title: DNA sequence determines epigenetic bistability at imprinting control regions [WGBS]

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

institute: Utrecht University

summary: Genomic imprinting is regulated by parental-specific epigenetic marks that differentiate between maternal and paternal chromosomes. Despite identical DNA sequence, the presence or absence of DNA methylation leads to the establishment of two distinct epigenetic states at Imprinting Control Regions (ICR). Here we combine targeted epigenome engineering to generate ectopic loci in the mouse embryonic stem cell genome that recapitulate the epigenetic properties of ICRs. We describe these ectopic ICRs as strong cis-regulatory sequences that can adopt and memorise one of two opposing epigenetic states, dependent of pre-imposed DNA methylation. This bistability is unique to ICRs and enabled us to systematically study the genetic and epigenetic determinants required for creating and maintaining the observed states. Through sequence manipulation we show that the ICR DNA sequence confers autonomy of ICRs and is required for creating epigenetic bistability. Genetic screens using DNA-methylation-sensitive reporters identify key components involved in regulating maintenance of epigenetic states. Besides DNMT1, UHRF1 and ZFP57, we identify novel factors that prevent switching between methylated and unmethylated states and validate two of these candidates, ATF7IP and ZMYM2, to be important for epigenetic memory at ICRs. In summary we show that the DNA sequence of ICRs provides the prerequisite for establishment of two distinct epigenetic states, while DNA and histone modifications ensure their stable propagation.

overall_design: Whole genome bisulfite sequencing in Atf7ip KO and Zmym2 KO ES cells

first: Stefan

last: Butz


title: SmcHD1 underlies the formation of H3K9me3 blocks on the inactive X chromosome in mice [RNA-seq]

status: Public on Jul 20 2022

city: Toyonaka

first: Koji

last: Nagao

state: Osaka

address: 1-1 Machikaneyama

department: Graduate School of Science

country: Japan

institute: Osaka University

type: Expression profiling by high throughput sequencing

summary: Stable silencing of the inactive X chromosome (Xi) in female mammals is crucial for the development of embryos and their postnatal health. SmcHD1 is essential for stable silencing of the Xi, and its functional deficiency results in derepression of many X-inactivated genes. Although SmcHD1 has been suggested to play an important role in the formation of higher-order chromatin structure of the Xi, the underlying mechanism is largely unknown. Here, we explore the epigenetic state of the Xi in SmcHD1-deficient epiblast stem cells and mouse embryonic fibroblasts in comparison with their wild-type counterparts. The results suggest that SmcHD1 underlies the formation of H3K9me3-enriched blocks on the Xi, which, although the importance of H3K9me3 has been largely overlooked in mice, play a crucial role in the establishment of the stably silenced state. We propose that the H3K9me3 blocks formed on the Xi facilitate robust heterochromatin formation in combination with H3K27me3, and that the substantial loss of H3K9me3 caused by SmcHD1 deficiency leads to aberrant distribution of H3K27me3 on the Xi and derepression of X-inactivated genes.

overall_design: Allele-specific RNA-seq analysis of epiblast stem cells (EpiSCs) prepared from female fetuses deficient for SmcHD1

first: Saya

last: Ichihara

first: Takehisa

last: Sakaguchi

first: Chikashi

last: Obuse

first: Takashi

last: Sado


title: PAI-1 is a potential transcriptional silencer that supports bladder cancer cell activity [ChIP-Seq]

city: Los Angeles

first: Hideki

last: Furuya

state: CA

address: 110 N. George Burns Road, Davis 2025

department: Surgery

country: USA

institute: Cedars Sinai Medical Center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The extracellular activity of Plasminogen activator inhibitor-1 (PAI-1) is well described, acting as an inhibitor of tissue plasminogen activator and urokinase-type plasminogen activator, impacting fibrinolysis. Recent studies have revealed a pro-tumorigenic role of PAI-1 in human cancers, via the regulation of angiogenesis and tumor cell survival. In this study, immunohistochemical staining of 939 human bladder cancer specimens showed that PAI-1 expression levels correlated with tumor grade, tumor stage and overall survival. The typical subcellular localization of PAI-1 is cytoplasmic, but in approximately a quarter of the cases, PAI-1 was observed to be localized to both the tumor cell cytoplasm and the nucleus. To investigate the potential function of nuclear PAI-1 in tumor biology we applied chromatin immunoprecipitation (ChIP)-sequencing, gene expression profiling, and rapid immunoprecipitation mass spectrometry to a pair of bladder cancer cell lines. ChIP-sequencing revealed that PAI-1 can bind DNA at distal intergenic regions, suggesting a role as a transcriptional coregulator. The downregulation of PAI-1 in bladder cancer cell lines caused the upregulation of numerous genes, and the integration of ChIP-sequence and RNA-sequence data identified 57 candidate genes subject to PAI-1 regulation. Taken together, the data suggest that nuclear PAI-1 can influence gene expression programs and support malignancy.

overall_design: Two biological replicates of ChIP-seq in 2 human bladder cancer cell lines

first: Charles

last: Rosser


title: Gene profiling using microarray analysis between the ΔMet treated and control groups at different stages

status: Public on Jul 21 2022

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

institute: Tokyo Institute of Technology

summary:
Undifferentiated cells, hiPSC-derived differentiated cells on day3 DE cells, day 5 PG cells, day 11 PP cells and day 25 EC cells were compared, using GeneChip™ Human Gene 2.0 ST Array
Methionine deprivation (ΔMet) pretreatment potentiates late-stage differentiation of human iPS cells into insulin-expressing β cells

overall_design: Cells were harvested at undifferentiated or differentiated stages for RNA extraction and hybridization on Affymetrix microarrays. We performed gene expression profiles of hiPSCS derived pancreatic cells cultured in complete (comple) or Met-deprived conditions (deltaMet) for 5h before differentiation.  And human islte were used as a comparison

first: Nobuaki

last: Shiraki

first: Tomonori

last: Tsuyama


title: Vascular Regulation by Super Enhancer-Derived LINC00607 (scRNA-Seq)

city: Duarte

first: Zhen

last: Chen

address: 1500 E Duarte Rd

department: DMRI

institute: City of Hope

summary: Vascular endothelial cells play a pivotal role in whole body homeostasis. Recent advances have revealed enhancer-associated long non-coding RNAs as essential regulators in endothelial function. We investigated LINC00607, a super enhancer-derived in human arteries with an emphasis on endothelial cells. Using a series of RNA-sequencing, we characterized the transcriptomes regulated by LINC00607 in endothelial cells and vascular smooth muscle cells, and in basal and diabetic conditions in endothelial cells. Furthermore, using scRNA-seq, we demonstrated that modified antisense oligonucleotide inhibitor of LINC00607 can reverse key dysfunctional changes induced by high glucose and TNF-alpha in endothelial cells.

overall_design: Performing single-cell RNA-seq in human umbilical vein endothelial cells exposed to high glucose and TNF-alpha treatment for 7 days and then inhibit LINC00607 for the last 3 days.

first: Kiran

last: Sriram

first: Yingjun

last: Luo

first: Dongqiang

last: Yuan

first: Naseeb

middle: K

last: Malhi

first: Alonso

last: Tapia

first: Vishnu

middle: A

last: Samara

first: Rama

last: Natarajan

middle: B


title: Vascular Regulation by Super Enhancer-Derived LINC00607

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

overall_design: Refer to individual Series


title: NfκB signaling dynamics and their target genes differ between mouse blood cell types and induce distinct cell behavior

city: Basel

first: Tobias

last: Kull

address: Mattenstrasse 26

country: Switzerland

institute: ETH Zurich

summary: Cells can use signaling pathway activity over time (i.e., dynamics) to control cell fates. However, little is known about the potential existence and function of signaling dynamics in primary hematopoietic stem and progenitor cells (HSPCs). Here, we use time-lapse imaging and tracking of single murine HSPCs from GFP-p65/H2BmCherry reporter mice to quantify their nuclear factor κB (NfκB) activity dynamics in response to TNFα and IL1β. We find response dynamics to be heterogeneous between individual cells, with cell type specific dynamics distributions. Transcriptome sequencing of single cells physically isolated after live dynamics quantification shows activation of different target gene programs in cells with different dynamics. Finally, artificial induction of oscillatory NfκB activity causes changes in GMP behavior. Thus, HSPC behavior can be influenced by signaling dynamics, which are tightly regulated during hematopoietic differentiation and enable cell type specific responses to the same signaling inputs.

overall_design: Single-cell mRNA profiles of GMPs, isolated from 12–19 week old, male and female GFP-p65/H2BmCherry mice and cultured for 8h under a confocal microscope.

first: Arne

last: Wehling

first: Martin

last: Etzrodt

first: Markus

last: Auler

first: Philipp

last: Dettinger

first: Nicola

last: Aceto

first: Timm

last: Schroeder


title: Vascular Regulation by Super Enhancer-Derived LINC00607 (bulk RNA-Seq)

overall_design: Performing polyA-enriched RNA-seq in HUVECs and HVSMC with LINC00607 knockdown by LNA


title: Altered regulation of mRNA and miRNA expression in epithelial and stromal tissue of keratoconus corneas [RNA]

city: Homburg

first: Tanja

last: Stachon

address: Kirrergerstr. 100

department: Dr. Rolf  M. Schwiete Center

country: Germany

institute: Saarland University

summary: Purpose:  To evaluate conjunctival cell microRNA and mRNA expression in relation to observed phenotype and genotype of aniridia-associated keratopathy (AAK) in a cohort of subjects with congenital aniridia.  Methods:  Using impression cytology, bulbar conjunctival cells were sampled from 20 subjects with congenital aniridia and 20 age and sex-matched healthy control subjects. RNA was extracted and microRNA and mRNA analysis was performed using microarrays. Results were related to the presence and severity of AAK determined by a standardized clinical grading scale and to the genotype (PAX6 mutation?) determined by clinical genetics.   Results:  Of the 2549 microRNAs analyzed, 21 were differentially expressed relative to controls. Among these miR-204-5p, an inhibitor of corneal neovascularization, was downregulated 26.8-fold, while miR-5787 and miR-224-5p were upregulated 2.8 and 2.4-fold relative to controls, respectively. At the mRNA level, 539 transcripts were differentially expressed, among these FOSB and FOS were upregulated 17.5 and 9.7-fold respectively, and JUN by 2.9-fold, all components of the AP-1 transcription factor complex. Pathway analysis revealed dysregulation of several enriched pathways including PI3K-Akt, MAPK, and Ras signaling pathways in aniridia. For several microRNAs and transcripts, expression levels aligned with AAK severity, while in very mild cases with missense or non-PAX6 coding mutations, gene expression was only minimally altered.  Conclusion:  In aniridia, specific factors and pathways are strongly dysregulated in conjunctival cells, suggesting that the conjunctiva in aniridia is abnormally maintained in a pro-angiogenic and proliferative state, promoting the aggressivity of AAK in a mutation-dependent manner. Transcriptional profiling of conjunctival cells at the microRNA and mRNA levels presents a powerful, minimally-invasive means to assess the regulation of cell dysfunction at the ocular surface.

overall_design: MiRNA and mRNA expression profiles of epithelial and stromal cells from 8 patients with keratoconus compared to controls

first: Nicole

last: Ludwig


title: "Stripe" transcription factors provide accessibility to co-binding partners in mammalian genomes.

city: Bethesda

first: Yongbing

last: Zhao

state: Maryland

address: 10 Center Drive RooM 13C101A

department: NIAMS

institute: National Institutes of Health

type: Genome variation profiling by high throughput sequencing


title: Metabolic Transitions Define the Spermatogonial Stem Cell Maturation [mouse]

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

summary: Spermatogonial stem cells (SSCs) are the basis of spermatogenesis and therefore of male fertility. Transplantation of SSCs, isolated before treatment for cancer, and cultured in vitro, could be a potential treatment for infertility.  Such clinical usage requires an understanding of the metabolic requirements during SSC development. Adult SSCs mainly use glycolysis for their maintenance in the mouse and human. However, SSCs embryonic precursors, primordial germ cells (PGCs), require a high mitochondrial metabolism in the mouse. Similarly, pig neonatal SSC precursors have been described to rely on oxidative phosphorylation (OXPHOS) for the first 2 months of development, when a transition to an adult SSC metabolic phenotype is initiated. When and if such a metabolic transition occurs in humans is ambiguous. We show here for the first time using single-cell RNA sequencing, that human PGCs and prepubertal human spermatogonia have an enrichment of oxidative phosphorylation associated genes, which is downregulated by 13 years of age. Furthermore, we show, that similar metabolic differences are detectable after birth also in mouse. The metabolic transition in humans with puberty was preceded by a drastic change of SSC shape. Using a pig model, we reveal that these metabolic changes could be regulated by IGF-1 dependent signaling via mTOR and proteasomic inhibition. Understanding the metabolic requirements of SSCs during development is crucial to establish a culture system and enable clinical use of SSCs.

overall_design: Testicular cells were collected from 6-8 day (n=3) and 4-month-old mouse testes (n=2)  by 2 step enzymatic digestion as previously described (Yeh et al., 2007). Spermatogonia from 6-8 old mice were then isolated by size exclusion and granularity using FACS light scatter properties. The primary contaminating cell type in the enriched spermatogonia population were somatic peritubular myoid and Sertoli cells. Spermatogonia from 4-month-old  were isolated by fluorescence assisted cell sorting (FACS) (FACSAria II, BD Biosciences), using antibodies against GFR⍺1 ([1:100] Neuromics, goat polyclonal) and cKIT ([1:100] AbCam, rat polyclonal). The primary contaminating cell type in the enriched spermatogonia population after FACS was further differentiating germ cells (spermatocytes and round spermatids). Porcine cells were isolated from the testis by a two-step enzymatic digestion, as previously described (Sakib et al. 2019). Enrichment was performed by differential plating in  alpha MEM advanced (ThermoFisher,#12492013), 5% FBS, 1x P/S with subsequent sort as previously described (Voigt et al. 2021). Isolated primary murine spermatogonia samples were resuspended in PBS supplemented with 1% BSA and 6000–10,000 cells per sample were processed using ChromiumTM Single Cell 3′ v2 Chemistry library prep kit according to the manufacturer’s instructions (10X Genomics, San Francisco, CA, USA). Samples were sequenced on an Illumina HiSeq4000 with paired-end 50 base pair reads by Genome Quebec (Montreal, QC, Canada). The raw counts were subsequently processed with a 10x Genomics CellRanger pipeline using default settings, after which the outputs from the individual samples were combined using the CellRanger aggr function to normalize the sequencing depth and produce aggregated gene-cell UMI count matrix. Sequencing data was analyzed using the cell ranger pipeline. A total of 19,166 cells were included in the analysis and normalized to a read depth of 104,230 reads per cell.

first: Anna

middle: L

last: Voigt

first: Rkia

last: Dardari

first: Lin

last: Su

first: Antoine

last: Dufour

first: Sarthak

last: Sinha

first: Sarah

last: Munyoki

first: Whitney

last: Alpaugh

first: Kyle

middle: E

last: Orwig

first: Ina

last: Dobrinski


title: Stromal HIF2 Regulated Immune Suppression in the Pancreatic Cancer Microenvironment

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary:
We used a dual recombinase mouse model to delete Hif2a in α-smooth muscle actin (αSMA)-expressing cancer-associated fibroblasts (CAFs) arising within spontaneous pancreatic tumors. The effects of CAF-Hif2a expression on tumor progression and composition of the tumor microenvironment were evaluated by Kaplan-Meier analysis, quantitative real-time polymerase chain reaction, histology, immunostaining, and by both bulk and single-cell RNA sequencing. CAF-macrophage crosstalk was modeled ex vivo using conditioned media from CAFs after treatment with hypoxia and PT2399, a HIF2 inhibitor currently in clinical trials. Syngeneic flank and orthotopic PDAC models were used to assess whether HIF2 inhibition improves response to immune checkpoint blockade.
Results. CAF-specific deletion of HIF2, but not HIF1, suppressed PDAC tumor progression and growth, and improved survival of mice by 50% (n = 21-23 mice/group, Log-rank P = 0.0009). Deletion of CAF-HIF2 modestly reduced tumor fibrosis and significantly decreased the intratumoral recruitment of immunosuppressive M2 macrophages and regulatory T cells. Treatment with the clinical HIF2 inhibitor PT2399 significantly reduced in vitro macrophage chemotaxis and M2 polarization, and improved tumor responses to immunotherapy in both syngeneic PDAC mouse models.
Conclusions. Together, these data suggest that stromal HIF2 is an essential component of PDAC pathobiology and is a druggable therapeutic target that could relieve tumor microenvironment immunosuppression and enhance immune responses in this disease.

overall_design: Examination of Hif2a deletion in aSMA-expressing cancer-associated fibroblasts to understand the role of hypoxia-inducible factors within the PDAC tumor microenvironment. Single-cell RNA sequencing allowed for the identification and deep characterization of multiple cell types in the PDAC tumor microenvironment, such that aSMA-expressing CAFs could indeed be distinguished from other cell types in the scRNA assay.

first: Carolina

middle: J

last: Garcia Garcia

first: Yanqing

last: Huang

first: Natividad

middle: R

last: Fuentes

first: Madeleine

middle: C

last: Turner

first: Maria

last: Monberg

first: Daniel

last: Lin

first: Nicholas

middle: D

last: Nguyen

first: Tara

middle: N

last: Fujimoto

first: Jun

first: Jaewon

last: Lee

first: Vincent

last: Bernard

first: Meifang

last: Yu

first: Abagail

middle: M

last: Delahoussaye

first: Iancarlos

last: Jimenez Sacarello

first: Emily

last: Caggiano

first: Jae

last: Phan

first: Amit

last: Deorukhar

first: Jessica

last: Molkentine

first: Dieter

last: Saur

first: Cullen

last: Taniguchi


title: Comparative analysis of gut bacteriophage between older and young people

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

summary: Given the gut microbiota involve aging processing, we performed comparative analysis of gut bacteriophage between older and young subjects using next-generation sequencing (NGS). In our previous study, we found that the Ruminococcaceae is higher in aged subjects comparing to young one. To identify the bacteriophage targeting to the Ruminococcaceae, we also access the composition of phage in the Ruminococcaceae (ATCC, TSD-27) after incubated with human stool samples. The Lactobacillus (ATCC, LGG) targeting phage was used as the control. The virome sequencing analysis using NGS indicated that Myoviridae are high enrich in young subjects and predominate in TSD-27 targeting phage.

overall_design: The study involved 24 healthy volunteers divided into a young group (25.6 ± 4.2 years old, n=12) and an older group (65.3 ± 5.6 years old, n=12) by age. The participants in the two groups were matched for age and gender. Six of samples was mixed as one group for DNA sequencing.

first: Yun

last: Teng


title: Design of a gene signature to analyze the proinflammatory and the profibrotic polarization of murine fibroblasts and validation in an experimental murine model of scleroderma.

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

summary: Effect of TGFb1, TNFa, IL6-IL6R, IL1b on gene expression in Mouse Embryonnic Fibrobroblasts (3T3) using RNA microarrays.

overall_design: Enrichment analysis of the differentially expressed genes (DEGs) regulated by  TGFb1, TNFa, IL6-IL6R, or IL1 compared to control in Mouse Embryonnic Fibroblasts (3T3).

first: Emmanuel

last: Ledoult

first: David

last: Launay


title: Metabolic Transitions Define the Spermatogonial Stem Cell Maturation [human]

first: Jeff

last: Biernaskie

overall_design: Human samples (homo sapiens) were obtained from the Fertility Preservation Program in Pittsburgh and processed at the University of Pittsburgh. Testes were collected from 1-, 2- and 7-year-old males through the University of Pittsburgh Health Sciences Tissue Bank and Center for Organ recovery under the University of Pittsburgh CORID 686. Human samples were enzymatically digested and processed as previously described (Shami et al. Dev Cell . 2020 Aug 24;54(4):529-547.e12). Human samples were processed with approval from the University of Pittsburgh Institutional Review Board (Protocol #STUDY09020220). Isolated primary human testicular cells were processed using Chromium TM Single Cell 3′ v3 Chemistry library prep kit according to the manufacturer’s instructions (10X Genomics, San Francisco, CA, USA). Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. A shallow sequencing was performed first using Illumina MiSeq SR50 to estimate the number of recovered cells in each sample (a total of 5089, 8447 and 7851 cells were collected from 1-, 2- and 7-year-old males, respectively). The sequencing of the libraries was performed a second time with a targeted sequencing depth of ~ 50,000 reads/cell using an Illumina NovaSeq 6000 sequencer (100pb single end reads) (CHGI, University of Calgary, Alberta, Canada). The raw reads were subsequently processed with a 10x Genomics CellRanger pipeline (version 3.1.0) using default settings. The outputs from the three human samples were combined using the CellRanger aggr function to normalize for the sequencing depth and produce aggregated gene-cell UMI count matrix for the downstream analysis.

first: Anna

last: Voigt

first: Rkia

last: Dardari

first: Lin

last: Su

first: Antoine

last: Dufour

first: Sarthak

last: Sinha

first: Sarah

last: Munyoki

first: Whitney

last: Alpaugh

first: Kyle

last: Orwig

first: Ina

last: Dobrinski


title: Gene expression profile of cardiac stromal cells from ACM patients in adipogenic medium with and without MB-3 treatment

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

country: Italy

institute: Eurac Researc

summary: Human primary cardiac stromal cells were isolated from arrhythmogenic cardiomyopathy patients and were cultured either in adipogenic medium (ADIPO, A) or in adipogenic medium supplemented with MB-3 (MB-3, M), that is a specific inhibitor of GCN5. The gene expressiona analysis was aimed to investigate the molecular effect of GCN5 inhibition.

overall_design: Gene expression profiles of ACM samples treated with MB3 were compared against ACM samples without MB-3 treatment.

first: Alessandra

last: Pagliaro

first: Chiara

last: Volani

first: Giuseppe

last: Paglia

first: Benedetta

last: Porro

first: Ilaria

last: Stadiotti

first: Luisa

last: Foco

first: Elisa

last: Cogliati

first: Adolfo

last: Paolin

first: Costanza

last: Lagrasta

first: Caterina

last: Frati

first: Emilia

last: Corradini

first: Angela

last: Falco

first: Theresa

last: Matzinger

first: Anne

last: Picard

last: Ermon

first: Silvano

last: Piazza

first: Marzia

last: DeBortoli

first: Claudio

last: Tondo

first: Giulio

last: Pompilio

first: Elena

last: Sommariva

first: Peter

middle: P

last: Pramstaller

first: Viviana

last: Meraviglia

last: Rossini


title: SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1a/XBP1 ER stress pathway in human lung-derived cells

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

summary: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available, or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the master UPR sensor IRE1a kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1a-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1a as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1a through autophosphorylation, but its RNase activity fails to splice XBP1. Moreover, while IRE1a was dispensable for replication in human cells for all coronaviruses tested, it was required for maximal expression of genes associated with several key cellular functions, including the interferon signaling pathway, during SARS-CoV-2 infection. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1a, perhaps as a strategy to eliminate detection by the host immune system.

overall_design:
A549 cells expressing the MERS-CoV receptor DPP4 were cultured in 10% FBS RPMI media. At 70% cell confluence, cells were washed once with PBS before being mock infected or infected with MERS-CoV (EMC/2012) at MOI = 1. Virus was absorbed for 1 hour at 37 degrees Celsius in serum-free RPMI media. After one hour, virus was removed, cells washed three times with PBS, and 2% FBS RPMI was added. The cells were incubated for another 24 hours or 36 hours, then washed once with PBS and lysed using RLT Plus lysis buffer before genomic DNA removal and total RNA extraction using the Qiagen RNeasy Plus Mini Kit (Qiagen 74134). Three independent biological replicates were performed per experimental condition. RNA sample quality check, library construction, and sequencing were performed by GeneWiz following standard protocols. All samples were sequenced by an Illumina HiSeq sequencer to generate paired-end 150bp reads. Read quality was assessed using FastQC v0.11.2 as described by Andrews, S. (2010) “FastQC:  A Quality Control Tool for High Throughput Sequence Data” (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Raw sequencing reads from each sample were quality and adapter trimmed using BBDuk 38.73 as described by Bushnell, B at "BBTools software package" (http://sourceforge.net/projects/bbmap). The reads were mapped to the human genome (hg38 with Ensembl V98 annotation) using RNA STAR 2.7.1a. The resulting BAM files were counted by featureCounts 1.6.4 to count the number of reads for each gene.

For SARS-CoV-2 and OC43 infections, ACE2-A549 control or IRE1 KO cells were cultured in 10% FBS RPMI to 70% confluence. Cells were washed once with PBS before being mock infected or infected with each virus at MOI = 1 for one hour in serum-free RPMI at 33C. Cells were then washed three times with PBS before 2% FBS RPMI was added. At 48 hours post infection, cells were lysed with RLT Plus lysis buffer before genomic DNA removal and total RNA extraction using the Qiagen RNeasy Plus Mini Kit (Qiagen 74134).  Three independent biological replicates were performed per experimental condition. RNA sample quality check, library construction, and sequencing were performed by the University of Chicago Genomics Facility following standard protocols. All samples were sequenced in two runs by a NovaSeq 6000 sequencer to generate paired-end 100bp reads. For each sample, the reads from two flow cells were combined before downstream processing. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3 (https://github.com/FelixKrueger/TrimGalore). The reads were mapped to the human genome (UCSC hg19 with GENCODE annotation).

first: David

last: Renner

first: Susan

last: Weiss

first: Marsha

last: Rosner


title: Increased H3K27 trimethylation contributes to cone survival in a mouse model of cone dystrophy

city: Perth

first: Livia

last: Carvalho

state: Western Australia

address: 2 Verdun St

country: Australia

institute: Lions Eye Institute

summary: Inherited retinal diseases (IRDs) are a heterogeneous group of blinding disorders, which result in dysfunction or death of the light-sensing cone and rod photoreceptors. Despite individual IRDs being rare, collectively they affect up to 1:2000 people worldwide, causing a significant socioeconomic burden, especially when cone-mediated central vision is affected. This study uses the Pde6ccpfl1 mouse model of achromatopsia, a cone-specific vision loss IRD, to investigate the potential gene-independent therapeutic benefits of a histone demethylase inhibitor GSK-J4 on cone cell survival. We investigated the effects of GSK-J4 treatment on cone cell survival in vivo and ex vivo and changes in cone-specific gene expression via single-cell RNA sequencing. A single intravitreal GSK-J4 injection led to transcriptional changes in pathways involved in mitochondrial dysfunction, endoplasmic reticulum stress, among other key epigenetic pathways, highlighting the complex interplay between methylation and acetylation in healthy and diseased cones. Furthermore, continuous administration of GSK-J4 in retinal explants increased cone survival. Our results suggest that IRD-affected cones respond positively to epigenetic modulation of histones, indicating the potential of this approach in the development of a broad class of novel therapies to slow cone degeneration.

overall_design: Single cell RNA sequencing was performed on isolated GFP-containing cone photoreceptors from Pde6ccplf1. Cone cells were collected 10 days after intravitreal injection of GSK-J4 and FAC-sorted into 96 well plates. Single cells were processed in wells and sequenced using an adapted version of SMARTseq2 and Mars-seq.

first: Paula

middle: I

last: Fuller-Carter

middle: S

first: Annie

last: Miller

first: Dragana

last: Trifunovic

first: Abha

last: Chopra

first: Ramesh

last: Ram

first: Klaudija

last: Masarini

first: Marijana

last: Samardzija

first: Kim

middle: W

last: Carter

first: Rabab

last: Rashwan

first: Alicia

last: Brunet

first: Christian

last: Grimm

first: Marius

last: Ueffing


title: CRAC of yeast RNA polymerase II and RNases H in asynchronous, G1-arrested, and S-phase cells.

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

summary: We obtained  RNA polymerase II and RNases H occupancy profiles across the genome of S.cerevisiae strains:   Sen1 depleted cells using the degron system (including no addition of IAA); sen1-3, RNases H deleted, and wild-type cells.  This allowed us to compare RNAPII and RNases H occupancy profiles in different genetic context and/or phases of the cell cycle.

overall_design: The nascent RNA was crosslinked to Rpb1 (RNAPII) or to RNases H (Rnh1 or Rnh201) and sequenced after purification of the target protein under stringent and denaturing conditions. This reveals the position of the target protein at the nucleotide resolution level.

first: Umberto

last: Aiello

first: Drice

last: Challal

first: Griselda

last: Wentzinger

first: Armelle

last: Lengronne

first: Rowin

last: Appanah

first: Philippe

last: Pasero

first: Benoit

last: Palancade


title: Comprehensive maps of transcription factor (TF) binding sites in mouse (ATAC-Seq)

first: Yongbing

last: Zhao

summary: Mammalian genome encodes approximately 1,700 transcription factors (TFs), 1,300 out of which have sequence specific binding motifs. Transcription in mammalian cells is regulated by the recruitment of TFs to specific cis-regulatory elements. In spite of consistent efforts on the function of individual TF, the question still remains how TFs bind to DNA and form enhancer. Here, we try to solve this problem by investigating the relationship between TF binding pattern and chromatin accessibility (ATAC-Seq). We first systematically acquired ATAC-Seq dataset as well as matched RNA-Seq dataset from different mouse primary tissues. A comprehensive TF binding map was built for each tissue/cell type by genomic approaches.

overall_design:
We have analyzed 239 ATAC-Seq samples from mouse primary cells and tissues, which include 151 samples from ENCODE and GEO (listed in metadata_ALLsamples.xlsx - YELLOW), and 88 newly generated samples.
Third-party reanalysis was performed on 151 samples from ENCODE and GEO.  The 151 processed data files are linked below as supplementary files.

first: Andrea

last: Conte

first: Supriya

last: Vartak

first: Rafael

last: Casellas


title: tsRNAs Are Potential Biomarkers of Acute Rejection in Vascularized Composite Allotransplantation

city: chang sha

first: yuan

last: fang

address: 138 TongZiPo road

country: China

institute: The Third Xiangya Hospital of Central South Uniiversity

summary:
Purpose: to explore the function and mechanism of acute rejection in vascularized composite allotransplantation
Method: tRF & tiRNA profiles of acute rejection in vascularized composite allotransplantation were generated by deep sequencing, using Illumina NextSeq 500. qRT–PCR validation was performed using SYBR Green assays.
Results:Sequencing was used to screen expression profiles and predict target genes. Compared with the control group, there were significant differences in the expression levels of 16 tRFs & tiRNAs, including 5 up-regulated target genes and 11 down-regulated target genes. Bioinformatics analysis and RT-qPCR revealed potential up regulation of tRFs & tiRNAs(tiRNA-1-33-Gly-GCC-1, tiRNA-1-34-Glu-CTC-1, tRF-1-32-Gly-GCC-2-M2) and down regulation of tRFs & tiRNAs (tRF-59:75-Gln-CTG-2-M2, tRF-59:76-Val-AAC-1-M2).
Conclusion: In conclusion, it is speculated that tiRNA-1-34-Glu-CTC-1 plays an important role in VCA induced acute rejection by regulating CACNA1D gene in MAPK signaling pathway. This provides a new insight into the mechanism and therapeutic targets of acute rejection.

overall_design: tRF & tiRNA profiles of normal skin and UV damage skin mice

first: Yuan

last: Fang

first: Shoubao

last: Wang


title: Transcriptomic profiles of gastrocnemius muscles from hindlimb unloaded mice treated with 4-phenylbutyrate

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

summary: Transcriptomic profiles of gastrocnemius muscles from 18 weeks old, male, hind muscles unloaded mice treated with vehicle or4-phenylbutyrate (4-PBA)

overall_design: 16 weeks old, male C57bl6/J mice were hindlimb-unloaded (HU) for three weeks, and treated with vehicle or 4-phenylbutyrate for prevention of muscle atrophy. The muscle from the ground mice were used as control.

first: Rizwan

last: Qaisar

first: Muhammad

middle: T

last: Gul


title: ChIPseq for pediatric AML patients

city: Suzhou

first: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to explore ChIPseq results for pediatric AML patients.

overall_design: 11 pediatric AML samples


title: Bone marrow adipocyte (BMAd)-specific deletion of Pnpla2 reveals local roles for lipolysis to fuel cells of bone and the marrow niche

city: Ann Arbor

first: Ziru

last: Li

state: MI

address: 2800 Plymouth Rd.

department: Molecular & Integrative Department

institute: University of Michigan

summary:
Purpose: To determine mechanisms by which BMAd-Pnpla2 deficiency-causes bone loss in calorie restricted (CR) mice, we profiled global gene expression in bone marrow plugs from distal tibiae, a location highly enriched with bone marrow adipose tissue.
Methods: Male control and BMAd-Pnpla2-/- mice at 24 weeks of age were either fed AL or underwent 30% CR for 6 weeks. Distal tibial cBMAT was flushed and cBMAT from two mice was pooled as one sample for RNAseq analyses (n of 3 or 4 per treatment).
Results: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the mouse genome (UCSC mm10) and identified 23,441 transcripts in the bone marrow adipose tissue of WT and Pnpla2 deficiency mice using STAR with default parameters. PCA plots show that RNA profiles from CR groups are distinct from their Ad libitum (AL) controls. Whereas Pnpla2 deficiency in mice fed AL does not cause gene expression to diverge substantially, loss of Pnpla2 interacts with CR resulting in a well-segregated pattern of gene expression
Conclusion: Caloric restriction induces dramatic elevations in extracellular matrix organization and skeletal development genes, and energy from BMAd is required for these adaptations.

overall_design: Gene profiling of bone marrow adipose tissue from WT and BMAd-Pnpla2-/- mice fed an ad libitum or a caloric restricted diet for 6 weeks.

first: Hui

last: Yu

first: Ormond

last: MacDougald


title: mRNAs sequestered in stress granules recover nearly completely for translation

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: SG-sequestered mRNAs disassemble nearly completely and the m6A modification may display some advantage to the mRNAs in their recovery

overall_design: RNA Sequencing of Human Embryonic Kidney 293 cells expressing N-terminally FLAG tagged TIA1 (HEK-TIA1-FLAG) to determinde the trnsalting pool of RNA upon arsenite stress relief

first: Sarada

last: Das

first: Leonardo

last: Santos


title: Transcriptional data of tissues in pacients with nasopharyngeal carcinoma

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

summary: Transcriptional data of 12 pairs NPC tissues with high or low intratumoural bacteria load

overall_design: 12 pairs NPC tissues with high or low intratumoural bacteria load were randomly selected for host transcriptional analysis to analyze the correlation between bacterial load and enrichment pathways, especially the immune pathways.

last: Liu

first: Han

last: Qiao

first: Xi-Rong

last: Tan


title: RNA-seq for NB4 cell line in either the absence or presence of GNE987

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare RNA-seq results for NB4 cell line in either the absence or presence of GNE987

overall_design: 2 NB4 samples with no treatment and 2 NB4 samples with GNE987


title: DNA sequence determines epigenetic bistability at imprinting control regions [BS-Seq]

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

country: Netherlands

institute: Utrecht University

type: Methylation profiling by high throughput sequencing

summary: Genomic imprinting is regulated by parental-specific epigenetic marks that differentiate between maternal and paternal chromosomes. Despite identical DNA sequence, the presence or absence of DNA methylation leads to the establishment of two distinct epigenetic states at Imprinting Control Regions (ICR). Here we combine targeted epigenome engineering to generate ectopic loci in the mouse embryonic stem cell genome that recapitulate the epigenetic properties of ICRs. We describe these ectopic ICRs as strong cis-regulatory sequences that can adopt and memorise one of two opposing epigenetic states, dependent of pre-imposed DNA methylation. This bistability is unique to ICRs and enabled us to systematically study the genetic and epigenetic determinants required for creating and maintaining the observed states. Through sequence manipulation we show that the ICR DNA sequence confers autonomy of ICRs and is required for creating epigenetic bistability. Genetic screens using DNA-methylation-sensitive reporters identify key components involved in regulating maintenance of epigenetic states. Besides DNMT1, UHRF1 and ZFP57, we identify novel factors that prevent switching between methylated and unmethylated states and validate two of these candidates, ATF7IP and ZMYM2, to be important for epigenetic memory at ICRs. In summary we show that the DNA sequence of ICRs provides the prerequisite for establishment of two distinct epigenetic states, while DNA and histone modifications ensure their stable propagation.

overall_design: Targeted bisulfite sequencing for Airn, Kcnq1ot1 and Peg10 ICRs in wild type and Atf7ip KO cells

first: Stefan

last: Butz


title: Global gene expression of canine bladder K9TCC cells and cancer stem cells after COX-2 inhibition

city: Edinburgh

first: Emma

last: Hurst

address: Easter Bush Campus

country: United Kingdom

institute: University of Edinburgh

summary: Cancer stem cells (CSCs) are fundamental to bladder cancer progression and the cyclooxygenase-2 (COX-2) pathway has a pro-tumorigenic role in CSC function. Naturally occurring bladder cancer in dogs has the potential to be a natural model of the human disease. Here, we used canine specific microarrays to determine changes in global gene expression of canine bladder cancer cells (the K9TCC cell line) and bladder cancer stem cells isolated from the K9TCC cell line after treatment with the selective COX-2 inhibitor mavacoxib or a COX-2 siRNA.

overall_design: K9TCC cells were grown as aherent cells or in anchorage dependent conditions to form cancer stem cell spheres for at least 5 passages to maintain self-renwal properties. Both adherent cells (Adh) and cancer stem cell spheres (Sphs) were treated with either 0 or 50uM mavacoxib (0uM treatment was DMSO, the vehicle control for the drug) for 24 hours, or transfected with a COX-2 siRNA or negative control siRNA for 48 hours. Cells were harvested and RNA extracted for microarray analysis on the Affymetrix Canine Gene 1.1 ST microarray (by Edinburgh Genomics). 3 replicates of each condition and cell type were assessed.

first: Lisa

middle: Y

last: Pang

first: David

last: Argyle


title: Next generation sequencing analysis of Arabidopsis thaliana transcriptomes in response to Botrytis cinerea infection

city: Changchun

first: Shouan

address: Xi-An-Da Road 5333

institute: Jilin University

summary: Next generation sequencing was performed to identify genes changed in Arabidopsis thaliana upon Botrytis cinerea infection. The goal of the work is to find interesting genes involved in plant defense. The object is to reveal the molecular mechanism of plant defense.

overall_design: mRNA profiling of Arabidopsis thaliana in response to Botrytis cinerea infection.


title: Metabolic Transitions Define the Spermatogonial Stem Cell Maturation

city: Calgary

first: Jeff

last: Biernaskie

address: 3330 Hospital Drive NW

institute: University of Calgary

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: Next Generation Sequencing Facilitates Quantitative Analysis of NC and shMETTL14 Transcriptomes

first: hongbo

last: li

state: Guangdong

address: No.58, Zhongshan Rd.2

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

summary: The goals of this study are to compare the differentially expressed genes between NC and shMETTL14 groups

overall_design: Cells were infected with lentiviral shRNA targeting METTL14.  We compared the differentially expressed genes between NC and shMETTL14 groups.

first: Hongbo


title: Transcriptome sequencing of Trichoderma guizhouense NJAU4742 and its mutants when induced by different polysaccharides or carbon starvation

city: Nanjing

first: Youzhi

last: Miao

address: WeiGang NO.1

institute: Nanjing Agricultural University

summary: The goal of this study is to find novel regulatory details of plant biomass-degrading enzymes in filamentous fungus Trichoderma guizhouense NJAU4742. Strain NJAU4742 and its mutants (∆Tgxyr1,∆Tgace1 and ∆Tgace2) were firstly incubated using 2% glucose, and then transfered into the medium containing different polysaccharides (xylan or cellulose) or carbon starvation. After 0h, 4h, 24h or 72h, samples were extracted and used for transcriptome sequencing in Illumina platform.

overall_design: Total 34 RNA-seq data from Trichoderma guizhouense NJAU4742 and its mutants


title: Periostin induces early articular cartilage degeneration in developmental dysplasia of the hip

city: Toon

first: Yuuki

last: Imai

state: Ehime

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

summary: Developmental dysplasia of the hip (DDH) is one of the significant risk factors for hip osteoarthritis. In order to investigate the factors that induce early articular cartilage degeneration of the hip joints that are exposed to reduced dynamic loads arising from hip dislocation , we created rodent models of hip dislocation by swaddling. Notably, expression of periostin (Postn) was increased in the acetabular articular cartilage of the DDH models; Postn was a candidate gene associated with early articular cartilage degeneration. We showed that early articular cartilage degeneration was suppressed in Postn-/- DDH mice. Furthermore, a microgravity environment induced the expression of Postn in chondrocytes through STAT3 signaling. Postn induced catabolic factors, interleukin-6 and matrix metalloproteinase 3, in articular chondrocytes through integrin-nuclear factor κB signaling. Additionally, interleukin-6 stimulated Postn expression through STAT3 signaling. Thus, Postn plays a critical role in early articular cartilage degeneration associated with hip dislocation.

overall_design: mRNA profiles of the acetabular cartilage obtained from 3-week-old control and DDH rats were generated by deep sequencing using Illumina Miseq.

first: Haruhiko

last: Akiyama


title: Copra β-mannooligosaccharide utilization by Bifidobacterium adolescentis ATCC 15703

city: Mysuru

first: Mukesh

last: Kapoor

state: Karnataka

address: CFTRI

department: Protein Chemistry and Technology

country: India

institute: CSIR-Central Food Technological Research Institute

summary: In order to understand gene expression profile of Bifidobacterium adolescentis ATCC 15703, it was grown in minimal media upto late log phase in the presence of β-mannooligosaccharide from copra till OD A600 = 0.800

overall_design: Agilent custom Bifidobacterium_adolescentis_ATCC15703 Gene Expression  8x15k Array designed by Genotypic Technology Private Limited  AMADID: 866021

first: Priyanka

last: Mary


title: Comprehensive analysis of pathological changes in tumor of B16 with CCND1 overexpression

city: Fuzhou

first: Jun

state: China

address: Department of Medical Oncology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou, Fujian Province, China

summary:
Aims: CCND1 amplification was an unfavorable prognostic factor for patients with melanoma. This study aimed to investigate the molecular changes in tumor of B16 with CCND1 overexpression.
Methods: High-throughput sequencing was used to identify genes that were differentially expressed in tumor between B16 controls and B16 with CCND1 overexpression. Tumors of B16 Ctrl (n=3) and B16 with CCND1 overexpression (n=3) were enrolled in this study.
Results: mRNA expression of genes associated with immunity, such as CD8, Gzm, B2m, and Tap1 were decreased in tumors with CCND1 overexpression.
Conclusion: CCND1 overexpression is associated with an immunosuppressive microenvironment.

overall_design: Three B16 Ctrl samples and three B16 with CCND1 overexpression samples.

first: Jing

last: Lin

first: Jiani

last: Xiong

first: Yu

last: Chen


title: DYSREGULATION OF THE m6A EPITRANSCRIPTOME AS A NEW MECHANISM INVOLVED IN HIPPOCAMPAL-DEPENDENT MEMORY DEFECTS IN HD MICE

city: Aarhus

first: Ulf

middle: Vang

last: Ørom

state: Aarhus

address: Aarhus University

department: MBG

country: Denmark

institute: Aarhus University

summary: Recent advances in RNA biology have focused on a new layer of gene expression regulation termed Epitranscriptomics. One of the most common mRNA modifications that is highly abundant in brain is N6-methyladenosine (m6A), which has been involved in learning and memory processes. Indeed, different studies have shown that m6A levels vary in response to cognitive tasks. This mark is dynamically regulated by a multicomplex of methyltransferases (METTL3, METTL14 and WTAP) as well as a series of demethylases (FTO and ALKBH5). Given the early cognitive symptomatology in Huntington’s Disease (HD), we aimed to determine whether expression of mutant huntingtin (mHtt) induces changes in the m6A epitranscriptome profile and signaling, leading to the memory and learning deficits observed in HD. For this purpose, genetically modified HdhQ7/Q111 mice were subjected to a hippocampal training task and relative levels of the m6A-modifying proteins were determined in different cellular compartments. In addition, identity of mRNAs with altered m6A profiles was determined through methylated RNA immunoprecipitation sequencing (meRIP-seq). Our results have shown that symptomatic HD mice display altered levels of FTO and METTL14, both in the nuclear as well as in the synaptic compartment. Moreover, transcriptome-wide profiling of m6A-modifed mRNAs has revealed a more prominent decrease in methylated peaks in HD mice in response to a training task when compared to age-matched wild type (WT) littermates. Interestingly, genes that show differential m6A peaks include immediate early genes and genes involved in synapse and neuronal function, among others. Thus, our results suggest that the altered levels of the m6A-modifying machinery in HD mice could be leading to a differential epitranscriptomic profile, contributing to the cognitive symptomatology observed in those animals. Altogether, our data uncover a promising role of m6A as a novel hallmark of the disease, pointing to this RNA chemical modification as a potential target to improve cognitive disturbances among HD patients

overall_design:
Input and m6A immunoprecipitated RNA from three biological replicates were analyzed for each of 8 conditions  (two genotypes; two ages, two treatments per genotype per age). Genotypes:HdhQ7/7 (wild-type) and HdhQ7/Q111 (KI) . Ages: 5 and  8 months. Conditions: Naive (non-trained) and trained
Differential binding analysis:
Metadata_v8_edited_8.10.bed.gz (KI_c8 vs KI_tr8 (all the replicates merged))
Metadata_v8_edited_8.1.bed.gz (KI_c5 vs WT_c5 (all the replicates merged))
Metadata_v8_edited_8.2.bed.gz (KI_c8 vs WT_c8 (all the replicates merged))
Metadata_v8_edited_8.3.bed.gz (KI_tr5 vs WT_tr5 (all the replicates merged))
Metadata_v8_edited_8.4.bed.gz (KI_tr8 vs WT_tr8 (all the replicates merged))
Metadata_v8_edited_8.5.bed.gz (WT_c5 vs WT_tr5 (all the replicates merged))
Metadata_v8_edited_8.6.bed.gz (KI_c5 vs KI_tr5 (all the replicates merged))
Metadata_v8_edited_8.7.bed.gz (c5 vs tr5 (all the replicates merged))
Metadata_v8_edited_8.8.bed.gz (c8 vs tr8 (all the replicates merged))
Metadata_v8_edited_8.9.bed.gz (WT_c8 vs WT_tr8 (all the replicates merged))

first: Anika

last: Pupak

first: Ankita

last: Singh

first: Marc

last: Espina

middle: A

last: Vang Ørom

first: Silvia

last: Gines

first: Veronica

last: Brito


title: SRC2 and SRC3 cooperatively promote pathogenic function of Th17 cells via regulation of epigenetic activation

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Steroid receptor coactivator 3 (SRC3) was reported to regulates pathogenic Th17 cell differentiation in vitro and in vivo.However, the role of SRC2, another member of SRC family, and its relationship with SRC3 in the regulation of Th17 cell differentiation remain unknown. We used RNA-seq to study the global function of SRC2 and SRC3. Naive CD4+ T cells were activated with 5ug/ml plate-bound anti-CD3/28, and  cultured with TGF-β+IL-6 or with IL-6+IL-1β+IL23. 4days later, cells were restimulated with plate-bound anti-CD3 for 4hrs for RNA-seq.

overall_design: To understand the overall function of SRC2 and SRC3 in Th17 cells, RNA-seq was performed with WT, Src2 KO and Src2/3 DKO in in vitro cultured Th17 cells.

first: Kenji

last: Ichiyama

first: Kentaro

last: Tanaka

first: Xinxin

last: Chi


title: MeRIP sequencing of human osteosarcoma cells

first: hongbo

last: li

summary: The goals of this study are to compare the differential m6A peaks between NC and shMETTL14 groups

overall_design: Cells were infected with lentiviral shRNA targeting METTL14.  We compared the differentially m6A peaks between NC and shMETTL14 groups.

first: Hongbo

last: Li


title: KDM6A(UTX) is an epigenetic gatekeeper of mTORC1 signalling in cancer

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

summary: Large-scale genome sequencing efforts of human tumors identified epigenetic modifiers as one of the most frequently mutated gene class in human cancer. However, how these mutations drive tumor development and progression is largely unknown. Here, we identify the histone demethylase KDM6A as an important tumor suppressor in solid cancers, such as liver cancer and pancreatic cancer. KDM6A-deficient tumors show hyperactivation of mTORC1 signaling, whereas endogenous KDM6A re-expression in established KDM6A-deficient tumors diminishes mTORC1 activity by fostering the expression of crucial negative pathway regulators, such as DEPTOR, TSC1, and TSC2, resulting in tumor regression. Importantly, KDM6A expression in human tumors correlates with mTORC1 activity and KDM6A-deficient tumors exhibit increased sensitivity to mTORC1 inhibition. Hence, our results link KDM6A-dependent epigenetic remodeling to mTORC1 signaling and provide a potential therapeutic strategy for KDM6A-deficient tumors.

overall_design: Examination of 2 different genotypes of primary liver cancer cell lines, Myc_Utx (derived from murine KDM6A-deficient tumor) and Myc_p53 (as control, derived from murine p53 knockout tumor). Three biological replicates (tumor from different mice) were used in this study for each genotype. For Myc_Utx: Myc_Utx_2A, Myc_Utx_2B and Myc_Utx_2D cell lines were used. As reference/control, Myc_p53: Myc_p53_1, Myc_p53_2 and Myc_p53_3 were used.

first: Steffie

last: Revia

first: Darjus

middle: F

last: Tschaharganeh


title: Identification of molecular signatures in multiple myeloma

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

country: Malaysia

institute: Institute for Medical Research

summary: The objective of this study is to identify genes involved in the pathogenesis of multiple myeloma (MM). In this study, we performed gene expression profiling of a total of 29 samples consisting of 19 clinical specimens, 7 myeloma cell lines and 3 normal samples. The microarray data were analysed by GeneSpring Software v14.9. A total of 5124 DEGs were identified in MM group vs control group (fold change≥2.0; P<0.05). Out of 5124 DEGs, 2696 and 2428 genes were up-regulated and down-regulated, respectively in MM group compared to the normal control group.

overall_design: Bone marrow aspirates of 19 clinical specimens and 7 myeloma cell lines were compared against  3 peripheral bloods from healthy individuals.

first: Ivyna Pau Ni

first: Ching Ching

last: Ng


title: Genome-wide maps of chromatin accessibility in Irf8+/+ and Irf8-/- mice LT-HSC cells

city: Shanghai

first: Qingsong

last: Qiu

address: Ruijin er road No.197

institute: SIH

summary: We describe an assay for transposase-accessible chromatin using sequencing (ATAC-seq), based on direct in vitro transposition of sequencing adaptors into native chromatin, as a rapid and sensitive method for integrative epigenomic analysis. ATAC-seq captures open chromatin sites using a simple two-step protocol with 1000–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. We discovered classes of DNA-binding factors that strictly avoided, could tolerate or tended to overlap with the nucleosome. Using ATAC-seq maps of chromatin accessibility in Irf8+/+ and Irf8-/- LT-HSC cells, we demonstrated the genome-wide activity of cis-regulatory elements (CREs) perturbation in IRF8 deficient mice bone marrow LT-HSC.

overall_design: Examination of the genome-wide activity of cis-regulatory elements (CREs) using Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) in Irf8+/+ and Irf8-/- mice LT-HSC cells.


title: A novel prognostic risk model for cervical cancer based on immune checkpoint HLA-G-driven differentially expressed genes

status: Public on Jul 19 2022

city: Linhai

first: Hui-Hui

last: Xu

state: Zhejiang province

institute: Taizhou Hospital


title: A novel prognostic risk model for cervical cancer based on immune checkpoint HLA-G-driven differentially expressed genes [SiHa]

summary:
The aim of this study was to construct and validate a prognostic risk model to predict the overall survival (OS) of patients with cervical cancer, providing a reference for individualized clinical treatment that may lead to better clinical outcomes.
HLA-G-driven DEG signature consisting of the eight most important prognostic genes CD46, LGALS9, PGM1, SPRY4, CACNB3, PLIN2, MSMO1, and DAGLB was identified as a key predictor of cervical cancer.
To summarize, we developed and validated a novel prognostic risk model for cervical cancer based on HLA-G-driven DEGs, and the prognostic signature showed great ability in predicting the overall survival of patients with cervical cancer.

overall_design: HLA-G-driven differentially expressed genes (DEGs) were obtained from two cervical carcinoma cell lines, namely, SiHa and HeLa, with stable overexpression of HLA-G by RNA sequencing (RNA-seq).


title: RNAseq dataset of murine NVU cells post ischemic stroke isolated using the SGD method from the same starting material.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

summary: The blood-brain barier (BBB) function is impaired in several neurological diseases such as stroke. To better study the BBB dysfunction in stroke and to identify novel therapeutic targets, a detailed analysis of the neurovascular unit (NVU) cells that together regulate the BBB function is needed. To this end, we isolated the NVU cells EC, PC, AC, MG post stroke in mice using our newly developed SGD (Spitzer, Guérit, Devraj) method from the same starting material followed by RNA sequencing. Cells were isolated from both healthy appearing contralateral hemisphere and ipsilateral stroke hemisphere post tMCAO (1h occlusion, 23h repurfusion) using the SGD method.  Each sample comprised 6 biological replicates with each replicate pooled from 3-4 male C57BL6 adult mouse brains either from contralateral or ipsilateral hemisphere post stroke. Only mice with neurological scores (mNSS) of atleast 8 were included for the NVU cell isolation. Our data showed regulation of several genes post stroke in each of the cell types analyzed with novel candidates that were co-regulated in the NVU cell types. As the blood-brain barrier (BBB) is co-regulated by several NVU cell types, we propose targeting the candidates co-regulated in multiple NVU cell-ytpes for novel and effective therapeutic options in stroke.

overall_design: NVU cells were isolated by the SGD method post experimental stroke (tMACO, 1h occlusion, 23h reperfusion) in mice followed by RNAseqencing from 6 biological replicates for each sample comprising 3-4 animal brains per replicate.

first: Devraj

last: Kavi

first: Günther

last: Stefan


title: Comparative analysis of gut microbiota profile between young people and aged people

city: Louisville

first: Huang-Ge

last: Zhang

address: 505 S Hancock Street

institute: University of Louisville

summary: Given the criticle role of gut bacteria involve in number of diseases, the gut microbiota from young and aged people were estimated using 16s rRNA next-generation sequencing. This study will benefit to identify the role of gut bacteria on the pathegenic mechasim of aging relative diseases.

overall_design: The feces DNA from 12 young people and 12 aged people was extracted and amplified on 16s rRNA gene for sequencing.

first: Yun

last: Teng

first: Fangyi

first: Xiangcheng

first: Jingyao

last: Mu


title: EXP2. Antitumor effect MVA-Combo

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

summary: RNA-seq analysis of ID8.OVA.Vegf/GFP omental metastases treated intraperitoneally with MVA expressing a tumor-associated antigen (TAA), CD40L and/or CD137L.

overall_design:
In vivo treated tumors were excised 7 days after intraperitoneally ijections with rMVA-TAA-CD40L,  rMVA-TAA-CD137L or rMVA-TAA-Combo. Tumor-bearing omenta were storaged in RNAlater at -80C until further processing. mRNA was isolated using Rneasy Mini Kit (Qiagen) following manufacture's instructions. RNAseq was performed by Macrogen using TruSeq Stranded mRNA library and NovaSeq 6000 sequencing system (Illumina)
contributor: Macrogen

first: Ángela

last: Bella

first: Fernando

last: Aranda

first: Pedro

last: Berraondo


title: Evolving a new electron transfer pathway to nitrogenase in an alphaproteobacterium

city: St. Paul

first: Kathryn

last: Fixen

state: MN

address: 1445 Gortner Ave

institute: University of Minnesota

summary: Nitrogenase is the key enzyme involved in nitrogen fixation and uses low potential electrons delivered by ferredoxin or flavodoxin to reduce dinitrogen gas (N2) to produce ammonia and hydrogen. Although the phototrophic alphaproteobacterium Rhodopseudomonas palustris encodes many proteins that can reduce ferredoxin, the electron bifurcating FixABCX complex is the only one shown to support nitrogen fixation. To gain insight into why R. palustris is unable to use these other enzymes to reduce ferredoxin in the absence of FixABCX, we isolated a suppressor of R. palustris DfixC that allowed this strain to grow under nitrogen-fixing conditions. We found two mutations were necessary and sufficient to restore growth under nitrogen-fixing conditions in the absence of a functional FixABCX. One mutation was in the primary ferredoxin involved in nitrogen fixation, fer1, and the other mutation was in rpa0678, a homolog of NAD+-dependent ferredoxin:NADPH oxidoreductase, which carries out flavin-based electron bifurcation to generate reduced Fd. We present evidence that Rpa0678 plays a role in electron transfer to benzoyl-CoA reductase, the key enzyme involved in anaerobic aromatic compound degradation. Together these findings indicate that the electron transfer pathway for anaerobic aromatic compound degradation was re-purposed to support nitrogen fixation in the suppressor strain.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for R. palustris CGA753 and suppressor mutant of CGA753 with a deletion in fixC

first: Nathan

last: Lewis

first: Abigail

last: Sarne


title: Single-nucleus RNA-sequencing reveals singular gene signatures of human ductal cells during adaptation to insulin resistance

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

summary: Adaptation to increased insulin demand is mediated by β-cell proliferation and neogenesis among other mechanisms. Although it is known that pancreatic β-cells can arise from ductal progenitors, these observations have been limited mostly to the neonatal period. We have recently reported that the duct is a source of insulin secreting cells in adult insulin resistant states. To further explore the signaling pathways underlying the dynamic β-cell reserve during insulin resistance we undertook human islet and duct transplantations under the kidney capsule of immunodeficient NOD SCID gamma (NSG) mouse models that were either pregnant, insulin resistant or had insulin resistance superimposed upon pregnancy  (pregnancy+insulin resistance), followed by single-nucleus RNA-sequencing (snRNA-seq) on snap-frozen graft samples. We observed an upregulation of proliferation markers (e.g., NEAT1), expression of islet endocrine cell markers (e.g., GCG and PPY) as well as mature β-cell markers (e.g., INS), in transplanted human duct grafts in response to high insulin demand. We also noted downregulation of ductal cell identity genes (e.g., KRT19 and ONECUT2) coupled with upregulation of β-cell development and insulin signaling pathways. These results indicate that subsets of ductal cells are able to gain β-cell identity and reflect a form of compensation during the adaptation to insulin resistance in both physiological and pathological states.

overall_design: Frozen grafts were transferred to dounce tissue grinder tubes (D8938; Sigma) containing 0.5 ml ice-cold Nuclei EZ lysis buffer (NUC-101; Sigma) and homogenized with pestles A and B on ice each for one minute. Samples were transferred to clean 15 ml tubes and homogenizers were rinsed with 1.5 ml buffer followed by 2 ml buffer and transferred to the same 15 ml tubes to get final 4 ml. The tubes were vortexed briefly at moderate speed and set on ice for 5 minutes for cell lysis. To separate nucleus and cytoplasm, the tubes were centrifuged at 500x g for 5 minutes at 4C. Supernatants containing cytoplasmic component were saved for later analysis. Pellet containing nuclei was resuspended in 0.5 ml cold buffer by vortex briefly at moderate speed and 3.5 ml cold buffer was added. Nuclei suspension was mixed by vortex briefly and set on ice for 5 minutes. The tubes were centrifuged at 500x g for 5 minutes, supernatant was saved for later analysis, pellet was resuspended in suspension buffer (0.5 ml PBS containing 0.01% non-acetylated BSA; Sigma and 0.1% RNase inhibitor; 2313A from Clontech). Nuclei suspension was pipetted ten times with a 1 ml tip, filtered through a 30 μm pre-separation filter (130-041-407; Miltenyi biotech), cell number and cell viability were determined by cell counter using 0.4% trypan blue stain. The average number of total nuclei obtained from one-half graft was approximately 8.5E+5 nuclei (1.7E+6 cells/ml) with 5-10 um size and 93.3 +/- 1.1% dead cell rate (n=32 samples across three independent experiments). Dead nuclei number was adjusted to 1000 nuclei/ul with suspension buffer and 10,000 nuclei were immediately used for generation of Gel Beads in Emulsion (GEMs) and barcoding. Leftover nuclei were saved for later analysis. GEMs were generated using the Chromium 3’ Single Cell Library Kit (v2, 10X Genomics, CA) according to the manufacturer’s instructions. Briefly, 10,000 nuclei were combined with Single Cell Master Mix and encapsulated into the barcoded Gel Beads through the Chromium™ Controller. After GEM-RT incubation, cDNA samples were recovered, purified and amplified through a cDNA Amplification Reaction. Quality controls on amplified cDNA samples were carried out through using a High Sensitivity DNA Kit (Agilent, CA) on a 2100 BioAnalizer (Agilent, CA) platform. Libraries were then constructed following Fragmentation and Adaptor Ligation and Sample Index incorporation. Finally, purified libraries were run on 2100 BioAnalizer (Agilent, CA) using a High Sensitivity DNA Kit (Agilent, CA) to evaluate the quality of the ~400bp fragments. The final single-cell libraries were sequenced using acoverage of 500,000 pair-ended reads targeted per cell, on a HiSeq 4000 platform (Illumina, CA, USA).

first: Ercument

last: Dirice

first: Giorgio

last: Basile

first: Rohit

last: Kulkarni


title: A novel prognostic risk model for cervical cancer based on immune checkpoint HLA-G-driven differentially expressed genes [HeLa]

first: Hui-Hui

last: Xu


title: Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation

city: Philadelphia

first: Desi

last: Alexander

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

summary: Histone acetylation is a key component in the consolidation of long-term fear memories, which are models for highly resilient and durable memory. Histone acetylation is fueled by acetyl-CoA and recently, nuclear-localized metabolic enzymes that produce this metabolite have emerged as direct and local regulators of histone acetylation. In particular, Acetyl-coA synthetase 2 (ACSS2) mediates histone acetylation in the mouse hippocampus. However, whether ACSS2 regulates long-term fear memory remains to be determined. Here, we show that Acss2 knockout is well-tolerated in mice, yet the Acss2 null mouse exhibits reduced acquisition of long-term fear memory. Loss of Acss2 leads to reductions in both histone acetylation and expression of critical learning and memory-related genes in the dorsal hippocampus, specifically following fear conditioning. Further, systemic administration of blood-brain-barrier (BBB)-permeable Acss2 inhibitors during the consolidation window reduces fear memory formation in mice and rats, and reduces anxiety in a predator-scent-stress (PSS) paradigm. Our findings suggest that nuclear acetyl-CoA metabolism via ACSS2 plays a critical, previously unappreciated role in the formation of fear memories.

overall_design: Included are two separately analyzed experiments that used RNA-seq to examine the transcriptome in the hippocampus from mice on a C57BL6/J background harboring a deletion of the metabolic gene Acss2. Experiment 1 (6 samples) consists of whole hippocampi processed from 3 genotypes (Acss2 WT[reference], Acss2 Het, and Acss2 KO), with two replicates each. All samples were processed together. Experiment 2 (17 samples) consists of 2 genotypes (Acss2 WT, Acss2 KO), 2 conditions (homecage-housed[reference], and fear conditioned). Replicates included are: 5 replicates WT untreated, 3 replicates WT fear conditioned, 5 replicates ACSS2- untreated, 4 replicates ACSS2- fear conditioned.

first: Tanya

last: Corman

first: Mariel

last: Mendoza

first: Andrew

last: Glass

first: Tal

last: Belity

first: Ranran

last: Wu

first: Rianne

last: Campbell

first: Joseph

last: Han

first: Ashley

last: Keiser

first: Jeffrey

last: Winkler

first: Marcelo

last: Wood

first: Thomas

last: Kim

first: Benjamin

last: Garcia

first: Hagit

last: Cohen

first: Philipp

last: Mews

first: Gabor

last: Egervari

first: Shelley

middle: L

last: Berger


title: Interactions between specific driver genes shape the signaling pathway landscape and direct the treatment of hepatocellular carcinoma

city: Hefei

first: yiqing

last: Shen

address: University of Science and Technology of China

summary: Hepatocellular carcinoma (HCC) is one of the most lethal malignancies, whose initiation and development are driven by alterations in driver genes. In this study, we identified four driver genes (TP53, PTEN, CTNNB1, and KRAS) that exhibit a high frequency of somatic mutations or copy number variations (CNVs) in patients with HCC. Four different spontaneous HCC mouse models were constructed to screen for changes in various kinase signaling pathways. The Trp53mut+Ptenmut tumor upregulated mTOR and noncanonical NF-κB signaling, which was shown to be strongly inhibited by rapamycin (an mTOR inhibitor) in vitro or in vivo. JAK-STAT signaling was activated in the Ctnnb1mut+Ptenmut tumor, the proliferation of which was strongly inhibited by napabucasin (a STAT3 inhibitor). MTOR, cytoskeleton, and AMPK signaling were upregulated while rapamycin and ezrin inhibitors exerted potent anti-proliferative effects in the Ptenmut+KrasG12D tumor. JAK-STAT, MAPK, and cytoskeleton signaling were activated in the Tp53mut+KrasG12D tumor and the combination of sorafenib and napabucasin led to the complete inhibition of tumor growth in vivo. In patients with HCC that had the same molecular classification as our mouse models, the downstream signaling pathway landscapes associated with genomic alterations were identical. Our research provides novel targeted therapeutic options for the clinical treatment of HCC, based on the presence of specific genetic alterations within the tumor.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for mice liver cancer tissues and normal liver tissues.

first: Yiqing

first: Xiaohu

last: Zheng

first: Yeben

last: Qian

first: Mantian

last: Liu


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells [PRO-seq early]

first: Stuart

middle: H

last: Orkin

address: 1 Blackfan Circle KFRB 07007H

department: Hematology/Oncology

institute: Dana-Farber Cancer Institute/Boston Children's hospital

summary: We acutely depleted the BCL11A protein by using the dTAG PROTAC technology, and assessed its immediate consequences on nascent transcription, DNA methylation, Protein expression and HIstone modification and chromatin accessibility.

overall_design: Examination of changes in Nascent transcription that occur imminently upon depletion of the repressive transcription factor BCL11A in two clones.

first: Stuti

last: Mehta

first: Yan

last: Kai


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells [Bisulfite-seq]

summary: We acutely depleted the BCL11A protein by using the dTAG PROTAC technology, and assessed its immediate consequences on DNA methylation at the HBG1/2 promoter region.

overall_design: Examination of changes in HBG1/2 promoter DNA methylation that occur imminently upon depletion of the repressive transcription factor BCL11A in two clones.


title: Affect of iPSC Passage Number on Neuronal Differentiation

city: Indianapolis

first: Guanglong

last: Jiang

state: IN

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

summary: Induced pluripotent stem cells (iPSCs) are a valuable resource for neurological disease-modeling and drug discovery, due to their ability to differentiate into neurons reflecting the genetics of the patient from which they are derived. iPSC-derived cultures, however, are highly variable due to differences in culture conditions. We investigated the effect of iPSC passage number on differentiation to optimize the generation of functional, mature sensory neurons (iPSC-dSNs). Three iPSC lines were differentiated into iPSC-dSNs at passage numbers within each of the following ranges: low (LP; 5-10), middle (MP; 20-26), and high (HP; 30-38). Morphology and pluripotency of the parent iPSCs were assessed prior to differentiation at each passage number. iPSC-dSNs were evaluated based on electrophysiological properties and expression of key neuronal markers.    All iPSC lines displayed the same morphology and were similarly pluripotent across passage numbers. iPSC-dSNs were also morphologically comparable across passage numbers. However, the expression levels of neuronal markers and an analysis of sodium channel function  indicated greater maturity in LP iPSC-dSNs. Our results demonstrate that lower passage numbers may be better suited for differentiation into peripheral sensory neurons. Further studies are warranted to elucidate factors that may contribute to the variability associated with iPSC passage number.

overall_design: Expression of pluripotency markers in three different iPSC lines, as well as expression of neuronal markers in the three lines after differentiation, at three different passage numbers each

first: Erica

last: Cantor

first: Fei

first: Geneva

last: Cunningham

first: Xi

last: Wu

first: Santosh

last: Philips

first: Bryan

last: Schneider


title: Adoptively transferred tumor-infiltrating lymphocyte immunotherapy following concurrent chemoradiotherapy in patients with advanced cervical cancer: a phase 1 trial

city: Guangzhou

first: jiang

last: li

address: 651 Dongfeng East Road, Yuexiu District, Guangzhou

institute: Sun yat-sen university

summary: Twenty-seven CC patients with stage III to IV were recruited in this a single-center, phase I study. TILs were isolated from local or metastatic CC lesions and generated under GMP conditions. Thirteen patients accepted TIL-based ACT and intramuscular IL-2 following CCRT or CT treatment. Outcomes were classified as patients with a poor outcome (nonresponders) and patients with a favorable outcome (responders). Single cell RNA sequencing (scRNA-seq) for infused TIL products in responder and non-responder.

overall_design: Using single-cell RNA sequencing, we profiled 8 TIL infusion products from CC patients with stage III to IV treated with CCRT or CT treatment and TIL (responder, n=5; nonresponder, n=3).

first: He

last: Huang

first: Cai-ping

last: Nie

first: Xiu-feng

first: Bin

last: Song

first: Jian-Hui

last: Yue

first: Jing-Xiao

last: Xu

first: Kui

last: Li

first: Yan-lin

last: Feng

first: Ting

last: Wan

first: Min

first: Yan-Na

last: Zhang

first: Wei-Jun

last: Ye

first: Jun-Dong

first: Yan-Fang

first: Jun-yun

first: Xin-Ping

last: Cao

first: Zhi-ming

first: Xiao-shi

first: Ji-Hong

first: Jiang


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells [PRO-seq washout]

first: Stuart

last: Orkin

summary: We acutely depleted the BCL11A protein by using the dTAG PROTAC technology, then performed a drug washout and and assessed its immediate consequences nascent transcription.

overall_design: Examination of changes in Nascent transcription that occur imminently upon washout of drug to restore transcription factor BCL11A in two clones.

first: Stuti

last: Mehta

first: Yan

last: Kai


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells [DNA methylation]

summary: We acutely depleted the BCL11A protein by using the dTAG PROTAC technology, and assessed its immediate consequences on DNA methylation, in the presence/absence of DNMT1 inhibitor AZAcytidine.


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells [ATAC-seq]

summary: We acutely depleted the BCL11A protein by using the dTAG PROTAC technology, and assessed its immediate consequences on chromatin accessibility by ATAC-seq,and compared this to changes in nascent transcription, DNA methylation, Protein expression and HIstone modification.

overall_design: Examination of changes in chromatin accessibility that occur imminently upon depletion of the repressive transcription factor BCL11A in two clones.


title: Identification of NPAS3 cistrome in the mouse cortical astrocytes (DIV 14).

first: liqiu

last: Liu

address: Yard 1, Beichen West Road, Chaoyang District, Beijing, China

institute: Beijing Institutes of Life Science, Chinese Academy of Sciences

summary: Genome-wide binding sites of NPAS3 were identified in mouse cortical astrocytes (DIV 14).

overall_design: ChIP-Seq analysis was performed to identify NPAS3 binding sites in mouse cortical astrocytes( DIV 14).

first: Li

last: Yuanyuan

first: Liu

last: Liqiu


title: Whole transcriptome sequencing of Npas3+/- and WT cortex at P0 stage

summary:
Purpose: To gain insight into the impact of NPAS3 deficiency on astrogenesis in mice, RNA-seq was used to analyze the genome-wide changes resulting from Npas3+/- and WT cortex at P0 stage.
Methods: Total RNA was extracted from Npas3+/- and WT cortex at P0 stage. Then, total RNA was quantified and quality controlled by Agilent Bioanalyzer 2100 system. After cDNA library construction, the library preparations were sequenced on an Illumina NovaSeq 6000 platform in Novogene.
Results: At significance cutoffs corresponding to FDR < 0.05, a total of 625 DEGs were identified in Npas3+/- mice.
Conclusions: Our results show that Npas3+/- mice exhibit defective astrogenesis and abnormal synapse function.

overall_design: Total mRNA profiles of Npas3+/- and WT cortex at P0 stage were generated by deep sequencing using Illumina NovaSeq 6000.


title: Whole transcriptome sequencing of mouse cortical astrocytes (DIV 14).

summary:
To gain futher insight into the Npas3 regulatory network in astrocytes, RNA-seq was used to analyze the genome-wide changes resulting from the days in vitro (DIV) 14 astrocytes of P0 wild-type (WT) mice and  littermate NPAS3-/- mice.
Total RNA was extracted from DIV 14 astrocytes of P0 Npas3-/- and WT mice. Then, total RNA was quantiﬁed and quality controlled by Agilent Bioanalyzer 2100 system. After cDNA library construction, the library preparations were sequenced on an Illumina NovaSeq 6000 platform in Novogene.

overall_design: Total mRNA profiles of DIV14 WT and Npas3-/- astrocytes (DIV14) were generated by deep sequencing using Illumina NovaSeq 6000.


title: Methionine oxidation of PKM2 promotes pancreatic cancer metastasis

first: Richard

last: Friedman

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University Irving  Medical Center

summary: We report that MSRA is a potent suppressor of pancreatic cancer metastasis. We performed global RNA sequencing to examine the transcriptome of pancreatic cancer cells that are proficient or deficient of MSRA

overall_design: Examination of transcriptome of pancreatic cancer cells expressing sgROSA or sgMSRA. Three biological replicates are compared in this experiment.

first: Iok

last: Chio

first: Dan

last: He


title: The molecular hallmarks of primary and secondary vitreoretinal lymphoma

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

institute: IDIBAPS

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Vitreoretinal lymphoma is a rare subtype of diffuse large B-cell lymphoma considered a variant of primary central nervous system lymphoma. Its diagnosis requires examination of vitreous fluid, but cytologic differentiation from uveitis remains difficult. Due to its rarity and difficulty in obtaining diagnostic material, little is known about the genetic profile of the disease.

overall_design: The aim of this study was to perform a genetic characterization of vitroretinal lymphoma. Copy number array analysis was performed on seven samples from six vitroretinal lymphoma cases.

first: Julia

last: Salmerón-Villalobos

first: Itziar

last: Salaverria


title: Next generation sequence data to elucidate the role of CHD8 in terminal erythropoiesis

city: Cincinnati

first: Zhaowei

last: Tu

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Medical Center

summary: To uncover how CHD8 regulates terminal erythropoiesis, we performed CUT&RUN assays to check the direct binding of CHD8 on the target genes in terminal erythroblasts. In addition, we perfromed RNA sequence in sorted ProEs from WT, P53 KO and Chd8 P53 DKO mice to identify the differentially expressed genes due to loss of CHD8.

overall_design: For CHD8 CUT&RUN assay, wild type CD44+TER119+ erythroblasts were sorted out from bone marrow and used for CHD8 binding, followed by Mnase binding and released DNA extraction. DNA were further used for library preperation with NEBNext DNA library preperation kit and send for sequencing. In analysis, after mapping, two replicates were merged into one and used for peak calling. For ProE RNA sequencing, WT, P53 KO and Chd8,P53 DKO mice bone marrow  were harvested at 2 weeks post pI:pC induction and ProEs were sorted out by BD sorter. The ProEs were lysed with Trizol and RNA extracted with Qiagen microRNeasy Kit. The RNAs were send to the core for library preperation and sequencing.

first: Yi

last: Zheng


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells

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

overall_design: Refer to individual Series


title: Endogenous expression profiles of HCT116 colorectal cancer cells and HCT116-derived ATF2 knockout (KO) clones [Version 02]

city: Erlangen

first: Regine

last: Schneider-Stock

address: Universitaetsstrasse 22

department: Department of Pathology

institute: University Hospital Erlangen

summary: Gene expression profiles were obtained via NanoString nCounter Gene Expression Assay (PanCancer Progression Panel, XT_PGX_HuV1_CancerProg_CSO, cat. no. XT-CSO-PROG1-12, NanoString Technologies, Hamburg, Germany). We aimed to decipher the role of activating transcription factor 2 (ATF2) in colorectal cancer, so-far masked by high intratumoral heterogeneity (ITH). To overcome ITH, we generated monoclonal ATF2 knockout (KO) cells (termed F9 and E5) using CRISPR/Cas9 gene editing and analyzed alterations of their gene expression profiles in comparison to the parental HCT116 cell line (HCT116 WT).

overall_design:
In this study, independent biological triplicates of HCT116 WT cells and ATF2 KO clones F9 and E5 (all n = 3) were investigated for gene expression alterations of genes related to tumor progression and metastasis using NanoString PanCancer Progression Panel (740 cancer-related genes plus 30 internal reference control genes). Tumor cells were cultured in a 10 cm cell culture dish in RPMI 1640 supplemented with 10% FBS and 1% penicillin/streptomycin for 48 h until cells reached 80% confluency. Cells were harvested and total RNA was extracted from frozen cell pellets using a QIAzol-chloroform-based isolation and RNeasy Mini Kit (Qiagen, Hilden, Germany) for purification. Gene expression profiling was performed on 100 ng total RNA with the human nCounter PanCancer Progression Panel (NanoString Technologies). Briefly, hybridization reaction was performed on the NanoString nCounter® Prep Station for 17 h at 65 °C according to the manufacturer’s instructions. Samples were further processed according to the manufacturer’s protocol and signal of reporter probes were counted on the nCounter Digital Analyzer (NanoString Technologies). Gene expression data was further processed and analyzed using the package NanoStringDiff v. 1.14.0 (Wang et al., 2019) within the R v. 3.6.1 environment (R-Core-Team, 2019). Obtained fold changes (FC) were further screened for our selected cut-off criteria to finally extract an ATF2 loss-dependent gene signature.
Endogenous expression profiles of HCT116 colorectal cancer cells and HCT116-derived ATF2 knockout (KO) clones [Version 02: all clones (n=6) vs WT (n=3)]

first: Kerstin

last: Huebner

first: Katharina

last: Erlenbach-Wuensch

first: Jan

last: Prochazka

first: Ilir

last: Sheraj

first: Chuanpit

last: Hampel

first: Blanka

last: Mrazkova

first: Tereza

last: Michalcikova

first: Jolana

last: Tureckova

first: Veronika

last: Iatsiuk

first: Anne

last: Weissmann

first: Fulvia

last: Ferrazzi

first: Philipp

last: Kunze

first: Enise

last: Nalli

first: Elisabeth

last: Sammer

first: Annemarie

last: Gehring

first: Marie

last: Cheema

first: Markus

last: Eckstein

first: Eva-Maria

last: Paap

first: Agnes

last: Soederberg

first: Corinna

last: Fischer

first: Sushmita

last: Paul

first: Vijayalakshmi

last: Mahadevan

first: Benardina

last: Ndreshkjana

first: Melanie

last: Meier

first: Susanne

last: Muehlich

first: Carol

last: Geppert

last: Merkel

first: Robert

last: Grutzmann

first: Adriana

last: Roehe

first: Sreeparna

last: Banerjee

first: Arndt

last: Hartmann

first: Radislav

last: Sedlacek


title: Inhibiting or depleting AHCY prevents senescence induction

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences


title: Effect of 3-deazaadenosine on the H3K36me3 chromatin landscape during senescence [ChIP-seq]

summary: We treated IMR90 ER:RAS cells with 4OHT to induce RAS activation or with vehicle (DMSO) as a non-senescent control. At the same time, cells were treated with 10 µM 3-deaazadenosine. 3-deazaadenosine is a SAM-dependent methyltransferase inhibitor. H3K36me3 is a mark enriched at actively transcribed genes. Our previous experiments showed that treatment with 3-deazaadenosine prevents senescence and reduces overall levels of H3K36me3. By performing ChIP-seq, we have unveiled that treatment with 3-deazaadenosine prevents deposition of H3K36me3 in genes essential for the secretory phenotype of senescent cells.

overall_design: Examination of H3K36me3 under 3 different treatments: non-senescent cells (DMSO), senescent cells (4OHT), 3DA cells (4OHT + 3DA).

first: Ana

last: Guerrero

first: Jesus

last: Gil

first: Oliver

last: Bischof

first: Pierre-François

last: Roux


title: Analysis of the senescence transcriptome after knockdown of AHCY

summary: IMR90 ER:RAS cells were infected with 2 different lentiviral pGIPZ shRNAs against AHCY or with an empty vector (EV). We treated IMR90 ER:RAS cells with 4OHT to induce RAS activation or with vehicle (DMSO) as a non-senescent control. RNA was collected 6 days after the start of the experiment once the senescence program has been fully implemented. Our previous experiments showed that knockdown of AHCY prevents senescence. By performing RNAseq, we have unveiled that AHCY knockdown prevents upregulation of a set of genes essential for the onset of senescence and its associated secretory phenotype.

overall_design: 16 samples examined from 4 different treatment (4 replicates each): non- senescent cells (EV), senescent cells (EV+4OHT), shAHCY_2 (+4OHT), shAHCY_4 (+4OHT).

first: Gopuraja

last: Dharmalingam

first: Husayn

last: Pallikonda


title: RNA-seq analysis in human Glioblastom Stem Cells in response to ADAR-KD

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

summary: Our observation suggest that ADAR may play important role to maintain GSC stemness. In order to address this hypothesis, we abrogated the expression of ADAR in GSCs using two distinct short and non-overlapping shot hairpin RNAs (shRNAs). A non-targeting control shRNA (shCONT) is used as control in these experiments. Both shRNAs significantly reduced ADAR protein expression. Depletion of ADAR impaired GSCs proliferation but did not affect matched DGCs. Similarly, lack of ADAR reduces GSC self-renewal capacity as assessed by in vitro limiting dilution assay . In order to identify the antitumor mechanisms triggered by ADAR depletion, we performed global transcriptional profiling through RNA-sequencing in GSCs upon ADAR knockdown. These analyses show that ADAR downregulation impairs the impairs the expression of genes involved in cancer proliferation, particularly those involved in cell cycle regulation

overall_design: Identification and characterization of DE genes after ADAR knockdown

first: Li

last: Jiang

first: Xiang-Dong

last: Fu

first: Jeremy

last: Rich


title: Temporal resolution of gene derepression and proteome changes upon PROTAC-mediated degradation of BCL11A protein in erythroid cells [ChIP-seq]

first: Stuart

last: Orkin

summary: We acutely depleted the BCL11A protein by using the dTAG PROTAC technology, and assessed its consequences on histone modification by ChIP-seq,and compared this to changes in nascent transcription, DNA methylation, Protein expression and chromatin accessibility.

overall_design: Examination of changes in histone modification that occur imminently upon depletion of the repressive transcription factor BCL11A.

first: Stuti

last: Mehta

first: Yan

last: Kai


title: Transcriptome map of dorsal root ganglion and spinal cord in mice with acute herpetic neuralgia induced by HSV-1

status: Public on Jul 18 2022

city: Shenzhen

first: Songbin

last: Wu

address: 89 Taoyuan Rd., Nanshan District,

department: Department of Pain Medicine

institute: Huazhong University of Science and Technology Union Shenzhen Hospital

summary:
To study the gene expression at the level of dorsal root ganglia and spinal cord in acute herpetic neuralgia mice, we induced acute herpetic neuralgia by subcutaneous injection of HSV-1 virus fluid into the tibia of C57/6J mice.
We collected data obtained from RNA-seq of dorsal root ganglia and spinal cord tissue in acute herpetic neuralgia mice (7 days after virus injection) and control mice for gene expression profiling.

overall_design: Comparative gene expression profiling of RNA-seq data in HSV-1-induced acute herpetic neuralgia mice (dorsal root ganglia and spinal cord) and control mice (dorsal root ganglia and spinal cord).


title: USP2 promotes experimental colitis and bacterial infections by inhibiting the proliferation of myeloid cells and remodeling the extracellular matrix network

city: 武汉

first: Ran

last: An

state: 湖北

address: 中国湖北武汉

institute: 武汉大学

summary: Inflammatory bowel disease (IBD) is closely associated with dysregulation of genetic factors and microbial environment. Here, we report a susceptible role of ubiquitin-specific protease 2 (USP2) in experimental colitis and bacterial infections. USP2 is upregulated in the inflamed mucosa of IBD patients and in the colon of mice treated with dextran sulfate sodium salt (DSS). Knockout or pharmacologic inhibition of USP2 promotes the proliferation of myeloid cells to activate IL-22 and IFNg production of T cells. In addition, knockout of USP2 in myeloid cells inhibits the production of pro-inflammatory cytokines to relieve the dysregulation of extracellular matrix (ECM) network and promote the gut epithelial integrity after DSS treatment. Consistently, Lyz2-Cre;Usp2fl/fl mice exhibit hyper-resistance to DSS-induced colitis and Citrobacter rodentium infections compared to Usp2fl/fl mice. These findings highlight an indispensable role of USP2 in myeloid cells to modulate T cell activation and epithelial ECM network and repair, indicating USP2 as a potential target for therapeutic intervention of IBD and bacterial infections in the gastrointestinal system.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Usp2 sufficient myeloid cells and Usp2 defficient myeloid cells from lamina propria of mice with DSS-induced colitis.

first: Peng

last: Wang

first: Bo

last: Zhong

first: Zhi-Dong

last: Zhang


title: Analysis of the senescent transcriptome after treatment with 3-deazaadenosine.

first: LMS

last: Bioinformatics Core

summary: We treated IMR90 ER:RAS cells with 4OHT to induce RAS activation or with vehicle (DMSO) as a non-senescent control. At the same time, cells were treated with 10 µM 3-deaazadenosine. RNA was collected 6 days after the start of the experiment once the senescence program has been fully implemented. 3-deazaadenosine is a SAM-dependent methyltransferase inhibitor. Our previous experiments showed that treatment with 3-deazaadenosine prevents senescence. By performing RNAseq, we have unveiled that treatment with 3-deazaadenosine prevents upregulation of a set of genes essential for the onset of senescence and its associated secretory phenotype.

overall_design: 12 samples examined from 3 different treatments (4 replicates each): non-senescent cells (DMSO), senescent cells (4OHT), 3DA cells (4OHT + 3DA).

first: Ana

last: Guerrero

first: Jesus

last: Gil


title: Effect of podoplanin depletion on gene expressions in canine melanoma cell lines

city: Tokyo

first: Masahiro

last: Shinada

address: Bunkyo-ku yayoi 1-1-1

institute: The University of Tokyo

summary:
To investigate the function of podoplanin, we established CMM2 and CMM12 canine melanoma cell lines in which podoplanin has been knocked out (KO) by CRISPR/Cas9.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control and podoplanin KO cell lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CMM2 and CMM12 cell lines and  its podoplanin KO cell lines.

first: Daiki

last: Kato

first: James

last: Chambers

first: Kazuyuki

last: Uchida

first: Tomoki

last: Motegi

first: Yousuke

last: Takahashi

first: Yuko

last: Hashimoto

first: Masaya

last: Tsuboi

first: Namiko

last: Ikeda

first: Susumu

last: Aoki

first: Takaaki

last: Iguchi

first: Toshio

last: Li

first: Yuka

last: Kodera

first: Shunsuke

last: Ota

first: Ryohei

last: Nishimura

first: Yukinari

first: Takayuki

last: Nakagawa