. Notably, rat PGCLCs transplanted into the seminiferous tubules of germline-less rats produce spermatids, leading to the birth of viable offspring. Insights from our rat model will elucidate conserved and divergent mechanisms essential for the broad applicability of in vitro gametogenesis.

overall_design: RNA-seq of rat embryonic stem cells (ESCs), epiblast-like cells (EpiLCs), and primordial germ cell like cells (PGCLCs).

first: Mami

last: Oikawa

first: Toshihiro


title: Exercise suppresses mouse systemic AApoAII amyloidosis through enhancement of the p38 MAPK signaling pathway

status: Public on Mar 04 2022

city: Matsumoto

first: Xiaoran

last: Cui

address: 3-1-1 Asahi

institute: Shinshu University

summary: Exercise interventions are beneficial for reducing the risk of age-related diseases, including amyloidosis, but the underlying molecular links remain unelucidated. Here, we investigated the protective role of interval exercise training in a mouse model of age-related systemic apolipoprotein A-II amyloidosis (AApoAII) and elucidated potential mechanisms. Mice subjected to sixteen weeks of exercise improved whole-body physiologic functions and exhibited substantial inhibition of amyloidosis, particularly in the liver and spleen. Exercise activated the hepatic p38 mitogen-activated protein kinase (p38 MAPK) signaling pathway and the downstream transcription factor tumor suppressor p53. This activation resulted in elevated expression and phosphorylation of heat shock protein beta-1 (HSPB1), a chaperone that defends against protein aggregation. In the amyloidosis-induced mice, the hepatic p38 MAPK-related adaptive responses were additively enhanced by exercise. We observed that with exercise, greatly increased amounts of phosphorylated HSPB1 accumulated at amyloid deposition areas, which we suspect to inhibit amyloid fibril formation. Collectively, our findings conclude exercise-activated, specific chaperone prevention of amyloidosis, and suggest that exercise may amplify intracellular stress-related protective adaptation pathways against age-associated disorders such as amyloidosis.

overall_design: Investigation liver mRNA profile in response to 16-week interventions of exercise and amyloidosis

first: Cui

last: Xiaoran

first: Keiichi

last: Higuchi


title: CIP, a cardioprotective factor, inhibits the transition from cardiac hypertrophy to heart failure

city: Guangzhou

first: Youchen

last: Yan

state: Guangdong

address: No.58 Zhongshan Road II

institute: The First Affiliated Hospital, Sun Yat-sen University

summary: Heart failure is characterized by the inability of the heart to pump effectively and generate proper blood circulation to meet the body's needs; it is a devastating condition that affects more than 100 million people globally. In spite of this, little is known about the mechanisms regulating the transition from cardiac hypertrophy to heart failure. Previously, we identified a cardiomyocyte-enriched gene, CIP, which regulates cardiac homeostasis under pathological stimulation. Here, we show that the cardiac transcriptional factor GATA4 binds the promotor of CIP gene and regulates its expression. We further determined that both CIP mRNA and protein decrease in diseased human hearts. In a mouse model, induced cardiac-specific overexpression of CIP after the establishment of cardiac hypertrophy protects the heart by inhibiting disease progression toward heart failure. Transcriptome analyses revealed that the IGF, mTORC2 and TGFβ signaling pathways mediate the inhibitory function of CIP on pathologic cardiac remodeling. Our study demonstrates GATA4 as an upstream regulator of CIP gene expression in cardiomyocytes, as well as the clinical significance of CIP expression in human heart disease. More importantly, our investigation suggests CIP is a key regulator of the transition from cardiac hypertrophy to heart failure. The ability of CIP to intervene in the onset of heart failure suggests a novel therapeutic avenue of investigation forthe prevention of heart disease progression.

overall_design: RNA-seq of CIP-OE mouse heart after 8 weeks of TAC operation. "KI" refered to CIP overexpression (CIP-OE) mice. CIP-KI-flox mice, which have a Rosa-CIP allele (the stop codon is present and floxed) were bred with aMHC-Mer-Cre-Mer mice to obtain CIP-OE (CIP-KI-flox;aMHC-Mer-Cre-Mer) mouse. Tamoxifen was administrated through intraperitoneal injection to activate the expression of Cre recombinase and the excision of the stop codon for the ectopic expression of CIP transgene in the heart in CIP-OE mice. “Ctrl” refered to CIP-KI-flox littermates.

first: Tianxin

last: Long

first: Yili

last: Chen

first: Yugang

last: Dong

first: Da-Zhi

last: Wang

first: Zhan-Peng

last: Huang


title: CREBBP/EP300 acetyltransferase inhibition targets lineage specific enhancers to inhibit the proliferation of ER+ breast cancer cells [ATAC-Seq]

city: Cambridge

first: David

last: Mayhew

state: MA

address: 500 Technology Square, Suite 700

institute: Foghorn Therapeutics

summary: MCF7 cells were treated with a CREBBP/EP300 acetyltransferase inhibitor CPI-1612 and chromatin status was measured via ATAC-seq

overall_design: MCF7 cells were treated with DMSO or CPI-1612 (50 nM).  Libraries were prepared with the Omni-ATAC-seq protocol.

first: Archana

last: Reddy

first: Sungmi

last: Park-Chouinard

first: Andy

last: Conery


title: CREBBP/EP300 acetyltransferase inhibition targets lineage specific enhancers to inhibit the proliferation of ER+ breast cancer cells [RNA-Seq]

summary: MCF7, T47D, or ZR751 cells were treated with a CREBBP/EP300 acetyltransferase inhibitor CPI-1612 and/or Fulvestrant and expression changes were measured via RNA-seq

overall_design: MCF7, T47D, or ZR751 cells were treated with DMSO, CPI-1612 (5 nM, 50 nM) or Fulvestrant (100 nM), or combinations of CPI-1612 + Fulvestrant.  Whole RNA was extracted and used for library construction and RNA-sequencing.


title: In-depth molecular profiling specifies human retinal microglia identity

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

summary: Microglia are the tissue-resident macrophages of the retina and brain, being critically involved in organ development, tissue homeostasis, and response to cellular damage. Until now, little is known about the transcriptional profile of human retinal microglia and how they differentiate from peripheral monocytes, as well as from brain microglia. Additionally, the degree to which mice are suitable models for human retinal microglia is still not clear. The present study applies fluorescence-activated cell sorting to isolate human retinal microglia from enucleated eyes and compares their transcriptional profile with that of whole retinal tissue, as well as classical, intermediate and non-classical monocytes. In addition, human retinal microglia are compared to murine retinal microglia, isolated from at least two-years old Cx3cr1GFP/+ mice, as well as human brain microglia obtained from the literature. Several overexpressed genes were identified in retinal microglia when compared to whole retinal tissue, as well as classical, intermediate, and non-classical monocytes, among them IL1B, C2, C3, TREM2, P2RY12 and SPP1. In relation to whole retina sequencing, several risk genes, such as APOE and TGBR1, as well as PLXDC2 and ARHGAP22 associated with age-related macular degeneration (AMD) and diabetic retinopathy (DRP), were preferentially expressed in retinal microglia, indicating their potential pathophysiological involvement. The top expressed genes exhibited a strong consistency between retinal and brain microglia, among them CD74, SPP1, ACTB, FTL and C3. There was a high degree of similarity between human and murine retinal microglia, although there were several species-specific genes, revealing for which genes mice are suitable models for human retinal microglia. This study provides detailed insights into the molecular profile of human retinal microglia and indicate a high similarity to brain microglia. It advances our under-standing about their role in human retinal disease, such as AMD and DRP. The similarities and differences between human and mice will facilitate the transferability of knowledge between both species.

overall_design: RNA sequencing of 5 retinal microglia (FACS: CD45+ CD11b+ CX3CR1+ MatMac+ CCR2-), 6 classical monocytes (FACS: CD45+ CD11b+ CX3CR1+ CD14++ CD16- ), 5 intermediate monocytes (FACS: CD45+ CD11b+ CX3CR1+ CD14++ CD16+), 5 non-classical monocytes (FACS: CD45+ CD11b+ CX3CR1+ CD14- CD16++ cells), 6 retinal samples

first: Julian

last: Wolf

first: Stefaniya

last: Boneva

first: Dennis-Dominik

last: Rosmus

first: Hansjürgen

last: Agostini

first: Günther

last: Schlunck

first: Peter

last: Wieghofer

first: Anja

last: Schlecht


title: CREBBP/EP300 acetyltransferase inhibition targets lineage specific enhancers to inhibit the proliferation of ER+ breast cancer cells [ChIP-Seq]

summary: MCF7  were treated with a CREBBP/EP300 acetyltransferase inhibitor CPI-1612 or DMSO and ChIP-seq was performed for H3K27ac and H3K9ac.

overall_design: MCF7 cells were treated with DMSO or CPI-1612 (50 nM).  ChIP-seq was performed for histone markers H3K27ac and H3K9ac and peaks were called relative to input samples.


title: SHAPE-guided RNA structure homology search and motif discovery

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared RNA structural features within transcriptomes.

sample_organism: Severe acute respiratory syndrome-related coronavirus

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: SHAPE-MaP

first: Edoardo

last: Morandi

first: Martijn

last: van Hemert

first: Incarnato

last: Danny


title: CREBBP/EP300 acetyltransferase inhibition targets lineage specific enhancers to inhibit the proliferation of ER+ breast cancer cells

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


title: EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma

city: Lausanne

first: Nicolo

last: Riggi

state: VD

address: Bugnon 25

department: Département de Pathologie Expérimentale

institute: CHUV


title: EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma [HiChIP-seq]

summary: Chimeric proteins resulting from chromosomal translocations play a major role as driver oncogenes in cancer. Among them, fusions between EWSR1 and a set of transcription factors (TFs) generate oncogenes with powerful chromatin regulatory activities, capable of establishing complex gene expression programs. However, specific EWSR1 fusion proteins have been implicated in distinct tumor types, suggesting an enhancement of their functional properties by permissive precursor cells. Here we combined functional epigenomics with nuclear topology mapping to define the epigenetic and 3D connectivity landscape of Clear Cell Sarcoma (CCS), one of the most aggressive forms of human cancer, driven by the EWSR1-ATF1 fusion gene. We find that EWSR1-ATF1 display a distinctive binding pattern that depends on the EWSR1 prion-like domain, and is divergent from wild type ATF1, despite the physical interaction between wt and EWSR1-ATF1 proteins. This cooperativity promotes ATF1 retargeting to new distal sites, leading to chromatin activation and the establishment of a 3D network that controls oncogenic and differentiation signatures shared with primary CCS tumors.  Conversely, EWSR1-ATF1 depletion results in a marked reconfiguration of 3D connectivity, including the emergence of a new set of connections controlling neural crest-related developmental programs. Accordingly, interrogation of more than 160’000 single cell expression profiles from the human skin atlas reveals loss of EWSR1-ATF1 expression to induce a more differentiated tumor cell state. Taken together, our study uncovers the cooperativity network of EWSR1-ATF1, delineates the molecular underpinnings of its epigenetic function in CCS, and points to precursor cells along the Schwann cell-melanocytic axis as a candidate origin for these tumors.

overall_design: 4 HiChIP samples of CCS cell lines including wt cells, and cells transfected with siRNA directed against either EWSR1-ATF1 vs non-targeting siRNA control.

first: Emely

last: Möller

first: Viviane

last: Praz

first: Sanal

last: Rajendran

first: Rui

last: Dong

first: Alexandra

last: Cauderay

first: Yu-Hang

last: Xing

first: Carlo

last: Fusco

first: Liliane

last: Broye

first: Shruthi

last: Rengarajan

first: Mary

middle: E

last: Awad

first: Beverly

last: Naigles

first: Igor

last: Letovanec

first: Petur

last: Nielsen

first: Antonia

last: Diglika

first: Greg

last: Cote

first: Edwin

last: Choy

first: Ivan

last: Stamenkovic

first: Gaylor

last: Boulay

first: Miguel

last: Rivera


title: EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma [RNA-seq]

first: Nicolo

last: Riggi

summary: Chimeric proteins resulting from chromosomal translocations play a major role as driver oncogenes in cancer. Among them, fusions between EWSR1 and a set of transcription factors (TFs) generate oncogenes with powerful chromatin regulatory activities, capable of establishing complex gene expression programs. However, specific EWSR1 fusion proteins have been implicated in distinct tumor types, suggesting an enhancement of their functional properties by permissive precursor cells. Here we combined functional epigenomics with nuclear topology mapping to define the epigenetic and 3D connectivity landscape of Clear Cell Sarcoma (CCS), one of the most aggressive forms of human cancer, driven by the EWSR1-ATF1 fusion gene. We find that EWSR1-ATF1 display a distinctive binding pattern that depends on the EWSR1 prion-like domain, and is divergent from wild type ATF1, despite the physical interaction between wt and EWSR1-ATF1 proteins. This cooperativity promotes ATF1 retargeting to new distal sites, leading to chromatin activation and the establishment of a 3D network that controls oncogenic and differentiation signatures shared with primary CCS tumors.  Conversely, EWSR1-ATF1 depletion results in a marked reconfiguration of 3D connectivity, including the emergence of a new set of connections controlling neural crest-related developmental programs. Accordingly, interrogation of more than 160,000 single cell expression profiles from the human skin atlas reveals loss of EWSR1-ATF1 expression to induce a more differentiated tumor cell state. Taken together, our study uncovers the cooperativity network of EWSR1-ATF1, delineates the molecular underpinnings of its epigenetic function in CCS, and points to precursor cells along the Schwann cell-melanocytic axis as a candidate origin for these tumors.

overall_design:
18 RNAseq samples on CCS cell lines, CCS and AFH Primary tumor samples and MSC primary cells. The study also includes perturbed systems; cells transfected with siRNA directed against EWSR1-ATF1, or cells infected with an EWSR1-ATF1 overexpression construct, and their respective controls. DTC1 samples include three biological, and one technical, replicate experiments.

>>> Raw files unavailable for Samples GSM5455379 GSM5455380 GSM5455382 GSM5455383 because they were generated using old archival samples, which have IRB limitations in terms of data deposition.  These raw files are on Zenodo (http://doi.org/10.5281/zenodo.5112706). <<<

first: Emely

last: Möller

first: Viviane

last: Praz

first: Sanal

last: Rajendran


title: A coordinated regulatory network of ApiAP2 transcription factors involved in heterochromatic gene expression during Plasmodium falciparum blood-stage development

first: Mei

last: Jiang


title: Replication maps of HCT116 cells grown under various conditions

city: New York

first: Tony

middle: T

last: Huang

address: 450 East 29th St, Rm 807

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Okazaki fragments were purified and sequenced from HCT116 cells.  The sequencing data were used to infer sites and efficiencies of replication initiation and termination.

overall_design: To map sites of replication initiation and termination in HCT116 cells grown under various conditions

first: Sarah

last: Keegan

first: Kate

last: Coleman

last: Lui


title: EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma [ATAC-Seq]

overall_design: 9 ATACseq samples of CCS cell lines and MSC primary cells. The study also includes perturbed systems; cells transfected with siRNA directed against EWSR1-ATF1, or cells infected with EWSR1-ATF1 overexpression constructs, and their respective controls.

first: Rui

last: Dong

first: Alexandra

last: Cauderay

first: Yu-Hang

last: Xing

first: Carlo

last: Fusco

first: Liliane

last: Broye

first: Shruthi

last: Rengarajan

first: Mary

last: Awad

first: Beverly

last: Naigles

last: Letovanec


title: EWSR1-ATF1 dependent 3D connectivity regulates oncogenic and differentiation programs in Clear Cell Sarcoma [ChIP-Seq]

last: Riggi

overall_design:
100 histone mark or transcription factor ChIPseq samples of CCS cell lines, CCS primary tumors and MSC primary cells. The study also includes perturbed systems; cells transfected with siRNA directed against EWSR1-ATF1, or cells infected with EWSR1-ATF1/EWSR1(YS37)-ATF1/wtATF1 overexpression constructs, and their respective controls.

>>> Raw files unavailable for Samples GSM5455054-GSM5455065 and GSM5455072-GSM5455075 because they were generated using old archival samples, which have IRB limitations in terms of data deposition.  These raw files are on Zenodo (http://doi.org/10.5281/zenodo.5112706). <<<

last: Möller

first: Igor

first: Petur

last: Nielsen

first: Antonia

last: Diglika

first: Greg

last: Cote

first: Edwin

last: Choy

first: Ivan

last: Stamenkovic

first: Gaylor

last: Boulay

first: Miguel

last: Rivera


title: Human colon cancer cell line HCT116 stably transfected with EPXH2 was constructed and analyzed by RNA sequencing.

status: Public on Mar 02 2022

city: Kunming

first: Li

middle: ru

last: hong

address: 245 Huancheng East Road

institute: Yan 'an Hospital affiliated to Kunming Medical University

summary: We analyzed the molecular mechanism of regulation of EPHX2 on colon cancer by constructing colon cancer cell line HCT116 stably transfected with EPHX2.

overall_design: HCT116 cells stably transfected with overexpressed EPHX2 were used as overEXP group, and HCT116 transfected with empty vector was used as control (NC group).

first: Yiran

last: Zhou

first: Xiao

last: Li

first: Aoran

last: Guan

first: Haodong

first: Yankun

last: Zhu

first: Ruhong


title: Genome-wide maps of 8-oxodG in UV/NAC-treated MCF10A cells.

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

summary: 8-oxodG accumulation within super-enhancers marks fragile CTCF-mediated chromatin loops.

first: Giovanni

last: Scala

first: Francesca

last: Gorini

first: Susanna

last: Ambrosio

first: Andrea

last: Chiariello

first: Mario

last: Nicodemi

first: Luigi

last: Lania

first: Barbara

last: Majello


title: Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer

status: Public on Mar 03 2022

city: Paris

first: Maxime

last: Meylan

state: Paris

address: 15 rue de l'école de Médecine

institute: UMRS 1138 - Centre de Recherche des Cordeliers

summary: The presence of intratumoral tertiary lymphoid structures (TLS) is associated with positive clinical outcomes and responses to immunotherapy in cancer. Here, we used spatial transcriptomics to examine the nature of B cell responses within TLS in renal cell carcinoma (RCC). B cells were enriched in TLS, and therein, we could identify all B cell maturation stages toward plasma cell (PC) formation. B cell repertoire analysis revealed clonal diversification, selection, expansion in TLS, and the presence of fully mature clonotypes at distance. In TLS+ tumors, IgG- and IgA-producing PCs disseminated into the tumor beds along fibroblastic tracks. TLS+ tumors exhibited high frequencies of IgG-producing PCs and IgG-stained and apoptotic malignant cells, suggestive of anti-tumor effector activity. Therapeutic responses and progression-free survival correlated with IgG-stained tumor cells in RCC patients treated with immune checkpoint inhibitors. Thus, intratumoral TLS sustains B cell maturation and antibody production that is associated with response to immunotherapy, potentially via direct anti-tumor effects.

overall_design:
Spatial transcriptomics of fresh frozen ccRCC human tumors
*** Raw data has not been submitted at this time due to patient privacy concerns ***

first: Aurélien

last: de Reyniès

first: Catherine

last: Sautès-Fridman

first: Wolf

last: Fridman


title: Downregulation of Neurodevelopmental Gene Expression in iPSC-Derived Cerebral Organoids Upon Infection by Human Cytomegalovirus

status: Public on Mar 01 2022

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

summary: We report the application of bulk RNA sequencing on cerebral organoids infected with HCMV TB40eGFP virus or uninfected, within the infected groups the organoids were sorted into 3 distinct populations prior to sequencing based on GFP expression as a proxy for level of infection. These populations have been denoted GFP (+), GFP Inter, GFP (-), for each sorted population 3 organoids of the same line and from the same differentiation were combined to ensure sufficient cell numbers for bulk sequencing analysis.

sample_organism:
Homo sapiens
Human betaherpesvirus 5

platform_organism:
Homo sapiens
Human betaherpesvirus 5

overall_design: Examination of the effect of HCMV virus on iPSC derived cerebral organoids.

first: Benjamin

last: O'Brien

first: Rebekah

middle: L

last: Mokry

first: Megan

last: Schumacher

first: Kirthi

last: Pulakanti

first: Scott

last: Terhune

first: Allison

middle: D

last: Ebert


title: Molecular profiling reveals human biomarker signatures in patients after allogeneic stem cell transplantation suffering from invasive aspergillosis

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

institute: Hans-Knoell-Institute Jena

summary: Despite available diagnostic tests and recent advances, diagnosis of pulmonary invasive aspergillosis (IPA) remains challenging. By undertaking a longitudinal case-control study, we explored the possibility to identify novel non-invasive human biomarkers candidates for IPA in patients post allogeneic stem cell transplantation (alloSCT). Using both RNA-sequencing and immunoassays, we investigated 66 blood samples of 3 probable IPA cases and 3 matched controls without Aspergillus infection. Selected potential biomarker candidates were evaluated further in additional alloSCT (n=23) and patients suffering from COVID-19-associated pulmonary aspergillosis (CAPA) and their appropriate control patients (n=65). Profiling analysis suggested LGALS2, MMP1 and caspase-3 as potential biomarker candidates indicating IPA in investigated alloSCT patients. Significant differences in IL-8 and caspase-3 levels were observed among CAPA patients compared to control patients. Given our conceptual work we demonstrate the value of seeking human IPA indicating biomarkers, which together with already established fungal biomarkers potentially improve the accuracy of IPA diagnostic.

overall_design: We investigated 66 blood samples of 3 probable IPA cases (two male, one female) and three matched controls without Aspergillus infection. All had past allogeneic stem cell transplantation. Samples were gathered biweekly if possible.

first: Schäuble

last: Sascha

first: Antje

last: Häder

first: Philip

last: White

first: Sabrina

last: Kraus

first: Oliver

last: Kurzai

first: Jörg

last: Linde

first: Götz

middle: U

last: Grigoleit

first: Hermann

last: Einsele

first: Gianni

last: Panagiotou

first: Sascha

last: Schäuble

first: Löffler

last: Jürgen


title: RNA-sequencing of bicyclomycin treated Escherichia coli str. O157:H7 str. Sakai

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Enterohaemorrhagic E. coli (EHEC) is a significant human pathogens that cause outbreaks of haemorrhagic colitis and haemolytic uremic syndrome. During infection, pathogens compete for iron with the host, and one mechanism by which EHEC obtains iron is through haem uptake and utilitisation which is encoded by the chu operon. We have demonstrated that the haem receptor chuA is regulated by the Crp-cAMP-dependent sRNA CyaR. We further demonstrate that activation of chuA by CyaR is independent of the chuA RNA-thermometer and termination by Rho. These results highlight the ability of regulatory sRNAs to integrate multiple environmental signals into a layered hierarchy of signal input.

overall_design: Detecting rho-dependent transcripts in Escherichia coli str. O157:H7 str. Sakai

first: Brandon

last: Sy


title: Targeted NGS on artificial microRNAs expressed by a pool of heterogeneous Sindbis viruses

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

summary:
Purpose: Next-generation sequencing (NGS) on targeted locus in Sindbis genome to determine frequency changes of artificial microRNAs expressed by viruses after passaging in cancer and normal cells
Methods: RNA was harvested in Trizol 488 (Thermo Fisher). RNA was extracted using the manufacturer’s protocol and quantified by nanodrop. Sequencing was done by SeqMatic on a MiSeq v3 platform generating 75bp reads. Adapters were trimmed using Trimmomatic and adapter-free reads represent artificial microRNAs encoded by Sindbis virus in a sample.
Results: We have identified changes in artificial microRNA frequency after passaging virus pool in cancer and normal cells and have identified microRNAs increasing viral fitness in cancer cells.
Conclusions: Our study represents artificial microRNAs which target pathways that can aid oncolytic viral replication in cancer cells.

overall_design: artificial microRNA abundance profile before and after passaging of pooled Sindbis virus in cancer cells

first: Carolina

last: Ilkow


title: The WOPR family protein Ryp1 is a key regulator of gene expression, development, and virulence in the thermally dimorphic fungal pathogen Coccidioides posadasii

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

summary: Coccidioides spp. are fungal pathogens endemic to Southern California, Arizona, and other desert regions where they cause a spectrum of symptoms known as Valley Fever in otherwise healthy individuals. In the soil, Coccidioides grows in a hyphal form that produces vegetative spores (arthroconidia). When arthroconidia are inhaled by mammals they undergo an elaborate developmental transition consisting of germination, multiple rounds of nuclear division, and segmentation to form large spherules filled with vegetative endospores. Very little is understood about the molecular basis of spherule formation. Here we characterize the role of the conserved transcription factor Ryp1 in Coccidioides spherule formation. We show that Coccidioides ryp1 mutants are unable to form mature spherules, instead arresting at an early stage of spherulation. We analyze the transcriptional profile of wild-type and Δryp1 mutant cells under hyphal and spherule-promoting conditions, thereby defining a set of hyphal- or spherule-enriched transcripts that are dependent on Ryp1 for their expression. Ryp1-dependent transcripts include key virulence factors such as SOWgp, which encodes the spherule outer wall glycoprotein. In the mouse model of coccidioidomycosis, we find that the Δryp1 mutant is completely avirulent, indicating that Ryp1-dependent pathways are essential for the ability of Coccidioides to cause disease. Vaccination of C57BL/6 mice with live Δryp1 spores does not provide any protection from lethal C. posadasii intranasal infection, consistent with our findings that the Δryp1 mutant fails to make mature spherules. Taken together, this work identifies the first transcriptional regulator that drives mature spherulation and virulence in Coccidioides.

overall_design: Two biological replicates each of wild type C. posadasii var. Silveira and the ryp1 mutant were grown at 37C and RT, for a total of 8 samples.

first: M

last: Mandel

first: Sinem

last: Beyhan

first: Lisa

last: Shubitz

first: John

last: Galgiani

first: Marc

middle: J

last: Orbach

first: Anita

last: Sil


title: Characterization of BatIM, the cytosine methyltransferase of Bacillus anthracis

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

institute: Hokkaido University

summary: 5-methylcytosine is one of the major epigenetic modifications of DNA in living organisms. In bacteria, some species possess DNA methyltransferases that produce the cytosine modification in both strands or either strand of its target sequence. The purpose of this study is to characterize BatIM, the orphan cytosine methyltransferase coded on a prophage region of Bacillus anthracis.

overall_design: Genomic DNA was extracted from E. coli strains after an hour of the induction of BatIM, then prepared for Bisulfite-seq library with post-bisulfite adaptor tagging (PBAT) strategy.

first: Fumihito

last: Miura

first: Takashi

last: Ito

first: Hideaki

last: Higashi


title: muscle and white adipose tissue transcriptomes in obese WT mice after 12 weeks of prednisone regimens

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

summary: Exogenous glucocorticoids regulate the muscl-fat axis communication, but little attention is paid to their frequency of intake. Here we investigated the transcriptional effects of prednisone in  muscle and adipose tissue when dosed as intermittent once-weekly 1mg/kg i.p. versus once-daily 1mg/kg in  WT obese mice. Prior to treatment, mice were fed a high-fat diet for 12 weeks. After 12 weeks of treatment, we performed RNA-seq analysis in muscle (quadriceps) and white adipose tissue (ventral fat pad) to quantitate gene expression at isoform level.

overall_design: 3 muscle samples vehicle; 3 muscle samples  weekly prednisone; 3 muscle samples daily prednisone; 3 adipose samples vehicle; 3 adipose samples weekly prednisone; 2 adipose samples daily prednisone. Each sample was ~1ug RNA isolated through Trizol and further purifed through RNeasy columns.

first: Michelle

last: Wintzinger


title: Global SLAM-Seq for accurate mRNA decay determination and identification of NMD targets

status: Public on Feb 28 2022

city: Gothenburg

first: Per

last: Sunnerhagen

address: Box 462

department: Chemistry and Molecular Biology

country: Sweden

institute: University of Gothenburg

summary: Gene expression analysis requires accurate measurements of global RNA degradation rates, earlier problematic with methods disruptive to cell physiology. Recently, metabolic RNA labeling emerged as an efficient and minimally invasive technique applied in mammalian cells. Here, we have adapted SH-Linked Alkylation for the Metabolic Sequencing of RNA (SLAM-Seq) for a global mRNA stability study in yeast using 4-thiouracil pulse-chase labeling. We assign high-confidence half-life estimates for 67.5 % of expressed ORFs, and measure a median half-life of 9.4 min. For mRNAs where half-life estimates exist in the literature, their ranking order was in good agreement with previous data, indicating that SLAM-Seq efficiently classifies stable and unstable transcripts. We then leveraged our yeast protocol to identify targets of the Nonsense-mediated decay (NMD) pathway by measuring the change in RNA half-lives; instead of steady-state RNA level changes. With SLAM-Seq, we assign 580 transcripts as putative NMD targets, based on their measured half-lives in wild-type and upf3Δ mutants. We find 225 novel targets, and observe a strong agreement with previous reports of NMD targets, 61.2 % of our candidates being identified in previous studies.This indicates that SLAM-Seq is a simpler and more economic method for global quantification of mRNA half-lives. Our adaptation for yeast yielded global quantitative measures of the NMD effect on transcript half-lives, high correlation with RNA half-lives measured previously with more technically challenging protocols, and identification of novel NMD regulated transcripts that escaped prior detection.

overall_design: SLAM-Seq profiling of BY4741 and upf3Δ to calculate NMD targets based on half-life changes. Done in biological triplicates.

first: Hanna

last: Alalam

first: Jorge

last: Zepeda-Martínez


title: The genome organization of Neurospora crassa at high-resolution uncovers principles of fungal chromosome topology

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

institute: University of Colorado Colorado Springs

summary: For a eukaryotic genome to properly function, its chromatin must be precisely organized, as genome topology impacts transcriptional regulation, cell division, DNA replication, and DNA repair, among other essential processes. Disruption of human genome topology can lead to disease states, such as cancer. The advent of chromosome conformation capture with high-throughput sequencing (Hi-C) technologies to assess genome organization has revolutionized our understanding of the arrangement of chromosomes within the nuclear genome. Critical developments include chromosomal territories, active/silent chromatin compartments, Topologically Associated Domains (TADs), and chromatin loops. However, to fully elucidate folding principles at the gene level, Hi-C datasets at an extremely high resolution are required: while low resolution (e.g., 40 kb bin) heatmaps can provide important insights into chromosomal level contacts, lower resolution datasets cannot provide information about individual gene or promoter contacts. Thus, high-resolution Hi-C datasets can elucidate principles of folding, including those of model organisms whose chromosome conformation can elucidate the folding of the human genome. Here, we have examined the high-resolution genome topology of the model fungal organism Neurospora crassa: our composite Hi-C dataset, generated using two restriction enzymes to monitor euchromatin (DpnII) and heterochromatin (MseI), provides exquisite detail for both larger chromosomal structures and individual gene contacts, including how repressed euchromatic genes associate with constitutive heterochromatic regions. Our high-resolution Neurospora Hi-C datasets should be an outstanding resource to the fungal community and provide valuable insights to the folding of higher organism genomes.

overall_design: We analyzed genome organization of two wild type strains of filamentous fungus Neurospora crassa by chromosome conformation capture by paired-end high-throughput sequencing (Hi-C); Hi-C libraries were generated with the four-base cutters DpnII and MseI, which monitor euchromatic and heterochromatic regions of the Neurospora genome, respectively, due to the location of the recognition sequences of these restriction enzymes. Four DpnII replicates (three techincal replicates and a biological replicate) and three MseI replicates (two technical replicates, one biological) were generated using eight PCR cycles; replicates were merged into DpnII and MseI datasets, and those two datasets were merged into a comprehensive interaction matrix.

first: Sara

last: Rodriguez

first: Ashley

last: Ward

last: Reckard

first: Yulia

last: Shtanko

first: Clayton

last: Hull-Crew


title: CD90 marks a mesenchymal program in human thymic epithelial cells in vitro and in vivo

city: Melbourne

first: Jacky

middle: Yisheng

last: Li

state: Victoria

address: 50 Flemington Rd

department: Cellular Biology

institute: MCRI

summary: Thymic epithelium is critical for the structural integrity of the thymus and for T cell development. Within the fully formed thymus, large numbers of hematopoietic cells shape the thymic epithelium into a scaffold-like structure which bears little similarity to classical epithelial layers, such as those observed in the skin, intestine or pancreas. Here, we show that human thymic epithelial cells (TECs) possess an epithelial identity that also incorporates the expression of mesenchymal cell associated genes, whose expression levels vary between medullary and cortical TECs (m/cTECs). Using pluripotent stem cell (PSC) differentiation systems, we identified a unique population of cells that co-expressed the master TEC transcription factor FOXN1, as well as the epithelial associated marker EPCAM and the mesenchymal associated gene CD90. Using the same serum free culture conditions, we also observed co-expression of EPCAM and CD90 on cultured TECs derived from neonatal human thymus in vitro. Single cell RNA-sequencing revealed these cultured TECs possessed an immature mTEC phenotype and expressed epithelial and mesenchymal associated genes, such as EPCAM, CLDN4, CD90 and COL1A1. Importantly, flow cytometry and single cell RNA-sequencing analysis further confirmed the presence of an EPCAM+CD90+ population in the CD45- fraction of neonatal human thymic stromal cells in vivo. Using the human thymus cell atlas, we found that cTECs displayed more pronounced mesenchymal characteristics than mTECs during embryonic development. Collectively, these results suggest human TECs possess a hybrid gene expression program comprising both epithelial and mesenchymal elements, and provide a basis for the further exploration of thymus development from primary tissues and from the in vitro differentiation of PSCs.

overall_design: This dataset includes RNA samples from three independent donors as biological replicates. For each donor, we sequenced mRNA isolated from four fractions of cells based on the expression of EPCAM and CD104, as well as samples representing unsorted cells.

first: Shicheng

last: Sun

middle: Y

first: Hieu

last: Nim

first: Adam

last: Piers

first: Mirana

last: Ramialison

first: Enzo

last: Porrello

first: Ogor

last: Konstantinov

last: Elefanty

first: Edouard

last: Stanley


title: cART Treated monocyte derived macrophages

city: Chicago

first: Jennillee

last: Wallace

state: IL

address: 1735 W Harrison St

institute: Rush University Medical Center

summary: primary human monocyte derived macrophages (MDMs) treated with antiretrovirals, specifically Atripla (A) or Triumeq (T)

overall_design: Batches of cells derived from 7 donors. Each batch treated with 2 drugs (A and T), and 2 proteins (1 [M-CSF only] and 2 [M-CSF and addition of IL-4 to skew to M2a-MDMs]). 6 samples per batch, 42 samples total.

first: Hemil

last: Gonzalez

first: Reshma

last: Rajan

first: Srinivas

last: Narasipura

first: Amber

middle: K

last: Virdi

first: Arnold

middle: Z

last: Olali

first: Ankur

last: Naqib

first: Zarema

last: Arbieva

first: Mark

last: Maienschein-Cline

first: Lena

last: Al-Harthi


title: Antigen cross-presentation in young tumor-bearing hosts promotes CD8 T cell terminal differentiation

city: memphis

first: yiping

last: fan

state: tn

address: 262 Danny Thomas Place

institute: st jude children's hospital

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Antigen cross-presentation in young tumor-bearing hosts promotes CD8 T cell terminal differentiation [WGBS]

summary: The immune system undergoes a progressive functional remodeling with age, polarizing the immune responses toward a “killer” or “healer” phenotype. Understanding how the age bias shapes anti-tumor immunity is essential in designing effective immunotherapies. In this manuscript we explore the anti-tumor CD8+ T cell responses generated in young (prepubescent) and adult (pre-senescent) mice. Using an MHCI-deficient, trackable tumor model, we observed that tumor reactive CD8+ T cells that expanded in young tumor-bearing (TB) mice acquired a terminally differentiated phenotype characterized by overexpression of inhibitory receptors and the transcription factor Tox1. Furthermore, tumor infiltrating CD8+ T cells from young tumors yielded a poor cytokine response compared to CD8+ T cells infiltrating adult tumors. Young migratory dendritic cells (migDC) and mononuclear phagocytic cells (MPCs) infiltrating young tumors were more competent in capturing and cross-presenting tumor antigen, leading to enhanced priming of CD8+ T cells in the draining lymph nodes (dLNs), and their subsequent terminal differentiation in the tumors. Notably, single-cell transcriptional profiling of tumor infiltrating MPCs revealed that young MPCs are polarized toward an inflammatory, effector phenotype. Consistent with our observations in young vs adult TB mice, analysis of immune infiltrates from pediatric solid tumors revealed a significant correlation between tumor-infiltrating CD8+ T cells with an exhaustion phenotype and the frequency of PD-L1-expressing phagocytic cells. Collectively, these data indicate that the young microenvironment of an actively developing tissue contributes to the generation of an immune response skewed toward a terminal effector state, thus narrowing the window for immunotherapeutic interventions.

overall_design: Freshly resected tumor was digested (collagenase-4 and DNase) and processed to single cell suspension. The referenced cell subsets were flow sorted, gDNA extracted and BS treated.

first: Ardiana

last: Moustaki

first: Jeremy

middle: C

last: Crawford

first: Shanta

last: Alli

first: Yiping

last: Fan

first: Shannon

last: Boi

first: Anthony

last: Zamora

first: Natalie

middle: M

last: McDonald

first: Gang

last: Wu

first: Joy

last: Nakitandwe

first: Scott

last: Newman

last: Foy

first: Antonina

last: Silkov

first: Paul

middle: G

last: Thomas

first: Alberto

last: Pappo

first: Michael

middle: A

last: Dyer

first: Elizabeth

last: Stewart

first: Sara

last: Federico

first: Ben

last: Youngblood


title: Interacting effects of sea louse (Lepeophtheirus salmonis) infection and formalin-killed Aeromonas salmonicida in Atlantic salmon skin transcriptome

city: St. John's

first: Albert

last: Caballero Solares

state: NL

address: 0 Marine Lab Road

department: Ocean Sciences

institute: Memorial University of Newfoundland

summary: Lepeophtheirus salmonis (sea lice) and bacterial co-infection threatens wild and farmed Atlantic salmon performance and welfare. The present microarray-based study examined the dorsal skin transcriptome response to formalin-killed Aeromonas salmonicida bacterin (ASAL) in pre-adult sea lice-infected and non-infected Atlantic salmon to fill the existing knowledge gap and aid in developing anti-co-infection strategies. To this aim, sea lice-infected and non-infected salmon were intraperitoneally injected with either phosphate-buffered saline (PBS) or ASAL (i.e., 4 injection/infection groups: PBS/no lice, PBS/lice, ASAL/no lice, and ASAL/lice). The analysis of the dorsal skin transcriptome data [Significance Analysis of Microarrays (5% FDR)] identified 345 up-regulated and 2,189 down-regulated DEPs in the comparison PBS/lice vs. PBS/no lice, and 82 up-regulated and 3 down-regulated DEPs in the comparison ASAL/lice vs. ASAL/no lice. The comparison ASAL/lice vs. PBS/lice identified 272 up-regulated and 11 down-regulated DEPs, whereas ASAL/no lice vs. PBS/no lice revealed 27 up-regulated DEPs. The skin transcriptome differences between the co-stimulated salmon (i.e., ASAL/lice) and PBS/no lice salmon accounted for 1,878 up-regulated and 3,120 down-regulated DEPs.

overall_design:
Groups of 35 salmon smolts [238.9 ± 45.2 g; mean weight ± standard deviation (SD)] were allocated in four 620-L tanks and exposed to Lepeophtheirus salmonis (sea lice) copepodids (at a ratio of 50 lice/fish). In parallel, groups of 15 salmon from the same population were distributed into two 620-L tanks to serve as no-lice infection controls. Four weeks after sea lice exposure, when lice were at the pre-adult stage, lice-infected salmon and non-infected salmon were subjected to an intraperitoneal injection of either phosphate-buffered saline (PBS), a solution of polyriboinosinic polyribocytidylic acid (pIC) or a PBS suspension of formalin-killed Aeromonas salmonicida (ASAL). For each tank holding infected salmon, 6 fish were injected with PBS, 6 with pIC, and 6 with ASAL. For each tank with non-infected salmon, 4 fish were injected with PBS, 4-5 fish with pIC, and 4-5 fish with ASAL. Samples of dorsal skin around louse attachment sites and adjacent intact skin were collected at 24 h post-injection. The microarray experiment analyzed the general skin transcriptome response to sea lice and ASAL co-stimulation, so it only used dorsal skin samples adjacent to louse attachment sites. The analysis employed a common reference microarray experiment design. The test RNA samples included in the experiment came from 6 PBS/no lice, 6 PBS/lice, 6 ASAL/no lice, and 6 ASAL/lice (24 samples in total). The common reference was prepared using pools of equal quantities of RNA from the 24 selected salmon for the present study, plus 6 pIC/no lice and 6 pIC/lice salmon. This design will allow future analyses of the shared molecular responses of Atlantic salmon dorsal skin to ASAL and pIC IP-injections, alone or in combination with lice infection.
variable - other: PBS/no lice
variable - other: ASAL/no lice
variable - other: PBS/lice
variable - other: ASAL/lice
biological replicate: PBS_NoLice_T30F1, PBS_NoLice_T30F3, PBS_NoLice_T30F4, PBS_NoLice_T33F2, PBS_NoLice_T33F3, PBS_NoLice_T33F4
biological replicate: ASAL_NoLice_T30F2, ASAL_NoLice_T30F3, ASAL_NoLice_T30F4, ASAL_NoLice_T33F2, ASAL_NoLice_T33F3, ASAL_NoLice_T33F5
biological replicate: PBS_Lice_T12F6, PBS_Lice_T2F2, PBS_Lice_T2F5, PBS_Lice_T5F3, PBS_Lice_T5F4, PBS_Lice_T8F4
biological replicate: ASAL_Lice_T12F1, ASAL_Lice_T12F4, ASAL_Lice_T2F2, ASAL_Lice_T5F4, ASAL_Lice_T8F5, ASAL_Lice_T8F7

last: Caballero-Solares

first: Navaneethaiyer

last: Umasuthan

first: Xi

last: Xue

first: Tomer

last: Katan

first: Surendra

last: Kumar

first: Jillian

last: DWestcott

first: Zhiyu

last: Chen

first: Mark

last: Fast

first: Stanko

last: Skugor

first: Richard

last: Taylor

first: Matthew

last: Rise


title: Antigen cross-presentation in young tumor-bearing hosts promotes CD8 T cell terminal differentiation [gene expression]

first: yiping

last: fan

overall_design: Total mCherry+ cells from pooled young and adult mouse tumors were FACS sorted. Single-cell gene expression libraries were generated using the Chromium Single Cell 3’ v2 kit (10X Genomics) with target outputs of 10,000 cells per library.

first: Ardiana

last: Moustaki

first: Jeremy

last: Crawford

first: Shanta

last: Alli

first: Yiping

last: Fan

first: Shannon

last: Boi

first: Anthony

middle: E

last: Zamora

first: Natalie

last: McDonald

first: Gang

last: Wu

first: Joy

last: Nakitandwe

first: Scott

last: Newman

last: Foy

first: Antonina

last: Silkov

first: Paul

last: Thomas

last: Pappo


title: KDM6B interacts with TFDP1 to activate P53 signalling in regulating mouse palatogenesis

city: Los Angeles

first: Tingwei

last: Guo

state: CA

address: 2250 Alcazar St

department: CCMB

institute: usc


title: Transcriptomic profiling uncovers key regulators during tulip bulb development

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary: The aim of this study was to determine transcriptomic level changes during tulip bulb growth. Bulbs of tulip genotypes 'Ad Rem' and 'Red Power' were harvested for RNA extraction at the indicated time points from S1 to S4. In total, 16 samples with two biological replicates per stage combination were used for RNA sequencing analysis. At least 6 G clean bases were generated for each sample. Comparative analysis identified genes involved in bulb development.

overall_design: In this study, five stages of a flower including buds, partial blooming, full blooming, early senescence and late senescence are collected individually. The whole flowers with different developmental stages were then used in RNA sequencing.

first: Qi

last: Sun


summary: The goal of this study is to assess genome-wide chromatin accessibility (ATAC-seq)of palatal tissue at E13.5

overall_design: Methods: Sequencing was performed using the NextSeq 500 platform (Illumina) and ATAC-seq reads were aligned to the UCSC mm10 reference genome using BWA-MEN. Then ATAC-seq peaks were called by MACS2 and annotated. Known transcription factor biding motifs were analyzed by HOMER.


title: For tRNA-related fragments and mRNAs of thyroid-associated ophthalmopathy patients and normal people

status: Public on Feb 27 2022

city: Shanghai

first: Zifan

last: Yue

address: No. 415 Fengyang Road, Hangpu District

department: Ophthalmology

institute: Shanghai Changzheng Hospital

summary: We measured the expression level of tRFs and mRNAs in thyroid-associated ophthalmopathy patients through high-throughput sequencing technology and verified the expression by quantitative real-time PCR. Then, the possible biological regulation and potential clinical significance of target genes of differentially expressed tRFs were assessed.

overall_design: Orbital adipose/connective tissue was obtained from 3 thyroid-associated ophthalmopathy patients with no history of thyroid disease, inflammatory disease, autoimmune disease, or orbital disease. All the thyroid-associated ophthalmopathy patients underwent orbital decompression for proptosis correction, and control subjects underwent cosmetic upper and lower blepharoplasty. The 3 control groups were obtained from the tissue remains of healthy people after plastic surgery.

first: Fei

last: Tong

first: Ruili

last: Wei


summary: The goal of this study is to compare transcriptome profiling (RNA-seq) of palatal tissue at E12.5 between control and Kdm6b mutant mice

overall_design: Methods: mRNA profiles of control and Kdm6b mutant mice were generated by deep sequencing, in triplicate, using Illumina Hiseq 4000. The quality of RNA samples was determined using an Agilent 2100 Bioanalyzer and all samples for sequencing had RNA integrity numbers >9.


title: CHARACTERIZING TOXICITY PATHWAYS OF FLUOXETINE TO PREDICT ADVERSE OUTCOMES IN ADULT PIMEPHALES PROMELAS

city: Saskatoon

first: Markus

last: Hecker

state: SK

address: 44 Campus Drive

institute: University of Saskatchewan

summary: Fluoxetine (FLX) is the most common selective serotonin reuptake inhibitor pharmaceutical used for the treatment of psychological disorders such as depression and anxiety. Increased prescription use of FLX by human populations has led to its pseudo-persistence in effluent-receiving waterways. Despite emerging concerns of FLX becoming a potential threat to the aquatic environment, there is currently limited information on effects of FLX on aquatic wildlife, including its specific mechanism of action and associated toxicity pathways in fish. The main goal of this study was to identify and validate key molecular toxicity pathways that are predictive of apical endpoints induced by exposure to FLX using the fathead minnow (Pimephales promelas), a model species common to North American freshwater systems. Adult fathead minnows were exposed to three concentrations of FLX (2.42, 10.7, and 56.7 µg/L) and a control for 21 days. After 96 hours, a subset of fish was sampled, and liver and brain tissue were collected to characterize molecular toxicity pathways using whole transcriptome and proteome analyses. In addition, at the end of the 21-day exposure, individuals were assessed for apical outcomes of regulatory relevance including histopathology and fecundity. Differential gene expression observed in the liver of fish exposed to the highest FLX treatment and revealed dysregulation of pathways associated with biosynthesis and metabolism of fatty acids, which may be an upstream molecular response that led to lipid-type vacuolation of hepatocytes, as observed in the histology analysis. Whole proteome analysis of the same fish revealed dysregulation of PPAR signalling, which may be associated with the enrichment of lipid-related pathways observed in the transcriptome. In addition, there was an indication of pathway enrichment of transcription- and translation-related pathways in the proteome. Common dysregulated genes in the brain of the treated fish were related to cellular signalling processes that are influenced by serotonin levels and shown to be involved in reproductive behaviour and, in turn, reproductive success. This was confirmed through a significant decrease in fecundity following the 21-day exposure. Pathways to measurable adverse outcomes are complex, however, this research does provide some important clues to the mechanistic toxicity that FLX inflicts.

overall_design: Fathead minnows (Pimephales promelas) were exposed to fluoxetine for 96h. Samples taken for transcriptomic analyses: Liver Samples: Negative Water Control (n=5, 2 individuals pooled per sample); 10.7µg FLX/L (n=5, 2 individuals pooled per sample); 56.7µg FLX/L (n=5, 2 individuals pooled per sample); Brain Samples: Negative Water Control (n=5, 2 individuals pooled per sample); 10.7µg FLX/L (n=5, 2 individuals pooled per sample); 56.7µg FLX/L (n=5, 2 individuals pooled per sample)

first: Carly

last: Colville

first: Alper

last: Alcaraz

first: Derek

last: Green

first: Bradley

last: Park

first: Jianguo

last: Xia

first: Othman

last: Soufan

first: Paval

last: Hruṧka

first: David

last: Potěšil

first: Zbyněk

last: Zdráhal

first: Doug

last: Crump

first: Niladri

last: Basu

first: Natacha

last: Hogan


title: Small intestinal mucosal transcriptomics in IBS

city: Rochester

first: Ting

state: MN

address: 507 3rd St SW

institute: Mayo Clinic

summary: Irritable bowel syndrome (IBS) patients often experience meal associated symptoms. Our objective was to determine small intestinal mechanisms of lipid-induced symptoms and rectal hypersensitivity in IBS based on RNA-seq.

overall_design: We recruited 26 IBS patients (12 IBS-C, 14 IBS-D) and 15 healthy volunteers (HV). In vivo permeability was assessed using saccharide excretion assay. Rectal sensitivity was assessed before and after a 1-hour small bowel lipid infusion (2 mL/min) and symptoms assessed throughout. Next, an extended upper endoscopy with probe-based confocal laser endomicroscopy (pCLE) was performed with changes assessed following application of intraluminal lipids. Mucosal biopsies from duodenum and jejunum were obtained for bulk RNA sequencing (RNA-seq). After library size selection of RNA-seq data, 11, 10, 12 Duodenum samples for HV, IBS-C and IBS-D were kept, and 12, 7, 8 Jejunum samples for HV, IBS-C and IBS-D were kept for further analysis.

first: Madhusudan

last: Grover

first: Lesley

last: Houghton

first: Stephanie

last: Peters

first: Surendra

last: Dasari


title: The human ion channel TRPM2 modulates cell survival in neuroblastoma through E2F1 and FOXM1

status: Public on Feb 25 2022

city: Hershey

first: Fernanda

last: Festa

state: PA

address: 500 University Dr BMR C7846

department: Pediatrics

institute: Penn State University

summary: Transient receptor potential channel melastatin 2 (TRPM2) is highly expressed in cancer and has an essential function in preserving viability through maintenance of mitochondrial function and antioxidant response. Here, the role of TRPM2 in cell survival was examined in neuroblastoma cells deleted of TRPM2 with CRISPR technology. Viability was significantly decreased in TRPM2 knockout after doxorubicin treatment. RNA sequence analysis and RT-qPCR revealed reduced RNAs encoding master transcription regulators FOXM1 and E2F1/2 and downstream cell cycle targets including Cyclin B1, CDK1, PLK1, and CKS1. CHIP analysis demonstrated decreased FOXM1 binding to their promoters. Western blotting confirmed  decreased expression, and increased expression of CDK inhibitor p21, a CKS1 target. In cells with TRPM2 deletion, cell cycle progression to S and G2/M phases was reduced after treatment with doxorubicin. RNA sequencing also identified decreased DNA repair proteins in cells with TRPM2 deletion after doxorubicin treatment, and DNA damage was increased. Wild type TRPM2  but not Ca2+-impermeable mutant E960D, restored live cell number and reconstituted expression of E2F1, FOXM1, and cell cycle/DNA repair proteins. FOXM1 expression alone restored viability.   TRPM2 is a potential therapeutic target to reduce tumor proliferation and increase doxorubicin sensitivity through modulation of FOXM1, E2F1, and cell cycle/DNA repair proteins.

overall_design: A total of 16 samples was analyzed (8 conditions in duplicate). Two control clones (SHSY5Y-SCR13 and SHSY5Y-SCR16) and two TRPM2 KO clones (SHSY5Y- TRPM2 KO11 and SHSY5Y- TRPM2 KO28) were analyzed in the presence or absence of Doxorubicin (3 uM for 24 h)

first: Iwona

last: Hirschler-Laszkiewicz

first: Suming

last: Huang

first: George-Lucian

last: Moldovan

first: Claudia

last: Nicolae

first: Ashna

last: Dhoonmoon

first: Lei

last: Bao

first: Kerry

last: Keefer

first: Shu-jen

last: Chen

first: Hong-Gang

last: Wang

first: Joseph

last: Cheung

first: Barbara

last: Miller


title: Transcriptome analysis of the symbiotic response of Arabidopsis at different temperatures.

status: Public on Feb 26 2022

city: Kunming

first: Jiajia

last: Han

state: Yunnan

address: Yunnan University (Chenggong Campus)

institute: Yunnan University

summary: High ambient temperature regulated the plant systemic response to the beneficial endophytic fungus Serendipita indica.  Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants.  The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high  ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild type plants.

overall_design: The aboveground parts of S. indica-inoculated Arabidopsis at 7 dpi were harvested for transcriptome.  Arabidopsis was grown on half-strength MS medium with 1.2% sucrose (½MS). The seeds were stratified at 4°C for 3 days and then first grown at 22°C under short-day growth condition (12 h: 12 h, day: night photoperiod, 7000 LX light) in growth chambers. Serendipita indica (syn. Piriformospora indica, DSM11827) fungus were grown and conserved in PDA medium (200 g L-1 potato, 20 g L-1 dextrose and 20 g L-1 agar). For cocultivation with S. indica, 9-day-old Arabidopsis seedlings were inoculated with S. indica in PNM medium plates. S. indica-incubated (Si) and control (CK) samples were grown at 22°C, 25°C or 28°C under short-day growth condition.

first: Xiaojie

first: Yueqing

last: Yin


title: Development of microRNA expression in exosomes derived from lncRNA HOTTIP overexpressed FaDu cells

first: Huaili

last: Jiang

state: 上海

address: 枫林路180号

institute: 复旦大学

summary:
Purpose: to detect the expression differences of miRNAs in exosomes derived from HOTTIP-overexpressed and NC FaDu cells
Methods: Total RNA containing small RNA was extracted from oe-HOTTIP FaDu-derived exosomes. Use Agilent miRNA array for miRNA analysis. Each slide of the Agilent array is designed as eight identical arrays (8×60K format), and each array contains probes for detecting 2549 human mature miRNAs from miRBase R21.0. Each miRNA was repeatedly detected by the probe 30 times. The array also contains 2164 Agilent control probes. GeneSpring software V13 (Agilent) was used to analyze the miRNA array data for data aggregation, standardization and quality control. Perform the default 90th percentile normalization method for date preprocessing. To select differentially expressed genes, we used thresholds of ≥2 and ≤−2 fold change, and the Benjamini-Hochberg corrected p vlaue was 0.05.
Results: The expression of 5000 miRNAs were tested and 257 miRNAs were significantly down-regulated.
Conclusion: 257 down-regulated miRNAs were candidates for HOTTIP-associated ceRNA network

overall_design: Examination of the expression differences of mircoRNAs in exosomes derived from HOTTIP-overexpressed and NC FaDu cells

first: Xinsheng


title: Loss of Vascular Endothelial Notch Signaling Induces Tertiary Lymphoid Structures in the Kidney

status: Public on Feb 24 2022

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

summary: Tertiary lymphoid structures (TLS are lymph node-like immune cell clusters that emerge during chronic inflammation in non-lymphoid organs like the kidney, but their origin remains not well understood. Here we show, using conditional deletion strategies of the canonical Notch signaling mediator Rbpj, that loss of endothelial Notch signaling in adult mice induces the spontaneous formation of bona fide TLS in the kidney, liver and lung, based on molecular, cellular and structural criteria. These TLS form in a stereotypical manner around parenchymal arteries, while secondary lymphoid structures remained largely unchanged. This effect is mediated by endothelium of blood vessels, but not lymphatics, since a lymphatic endothelial-specific targeting strategy did not result in TLS formation, and involves loss of arterial specification and concomitant acquisition of a high endothelial cell phenotype, as shown by transcriptional analysis of kidney endothelial cells. This indicates a so far unrecognized role for vascular endothelial cells and Notch signaling in TLS initiation.

overall_design: Bulk RNAseq of isolated kidney endothelial cells from mice with or without conditional endothelial-specific Rbpj deletion at 8wk of age, harvested 12wk after tamoxifen-mediated induction.

first: Susanne

last: Fleig

first: Florian

last: Limbourg


title: CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity (sgRNA distribution)

city: Cambridge

first: Julia

last: Joung

state: MA

address: 75 Ames St

institute: Broad Institute

summary: SgRNA library distributions of CRISPR activation screens for tumor immune evasion

overall_design: CRISPR activation sgRNA library was transduced in A375 cells and co-cultured with T cells before sequencing to determine sgRNA distribution

first: Feng

last: Zhang


title: Effect of Sirt6 deficiency on transcriptome in skeletal muscle of mice

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

country: South Korea

institute: Jeonbuk National University Medical School

summary: Expanding the exercise capacity is an emerging strategy to combat metabolic diseases. Skeletal muscle fiber type determination is critical for the exercise performance, but the regulatory basis is largely unknown. Here, we report that Sirt6 has a role in regulating myofiber configuration toward oxidative type and that Sirt6 activator can be an exercise mimetic. To elucidate molecular mechanisms, we performed RNA-sequencing analysis using WT and skeletal muscle-specific Sirt6 KO mice. Transcriptomic analysis enabled us to discover major signaling nodes altered by Sirt6 deficiency in close association with mitochondrial function and muscle phenotypes.

overall_design: Examination of RNA profile in gastrocnemius muscles of WT and skeletal muscle-specific Sirt6 KO mice.

first: Mi-Young

last: Song

first: Chang

first: Eun

last: Bae