title: Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [scRNAseq]

city: Melbourne

first: Ian

last: Parish

state: VIC

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection.  We conducted scRNAseq analysis on sorted virus-specific tetramer+ CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from either littermate control or EGR2 T cell conditional knock-out mice. Cells were labelled with hashtags and mixed prior to multiplexed analysis. The resulting data demonstrated that the exhausted cell subsets within EGR2 KO CD8+ T cells have an effector-like phenotype, suggesting that EGR2 stabilises the exhausted state.

overall_design: The subset composition and transcriptome of exhausted wild-type or EGR2 knockout CD8+ T cells were examined by scRNAseq.

first: Willem

last: Van Der Byl


title: Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [RNA-seq II]

status: Public on Mar 02 2021

country: Australia

type: Expression profiling by high throughput sequencing

summary: In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection.  Flow cytometric analysis indicated that EGR2 is expressed selectively within the progenitor exhausted subset, however a subpopulation of progenitor exhausted cells did not express in EGR2. To define the differences between the EGR2+ and EGR2- progenitor exhausted cells, GFP+ and GFP- polyclonal progenitor exhausted (ie. CD44int-hiPD-1+Slamf6+Tim3-) CD8+ T cells were sorted from Egr2-GFP reporter mice at day 20 p.i. with chronic LCMV-Cl13, and analysed by RNAseq. The resulting data demonstrated that GFP- progenitor cells have a more differentiated phenotype.

overall_design: The transcriptome of Egr2-GFP reporter positive and negative progenitor exhausted CD8+ T cells was examined by RNAseq.

first: Madison

last: Kelly


title: Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [RNA-seq I]

summary: In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection.  Flow cytometric analysis indicated that EGR2 deficient CD8+ T cells had a block in differentiation and failed to undergo terminal exhaustion. To confirm this at a whole transcriptome level, we conducted RNAseq analysis on sorted splenic virus-specific tetramer+ CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from either littermate control or EGR2 T cell conditional knock-out mice. The resulting data demonstrated that there was a global loss of the terminally exhausted gene signature within EGR2 KO CD8+ T cells.  This suggests that EGR2 promotes terminal CD8+ T cell exhaustion.

overall_design: The transcriptome of exhausted wild-type or EGR2 knockout CD8+ T cells was examined by RNAseq.


title: Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [CHIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection.  Flow cytometric and RNAseq analysis indicated that EGR2 deficient CD8+ T cells had a block in differentiation and failed to undergo terminal exhaustion. To examine the direct gene targets of EGR2 during exhaustion, we conducted ChIPseq analysis on enriched bulk splenic CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from C57BL/6J mice. The resulting data demonstrated that EGR2 directly controls expression of key gene targets, including Pdcd1, Tigit, Cxcr5, Tcf7, Bach2 and Bcl6.

overall_design: The genome-wide binding pattern of EGR2 was examined wtihin exhausted CD8+ T cells by ChIPseq.


title: Human plasmacytoid dendritic cells mount a distinct antiviral response to virus-infected cells

status: Public on Mar 01 2021

city: New York

first: Peter

middle: A

last: Sims

state: NY

address: 3960 Broadway, Lasker 203AC

country: USA

institute: Columbia University

summary: Plasmacytoid dendritic cells (pDCs) can rapidly produce interferons and other soluble factors in response to extracellular viruses or virus mimics such as CpG-containing DNA. pDCs can also recognize live cells infected with certain RNA viruses, but the relevance and functional consequences of such recognition remain unclear. We studied the response of primary DCs to the prototypical persistent DNA virus, the human cytomegalovirus (CMV). Human pDCs responded poorly to free CMV but strongly to live CMV-infected fibroblasts, in a process that involved integrin-mediated adhesion, transfer of viral DNA to pDCs and its recognition through TLR9. Compared to transient polyfunctional responses to CpG or free influenza virus, pDC response to CMV-infected cells was long-lasting, dominated by the production of type I (IFN-I) and type III (IFN-III) interferons, and lacked diversification into functionally distinct populations. Similarly, pDC activation by influenza-infected lung epithelial cells was highly efficient, prolonged and dominated by interferon production. Prolonged pDC activation by CMV-infected cells facilitated the activation of natural killer cells that are critical for CMV control. Finally, patients with CMV viremia harbored phenotypically activated pDCs and increased levels of IFN-I and IFN-III in circulation. Thus, recognition of live infected cells is a common mechanism of virus detection by pDCs that elicits a unique antiviral response program.

sample_organism:
Homo sapiens
blank sample

platform_organism:
Homo sapiens
blank sample

overall_design: RNA-sequencing of pDCs treated with CpG, CMV, and both infected and uninfected MRC5 cells using PLATE-seq 3'-tag sequencing

first: Tae

middle: J

last: Yun

first: Boris

last: Reizis


title: DNA methylation abnormal accumulation during cloned TSCs maintaining [RRBS]

city: shanghai

first: Jin

last: Sun

department: life science and technology

country: China

institute: Tongji University

type: Methylation profiling by high throughput sequencing

summary: Trophoblast stem cells (TSCs) are derived from the trophoectoderm of blastocysts and maintain ability to self-renewal and differentiation. TSC is a good model to research placenta development in vitro. It will contribute to understanding and improving cloned placentomegaly to compare the transcription and methylation between cloned and natural fertilized embryos throughout TSC derivation process. In the present study, we used SCNT (NT) and SCNT with HDACi treatment (SNT) as cloned groups and natural fertilized (NF) embryos to derive TSCs and chosed 5-time points to peform RNA-seq and RRBS. We found only NT got a barriar in TSC maintenace and both cloned groups exhited abnormal accumulating DNA methylation and it might be resiponsible for some malformations of cloned placentas.

overall_design: We generated embryos from 3 different sources natural fertilization (NF), somatic nuclear transfer (NT), and somatic nuclear transfer with HDACi Scriptaid treatment (SNT) and chosed 5-time points during the TSC maintaining, E3.5 blastocyst trophectoderm (TE3.5), E4.5 blastocyst trophectoderm (TE4.5), outgrowths at half-time progression (outgrowth), passage 1 TSCs (TS_P1), and passage 3-4 TSCs (TS_Pn) to perform RNA-seq and RRBS. For each sample, we performed several independent replicates.

first: Rui

last: Gao

first: Cizhong

last: Jiang


title: Human anogenital monocyte-derived dendritic cells and langerin+ cDC2 are major HIV target cells

city: Westmead

first: J

middle: Dinny

last: Graham

state: NSW

address: 176 Hawkesbury Rd

department: Westmead Institute for Medical Research

institute: University of Sydney

summary: Tissue mononuclear phagocytes (MNP) are specialised in pathogen detection and antigen presentation. They are the first cells of the immune system to encounter HIV and play a key role in transmission as they deliver the virus to CD4 T cells, which are the primary HIV target cell in which the virus undergoes replication. Most studies have investigated the role that epithelial MNPs play in HIV transmission but, as mucosal trauma and inflammation are strongly associated with HIV transmission, it is also important to examine the role that sub-epithelial MNPs play. Sub-epithelial MNPs are present in a diverse array of subsets which differ in their function and the pathogens they detect. Understanding how specific subsets interact with HIV and deliver the virus to CD4 T cells is therefore of key importance to vaccine and microbicide development. In this study we have shown that, after topical application, HIV can penetrate to interact with sub-epithelial resident myeloid cells in anogenital explants and defined the full array of MNP subsets that are present in all the human anogenital and colorectal sub-epithelial tissues that HIV may encounter during sexual transmission. In doing so we have identified two subsets that preferentially take up HIV, become infected and transmit the virus to CD4 T cells; CD14+CD1c+CD11c+ monocyte-derived dendritic cells and langerin-expressing conventional dendritic cells 2 (cDC2).

overall_design: The study contains RNA-seq data in 18 samples, representing analysis of gene expression in 6 distinct flow sorted immune cell populations, separately isolated from abdominal tissue from from 3 healthy human donors.

first: Andrew

middle: N

last: Harman

first: Jake

middle: W

last: Rhodes

middle: D

first: Grant

middle: P

last: Parnell


title: RNA-sequencing of regenerating planaria Dugesia japonica

city: Boston

last: Chiang

state: MA

address: 60 Fenwood Rd. 3016Q

department: Anesthesiology

institute: Brigham and Women's Hospital

summary: We employed RNA-sequencing with surgically resected planaria and cysteinyl-specialized pro-resolving mediators (cys-SPMs), including MCTR3, PCTR3 and RCTR3 to identify genes and pathways activated by cys-SPMs.

overall_design: Planaria (Dugesia japonica; Dj) were kept in water (Poland Spring) at 20°C and starved for 7 days before surgery. Briefly, head resection was performed (post-ocular surgical injury), and posterior portions were then placed in water together with MCTR3, PCTR3, RCTR3 (10 nM) or vehicle (0.1% ethanol v/v in water). Forty-eight hours later, planaria were collected, RNA isolated and submitted to Molecular Biology Core Facilities at Dana-Farber Cancer Institute (Boston, MA) for paired-end RNA sequencing using an Illumina NextSeq 500 sequencing system. Bioinformatics was carried out using Dj transcript sequences with the Bioinformatics and Biostatistics Core at Joslin Diabetes Center (Boston, MA).

first: Charles

last: Serhan

first: Hui

last: Pan

first: Jonathan

middle: M

last: Dreyfuss


title: DNA methylation abnormal accumulation during cloned TSCs maintaining

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

overall_design: Refer to individual Series


title: GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryo [ATAC-seq]

status: Public on Mar 03 2021

city: Madison

first: Melissa

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: Following fertilization, the genomes of the germ cells are reprogrammed to form the totipotent embryo. Pioneer transcription factors are essential for remodeling the chromatin and driving the initial wave of zygotic gene expression. In Drosophila melanogaster, the pioneer factor Zelda is essential for development through this dramatic period of reprogramming, known as the maternal-to-zygotic transition (MZT). However, it was unknown whether additional pioneer factors were required for this transition. We identified an additional maternally encoded factor required for development through the MZT, GAGA Factor (GAF). GAF is necessary to activate widespread zygotic transcription and to remodel the chromatin accessibility landscape. We demonstrated that Zelda preferentially controls expression of the earliest transcribed genes, while genes expressed during widespread activation are predominantly dependent on GAF. Thus, progression through the MZT requires coordination of multiple pioneer-like factors, and we propose that as development proceeds control is gradually transferred from Zelda to GAF.

overall_design: ATAC-seq profiling of chromatin accessibility was performed on single embryos from GAFdeGradFP embryos lacking GAF protein, or control embryos. 6 replicates were performed for both conditions.

first: Marissa

last: Gaskill

first: Tyler

last: Gibson

first: Elizabeth

last: Larson


title: The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells

city: Portland

first: Bret

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

summary: A common and shared biology across diverse animal species is that adult tissue homeostasis is ultimately regulated by stem cell proliferation, differentiation, and self-renewal. Aberrant activation of “stemness” programs is deleterious at organismal level, and commonly observed in human cancers. However, identifying key stemness genes in the milieu of thousands of genes dysregulated in a given human cancer is challenging. Here, using a comparative genomics approach between planarians and humans, we identify and functionally screen 76 highly conserved, putative stemness regulators in vivo that are also candidate drivers of stemness in human glioblastoma, a highly aggressive, stem-cell driven cancer with limited treatment options. We selected the helicase DDX56, and demonstrate a conserved role in regulating aspects of stemness across 4 normal and cancer stem cell systems: planarian adult stem cells; mouse embryonic neural stem cells; human glioma neural stem cells; and a fly model of glioblastoma. We demonstrate that DDX56 is required for self-renewal and survival of stem cells across the systems. Using planarians, we show that when DDX56 is lost, stem cells dysregulate expression of ribosomal RNAs and lose nucleolar integrity prior to stem cell death. Altogether, our study demonstrates the power of a comparative genomic approach to discover deeply conserved stemness regulators and actionable target genes relevant to human cancer.

overall_design:
Smed-ddx56(RNAi) animals were fed 3 times over 6 days and stem cells were collected 3 days after the last feed. Approximately 500,000 X1 cells from >100 animals were isolated at on a Becton–Dickinson FACS aria. Total RNA was purified using Trizol (Invitrogen 15596026), and poly-A-selected cDNA libraries were prepared using the TruSeq kits from Illumina. For RNA-seq, samples were sequenced to a depth of 250 million paired end 125 base pair reads, and multiplexed on an Illumina HiSeq2500.

Please note that the processed data file contains data compared to wild-type X1 cells previously published in GEO accessions GSE37910 (GSM929778), GSE68581 (GSM1675833) as described in the sample data processing field.

first: Michael

last: Pryszlak

first: Mallory

last: Wiggans


title: Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance

first: Ian

last: Parish


title: The Pif1 helicase is actively inhibited during meiotic recombination to prevent excess length of gene conversions

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

summary: Meiotic recombination ensures proper chromosome segregation to form viable gametes and results in gene conversion events between homologs. Conversion tracts are shorter in meiosis than in mitotically dividing cells. This results at least in part from the binding of a complex, formed of the Mer3 helicase and the MutL heterodimer, to meiotic recombination intermediates. The molecular actors inhibited by this complex are elusive. The Pif1 DNA helicase is known to stimulate DNA polymerase delta (Pol δ) -mediated DNA synthesis from D-loops in vitro, allowing long synthesis required for break-induced replication. We show that Pif1 is recruited genome wide to meiotic double-strand break (DSB) sites. We further show that Pif1, through its interaction with PCNA, is required for the long gene conversions observed in the absence of MutL recruitment to recombination sites. in vivo, Mer3 interacts with the PCNA clamp loader RFC, and in vitro, Mer3-MutL ensemble inhibits Pif1-stimulated D-loop extension by Pol δ and RFC-PCNA. Mechanistically, our results suggest that Mer3-MutL may compete with Pif1 for binding to RFC-PCNA. Taken together, our data show that Pif1’s activity to promote meiotic recombination-related DNA synthesis is restrained by the Mer3-MutL ensemble to prevent long gene conversion events and possibly associated mutagenesis.

overall_design: 4 samples total: 2 independent replicates of Pif1-Myc ChIP at 5 h in pCUP1-IME1 synchronized meiosis and 2 independent replicates of  Pif1-Myc ChIP in a spo11Y135F strain at 5 h in pCUP1-IME1-synchronized meiosis

first: Valérie


title: Identify genomic binding sites of Tfcp2l1 in mouse embryonic stem cells grown in 2i medium

city: Bethesda

first: Jing

last: Huang

state: MD

institute: National Cancer Institute

summary: Mouse embryonic stem cells (ESCs) grown in the 2i (an ERK inhibitor, PD0325901, and a GSK-3b inhibitor, CHIR99021) mimic pluripotent epiblasts in preimplantation blastocysts. Tfcp2l1 is a transcription factor highly expressed in ESCs grown in the 2i medium, suggesting that it plays in important role in ESC biology. To search for the putative role(s) of Tfcp2l1 in ESCs, we plan to use an integrated genomic approach--combing RNA-seq and ChIP-seq--to identify the direct targets of Tfcp2l1 in ESCs. ChIP-seq is used to identify the genomic bindings sites of Tfcp2l1 in ESCs grown in the 2i medium.

overall_design: Two repeats were performed and each repeat includes one input and one ChIP. 50 million of ESCs grown in 2i were subject to ChIP-seq with 10 ug custom-made antibody against mouse Tfcp2l1. To identify genomic peaks of Tfcp2l1, enrichment of ChIP versus input across the genome was calculated.

first: Hualong

last: Yan


title: GIMAP5 maintains liver sinusoidal endothelial cell identity and prevents portal hypertension

city: Seoul

first: Jungmin

last: Choi

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Biomedical Sciences

country: South Korea

institute: Korea University College of Medicine

summary: Chronic liver disease is a major leading cause of portal hypertension that affects approximately 1.5 billion people globally. We show that GIMAP5, a small organellar GTPase, is selectively expressed in liver endothelial cells and human GIMAP5 deficiency causes portal hypertension with capillarization of liver sinusoidal endothelial cells (LSECs).  LSEC capillarization is recapitulated in GIMAP5 loss-of-function (LOF) mice, and upon conditional Gimap5 deletion in endothelial cells. Single cell RNA-sequencing analyses reveals replacement of LSECs with capillarized endothelial cells and expansion of liver lymphatic endothelial cells in GIMAP5 LOF mice, and places GIMAP5 upstream of GATA4, a transcription factor required for LSEC-specification. Our studies reveal that GIMAP5 prevents portal hypertension by maintaining LSEC identity and suggest that LSEC is an induced endothelial cell state.

overall_design: single cell RNA-sequencing of sorted (CD45-CD31+) liver endothelial cells isolated from Gimap5sph/+ and Gimap5sph/sph mice

first: Silvia

last: Vilarinho


title: DNA methylation abnormal accumulation during cloned TSCs maintaining [RNA-seq]

first: Jin

last: Sun

first: Rui

last: Gao

first: Cizhong

last: Jiang


title: Human primary airway basal cells display a continuum of molecular phases from health to disease in COPD

city: Lund

first: Mattias

last: Magnusson

address: BMC A12

department: Molecular Medicine and Gene Therapy

country: Sweden

institute: Lund university

summary: Airway basal cells are crucial for regeneration of the human lung airway epithelium, and are thought to be important contributors to chronic obstructive pulmonary disease (COPD). However,  to reveal how basal cells contribute to disease, the basal cells need to be further characterized. We aimed to study  primary human basal cells from healthy donors and COPD patients in order to identify key differences that could further our understanding of the disease mechanisms. In this study, we optimized a sorting protocol for primary human basal cells dependent on cell size and NGFR expression. The basal cell population was found to be heterogeneous in contrast to cultured basal cells. In addition, significant differences such as KRT14 expression was found exclusively in cultured cells. Also, colony-forming capacity was significantly increased in cultured cells showing a clonal enrichment in vitro. Next, by single cell RNA sequencing on primary basal cells from healthy donors and COPD patients, the gene expression changes revealed a continuum ranging from healthy basal cell signatures to diseased basal cells phenotypes. We identified several upregulated genes that may be indicative of COPD, such as stress response related genes GADD45B and AHSA1, along with genes involved in the response to hypoxia such as CITED2 and SOD1. Taken together, the presence of both healthy and diseased basal cells in stage IV COPD demonstrates the potential for regeneration through the discovery of novel therapeutic targets. In addition, we show the importance of studying primary basal cells when investigating disease mechanisms in the human lung.

overall_design:
Comparing primary human basal cells from healthy and COPD donors
-----------------------------------------------------
Authors state "material from EU patients  are protected by GDPR and can therefore not be shared".  Thus, this dataset is incomplete.
Nextseq1.Sample2 in Raw_Reads.csv is COPD 1 to 3.  No additonal information to differentiate among the 3 is provided.

first: Sofia

last: WIjk

first: Pavan

last: Prabhala


title: m6A-RIP-seq of mRNA in yw, Mettl3, Mettl14 and Hakai flies

city: Shanghai

first: Dong

address: 2005 Songhu Road

department: School of life sciences

institute: Fudan University

summary: In order to obtain a stringent m6A methylome in Drosophila adults, we performed m6A-RIP-seq in yw control (male and female), Mettl3 (male), Mettl14 (male) and Hakai (male) mutant flies. We find that the effective m6A modification, which depends on the writer complex, is mostly distributed in 5’ UTR and near start codon in Drosophila, in contrast to the mammalian system. We define a set of high-confident m6A methylation sites shared by Mettl3, Mettl14 and Hakai, indicating that Hakai is a core component of the m6A writer complex. We also find differential methylation pattern in certain loci between male and female flies.

overall_design: Flies of 4 genotypes were analyzed with two replicates. For yw, experiments were performed on both male and female flies. For Mettl3, Mettl14 and Hakai, only males were used. Each RNA preparation was divided into input and IP samples, so total samples were 20.

first: Yanhua

last: Wang


title: m6A IP sequencing analysis of m6A mRNA methylation regulation by arsenic in keratinocytes

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

summary: N6-methyladenosine (m6A) RNA methylation is the most abundant internal chemical modifications in eukaryotic messenger RNA (mRNA) as well as long non-coding RNA (lncRNA). Recently, m6A RNA methylation research was revived by the discovery of the fat mass- and obesity-associated protein (FTO) as the first RNA demethylase, implicating that m6A RNA methylation is a reversible and dynamic modification and may have critical biological functions. Emerging evidence has shown that m6A modifications in mRNAs and lncRNAs play crucial roles in regulating RNA fate and function in biological processes in the past several years. The goal is to determine the targets of arsenic damage including m6A RNA methylation in keratinocytes.

overall_design: m6A IP seq of control, arsenic-treated (As) or arsenic-tumorigenic (As-T) HaCaT keratinocytes in duplicate

first: Jiangbo

last: Wei

first: Yan-Hong


title: RNA sequencing of blood-brain barrier (BBB) microvessels from mice with orthotopic GBM showing the benefit of triple therapy combining anti-immune checkpoint therapy with dual-anti angiogenic therapy.

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

summary: Glioblastoma multiforme (GBM) is a non T cell-inflamed cancer characterized by an immunosuppressive microenvironment that impedes dendritic cell maturation and T cell cytotoxicity. The alleviation of immunosuppression might be a prerequisite for succesful immune checkpoint therapy in GBM. We here combine anti-angiogenic and immune checkpoint therapy and demonstrate improved therapeutic efficacy in syngeneic, orthotopic GBM models. We observed that blockade of vascular endothelial growth factor (VEGF), Angiopoietin-2 (Ang-2) and programmed cell death protein-1 (PD-1) significantly extended survival compared to vascular targeting alone. In the GBM microenvironment, triple therapy increased the numbers of cytotoxic T-lymphocytes that inversely correlated with myeloid-derived suppressor and regulatory T cells. Furthermore, transcriptomic analysis of GBM microvessels indicates a global vascular normalization that was highest after triple therapy. Our results propose a rationale to overcome limitations of VEGF monotherapy by integrating the synergistic effects of VEGF/Ang-2 and PD-1 blockade to reinforce anti-tumor immunity through a normalized vasculature.

overall_design: Brain microvessels were isolated from treated and untreated adult WT BL6/57 mice from tumor bearing brain region at 21 days post transplation followed by RNA sequecning. Three biological replicates were included for each group pooling 3 mice for each set. Contra-lateral brain region within each group and sham operated mice served as controls.

first: Devraj

last: Kavi

first: Reiss

last: Yvonne

first: Günther

last: Stefan


title: Impact of glucose metabolism in postnatal cardiomyocytes

city: Los Angeles

first: Haruko

last: Nakano

state: CA

address: 615 Charles E. Young Dr. South

department: MCDB

institute: University of California, Los Angele

summary: We report RNA sequencing data from the postnatal cardiac myocytes of the wild type and Glucose transporter 1 (Glut1) overexpressed mouse

overall_design: Postnatal day 1 cardiomyocytes isolated and FACS sorted  from aMHC-cre;Rosa-YFPR of wild type or Glut1 overexpressed murine hearts

first: Viviana

last: Martinez

first: Baochen

last: Shi


title: Critical role of Lkb1 in the maintenance of alveolar macrophage self-renewal and immune homeostasis

city: Tianjin

first: li

last: tengda

address: Heping

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: Alveolar macrophages (AMs) are pivotal for maintaining lung immune homeostasis. We demonstrated that deletion of liver kinase b1 (Lkb1) in CD11c+ cells led to the greatly changed AMs abundance in lung. Transcriptomic sequencing revealed that Lkb1 inhibited the pro-inflammatory pathways, which might also contribute to the protective function of Lkb1 in AMs. We thus identified Lkb1 as a pivotal regulator to maintain immune function of AMs.

overall_design:
CD11ccrelkb1f/f mouse as the KO mouse and lkb1f/f mouse as WT mouse(2:2), the samples from the lung of the two KO mice and 2 WT mice
Wang qianqian (contributor), Chen Song (contributor)

first: Tengda

last: Li


title: One-shot analysis of translated mammalian lncRNAs with AHARIBO

status: Public on Feb 28 2021

city: Povo (TN)

first: Fabio

last: Lauria

address: Via alla Cascata 56

country: Italy

institute: Institute of Biophysics (Italian National Research Council)

summary: A vast portion of the mammalian genome is transcribed as long non-coding RNAs (lncRNAs) acting in the cytoplasm with largely unknown functions. Surprisingly, lncRNAs have been shown to interact with ribosomes, encode uncharacterized proteins, or act as ribosome sponges. These functions still remain mostly undetected and understudied owing to the lack of efficient tools for genome-wide simultaneous identification of ribosome-associated lncRNAs and peptide-producing lncRNAs. Here we present AHARIBO, a method for the detection of lncRNAs either untranslated, but associated with ribosomes, or encoding small peptides. Using AHARIBO in mouse embryonic stem cells during neuronal differentiation, we isolated ribosome-protected RNA fragments, translated RNAs and corresponding de novo synthesized polypeptides. Besides identifying mRNAs under active translation and associated ribosomes, we found and distinguished lncRNAs acting as ribosome sponges or encoding micropeptides, laying the ground for a better functional understanding of hundreds lncRNAs.

overall_design: We performed standard and AHARIBO (AHA-mediated RIBOsome isolation) RIBO-Seq on mouse embryonic stem cells. AHARIBO RIBO-Seq is based on the isolation of ribosomes trapped with their nascent peptides, by incorporating the non-canonical amino acid L-azidohomoalanine (AHA) followed by ribosome profiling. Experiment were performed in biological triplicate (standard RIBO-Seq) and duplicate (AHARIBO RIBO-Seq).

first: Luca

last: Minati

first: Claudia

last: Firrito

first: Alessia

last: Del Piano

first: Alberto

last: Peretti

first: Simone

last: Sidoli

first: Daniele

last: Peroni

first: Romina

last: Belli

first: Francesco

last: Gandolfi

first: Alessandro

last: Romanel

first: Paola

last: Bernabò

first: Jacopo

last: Zasso

last: Quattrone

first: Graziano

last: Guella

first: Gabriella

last: Viero

first: Massimiliano

last: Clamer


title: Transcriptome Investigation of Anti-inflammation and Immuno-Regulation Mechanism of Taurochenodeoxycholic acid

city: Hohhot

first: LiGe

last: Bao

address: Inner Mongolia Agricultural University, No. 306, Zhaowuda Road/Street

institute: College of Veterinary Medicine, Inner Mongolia Agricultural University

summary:
Background: Taurochenodeoxycholic acid (TCDCA) is one of the major active components in bile acid. It was proven to have inhibitory activities on inflammation and also participate in host immuno-regulation. TCDCA exerts anti-inflammatory and immuno-regulatory effects through the glucocorticoid receptor (GR) mediated genomic signaling pathway and the G protein-coupled bile acid receptor 5 (TGR5) mediated AC-cAMP-PKA signaling pathway. However, it is unclear whether GR or TGR5 plays an important role in the regulatory effects of TCDCA. In order to further investigate this effects mechanism of TCDCA, the research use the transcriptome to identify the major genes and pathway in the anti-inflammatory and immuno-regulatory effects.
Methods: After the Fibroblast-like synoviocytes (FLS) being treated by different concentrations (10-5, 10-6 and 10-7 M) of TCDCA for 12 hours, the resulting mRNA was analyzed by RNA-seq. The differentially expressed genes were screened from sequencing results using bioinformatics techniques. In the next step, other published literature were referred in order to find out whether those genes mentioned above are related to inflammation. The final selected differentially expressed genes associated with inflammation were then validated by q-PCR and western blot assays.
Results: Five genes associated with anti-inflammatory and immuno-regulatory effects, include Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Glutathione peroxidase 3 (GPX3), Serine/arginine-rich splicing factor-9 (SRSF9), Connective tissue growth factor (CTGF) and Cystatin B (CSTB) were identified. TCDCA at the concentrations of 10-5, 10-6 and 10-7 M significantly (p<0.05) up-regulate the mRNA and protein expression of SRSF9 and GPX3 and also up-regulate the mRNA expression of CSTB, CTGF and GAPDH. RNA-seq results of GPX3 and SRSF9 expression were consistent with q-PCR results, while q-PCR results of CTGF, GAPDH showed inconsistent with their RNA-seq results. Q-PCR result of CSTB expression also showed inconsistent with the RNA-seq result.
Conclusions: The anti-inflammatory and immuno-regulatory activities of TCDCA are proven to be related to the up-regulation expression of GPX3, SRSF9 and CSTB.

overall_design: mRNA profiles of the Fibroblast-like synoviocytes (FLS) treated with TCDCA (10-5, 10-6 and 10-7 M) and control cells were generated by sequencing, in triplicate, utilizing Illumina HiSeq 4000 platform.

first: Lige

first: Dacheng

last: Hao

first: Xu

last: Wang

first: Xiuling

last: He

first: Wei

last: Mao

first: Peifeng

last: Li


title: The effect of lncRNA PART1 knockdown on mature miRNA levels in HCC1806 and HCC1395 cells

city: Halifax

last: Marcato

state: Nova Scotia

address: 11F11, 5850 College Street

department: Pathology

country: Canada

institute: Dalhousie University

summary:
PART1 was knocked down down using GapmeRs specific to PART1.
The breast cancer cells used in this study were confirmed to have PART1 expression by qPCR and knockdown of PART was confirmed by qPCR.

overall_design: To assess the changes to mature miRNAs post PART1 knockdown, miRNA 4.0 microarray analyses were completed on HCC1806 and HCC1395 cells were treated with either control GapmeR, GapmeR#1 or GapmeR #2 for 48 hours and then collected and RNA purified using the mirVana™ miRNA Isolation Kit. Samples (in biological triplicate; n=3)  were sent to the Microarray Facility, The Centre for Applied Genomics (TCAG), The Hospital for Sick Children (Toronto, Canada) where the processed for  Affymetrix miRNA 4.0 microarray platform, and miRNA differences quantified. Data was collected in raw CEL format and processed through the Transcriptome Analysis Console (Affymetrix) to reveal differential miRNA levels.

first: Marie-Claire

last: Wasson


title: gd T-cells regulate transcriptional response to diet in the intestinal epithelium

first: Jaechul

last: Lim

state: CT

address: 1 Gwanak-ro, 1 Gwanak-gu

institute: Seoul National University

summary: As a site of direct encounter with the external environment, the intestine must balance nutrient uptake with barrier defense. This requires coordination between numerous cell types that engage whole tissue responses to changes in environmental variables. To investigate how nutrient uptake is regulated in the small intestine, we tested the effects of diets with different macronutrient composition on epithelial cell gene expression. We found that expression of enzymes and transporters required for digestion and absorption of carbohydrates, but not protein, was dependent on substrate availability. Surprisingly, the ‘on-demand’ induction of this machinery required gd Tcells, which regulated this program via suppression of IL-22 expression by ILC3s. We found that nutrient availability alters the tissue localization and transcriptome of gd T-cells and that transcriptional responses to diet involved cellular remodeling of the epithelial compartment. This work thus identified a novel role of intestinal gd T-cells in nutrient sensing.

overall_design: Bulk RNA-seq of intestinal epithelial cells, gd T cells, and ab T cells from mice fed with high carb or high protein diet, respectively.

first: Zuri

last: Sullivan

first: Ruslan

last: Medzhitov


title: Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [ATACseq]

city: Melbourne

first: Ian

last: Parish

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

summary: In this study, we examined the role of the transcriptional regulator EGR2 in CD8+ T cell exhaustion during chronic viral infection.  Flow cytometric and scRNAseq analysis indicated that EGR2 deficient CD8+ T cells had an abnormal effector-like phenotype. To examine whether this was due to epigenetic alterations, we conducted ATACseq analysis on sorted virus-specific tetramer+ CD8+ T cells isolated at day 20 post-infection with chronic LCMV-Cl13 from either littermate control or EGR2 T cell conditional knock-out mice. The resulting data demonstrated that there were substantial epigenetic changes within EGR2 KO CD8+ T cells, suggesting that EGR2 stabilises the exhausted epigenetic state.

overall_design: The open chromatin regions of exhausted wild-type or EGR2 knockout CD8+ T cells were examined by ATACseq.

first: Timothy

last: Peters


title: Actuation Enhances Patterning in Human Neural Tube Organoids

city: Heverlee

first: Adrian

last: Ranga

state: Flanders

address: Celestijnenlaan 200F - Room 03.349

department: Mechanical Engineering

country: Belgium

institute: KU Leuven

summary: Tissues achieve their complex spatial organization though physical interactions mediated by mechanical forces. Current strategies to generate in-vitro tissues have largely failed to implement such active, dynamically coordinated mechanical manipulations, relying instead on extracellular matrices which respond to, rather than impose mechanical forces. Here we develop devices which enable the actuation of organoids, and show that active mechanical forces increase growth and lead to enhanced patterning in an organoid model of the neural tube derived from single human pluripotent stem cells (hPSC). We demonstrate that organoid mechanoregulation due to actuation operates in a temporally restricted competence window, and that organoid response to stretch is mediated extracellularly by matrix stiffness and intracellularly by cytoskeleton contractility and planar cell polarity. Exerting active mechanical forces on organoids using the approaches developed here is widely applicable and should enable the generation of more reproducible, programmable organoid shape, identity and patterns, opening avenues for use of these tools in regenerative medicine and disease modelling applications.

overall_design: 5 samples are analyzed to compare the effect of stretching on human neural tube organoids. 2x day 11 samples of stretched and unstretched, 2x day 5 samples of stretched and unstretched (immediately after RA-SAG treatment and stretch completion) and 1 sample at day 3 (immediately before RA-SAG treatment and stretch initiation)

first: Abdel Rahman

last: Abdel Fattah

first: Brian

last: Daza

first: Gregorious

last: Rustandi

first: Miguel

last: Rubio

first: Benjamin

last: Gorissen

first: Suresh

last: Poovathingal

first: Kristofer

last: Davie

first: Yunping

last: Lei

first: Derek

last: Rosenzweig

first: Richard

last: Finnell

first: Catherine

last: Verfaillie

first: Maurilio

last: Sampaolesi

first: Peter

last: Dedecker

first: Hans

last: Van Oosterwyck

first: Stein

last: Aerts


title: SOX4 and SMARCA4 cooperatively regulate PI3K signaling through transcriptional activation OF TGFBR2 in triple negative breast cancer

city: Nutley

first: Kevin

last: Tong

state: NJ

address: 111 Ideation Way

department: CDI

institute: Hackensack Meridian Health

summary: Genomic and proteomic analyses coupled withmechanistic studies identified TGFBR2as a direct transcriptional target of SOX4and demonstrated that TGFBR2 is required to mediate SOX4-dependent PI3K signaling. We further reportthat SOX4 and the SWI/SNF ATPase SMARCA4, which are uniformly overexpressed in basal-like tumors,form a previously unreported complex that is requiredto maintain an open chromatin conformationat the TGFBR2regulatory regionsin order tomediateTGFBR2expressionand PI3K signaling.

overall_design: Total RNA was extracted from HCC1143 cells treated with either siRNA targeting SOX4 or non-targeting control siRNA for 96 hours. RNA libraries were prepared using theNuGen Ovation Universal RNA-Seq System (Catalog # 0343-32)and paired end (2x48bp) sequencing was performed usingthe Illumina NextSeq system. Paired-end FASTQ files were processed using default parameters of Kallisto version v0.43.1, with 100 bootstraps for the expectation-maximization algorithm. Kallisto transcriptome index was built using the Ensembl human genome reference build 38. Gene level summarization of Kallisto abundance (TPM) was established using the R package Tximport v1.0.3 and R v3.3.1.

first: Gaurav

last: Mehta

first: Steven

last: Angus

first: Christen

last: Khella

first: Michael

last: PVerzi

first: Gary

middle: L

last: Johnson

last: Gatza


title: The effect of lncRNA PART1 knockdown on gene expression in HCC1806 and HCC1395 cells

first: Paola

last: Marcato

overall_design: To assess the transcriptome post PART1 knockdown, microarray analyses were completed on HCC1806 and HCC1395 cells treated with either control GapmeR, GapmeR#1 or GapmeR #2 for 48 hours and then collected in TRIzol reagent before RNA purification, and RNA purification was performed. Samples (in triplicate; n=3)  were sent to the Microarray Facility, The Centre for Applied Genomics (TCAG), The Hospital for Sick Children (Toronto, Canada) where the processed for reverse transcribed into cDNA and hybridization ed to an Affymetrix Human Gene 2.0 ST microarray platform, and gene expression differences quantified. Data was collected in raw CEL format and processed through the Transcriptome Analysis Console (Affymetrix) to reveal differential gene expression.

first: Brianne

last: Cruickshank


title: Swine inflammation and necrosis syndrome is associated with plasma metabolites and liver transcriptome in affected piglets

status: Public on Feb 26 2021

city: Gießen

first: Robert

last: Ringseis

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

institute: JLU Gießen

summary: Swine Inflammation and Necrosis Syndrome (SINS) can lead to severe clinical signs, especially in tails, ears, teats and claws in pigs. Clinical and histopathological findings in newborn piglets with in-tact epidermis indicate a primarily endogenous etiology, and microbial-associated molecular pat-terns (MAMPs), such as lipopolysaccharide (LPS) are assumed to play a central role in the devel-opment of the syndrome. We hypothesized that swine inflammation and necrosis syndrome (SINS) is indirectly triggered by gut-derived MAMPs entering the circulatory system via the liver and thereby causing derangements on liver metabolism. To test this hypothesis, metabolomes, candidate genes of the liver and liver transcriptomes of 6 piglets with high-grade clinical signs of SINS  (SINS high) were examined and compared with 6 piglets without significant signs of SINS (SINS low). Several hepatic pro-inflammatory genes and genes involved in stress response were induced in piglets of the SINS high group. The most striking finding from hepatic transcript pro-filing and bioinformatic enrichment was that the most enriched biological processes associated with the approximately 220 genes induced in the liver of the SINS high group were exclusively related to metabolic pathways, such as fatty acid metabolic process. Within the genes (≈ 390) re-pressed in the liver of the SINS high group, enriched pathways were ribosome biogenesis, RNA processing, RNA splicing, spliceosome and RNA transport. The transcriptomic findings were supported by the results of the metabolome analyses. These results provide the first evidence for the induction of an inflammatory process in the liver of piglets suffering from SINS, accompanied by lipid metabolic derangement.

overall_design: For microarray analysis, n = 6 RNA samples each of the group SINS low and group SINS high were used for hybridization to the Affymetrix GeneChip Porcine Gene 1.0 Sense Target array.

first: Denise

middle: K

last: Gessner

first: Klaus

last: Eder

first: Gerald

last: Reiner


title: Next Generation Sequencing reveals different transcriptome induced by IL4-10 fusion protein (IL4-10 FP) compared to the combination of cytokines in mice with inflammatory pain

city: Utrecht

first: Niels

last: Eijkelkamp

address: Lundlaan 6

department: Center for Translational Immunology

country: Netherlands

institute: University Medical Center Utrecht

summary:
Purpose: The goalsof this study was to compare the transcriptome profiling of dorsal root ganglia (DRG) of animals injected intrathecally with IL4-10 FP, the combination of IL4+IL10 or vehicle, one week after induction of persistent inflammatory pain.
Methods: Mice received an intraplantar injection of carrageenan and one week developing inflammatory pain were intrathecally injected with IL4-10 FP, IL4+IL10 or PBS. DRGs were isolated and RNA libraries were prepared with the poly A selection method followed by multiplexing and sequencing on the Illumina NextSeq500® platform in a 1 × 75bp single-read and 350 million reads per lane (Utrecht Sequencing Facility)
Results: In vivo IL4-10 FP induces a differential transcriptome than the combination of cytokines in mice with persistent inflammatory pain.
Conclusions: The superior analgesic effect observed in mice treated with IL4-10 FP compared to mice injected with the naïve cytokines is derived from an induction of a different transcriptome on the lumbar DRGs.

overall_design: RNA was extracted from lumbar DRGs of mice injected intrathecally with IL4-10 FP (n=6), IL4+IL10 (n=5) or PBS; a week after induction of persistent inflammatory pain.

first: Judith

last: Prado

first: Remco

middle: H

last: Westerink

first: Jelena

last: Popov-Celeketic

first: Cristine

last: Steen-Louws

first: Aridaman

last: Pandit

first: Sabine

last: Versteeg

first: Wouter

last: van de Worp

first: Kris

last: Reedquist

first: Werner

last: Müller

first: C

middle: E

last: Hack

first: Leo

last: Koenderman


city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras. Mouse CD4+T cells in 21-day-old male WT and ∆Foxp3 mice were isolated from spleen by flow cytometry as DAPI–TCRβ+CD4+ cells for 10x Genomics Single Cell 3′ Reagent Kit (V2 chemistry, one sample per channel). For bone marrow chimera experiment: 7 week-old CD45.2-recipient mice were irradiated with 1000 Rad, reconstituted with 4 million CD3-depleted bone marrow cells: 50% CD45.1 x Foxp3-IRES-GFP (WT, 21d-old male) and 50% Foxp3DeltaEGFPiCre/RFP x ROSA-YFP x CD45.1/2 (scurfy, 21d-old male). 10 weeks later, spleen were harvested and tagged using a different Hashtags fo each mouse. ∆Foxp3 CD4+ T cells were sorted as DAPI–TCRb+CD4+CD45.1+CD45.2+. WT CD4+ T cells were sorted as DAPI–TCRb+CD4+CD45.1+CD45.2–. Control WT DAPI–TCRb+CD4+GFP+ Treg cells and GFP- Tconvs cells were also tagged and sorted. Samples with different hastags were pooled before single cell encapsulation using 10x Genomics Single Cell 3′ Reagent Kit (V3 chemistry).

first: David

last: Zemmour

first: Louis

last: Charbonnier

first: Juliette

last: Leon

first: Tala

last: Chatila

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Identify Tfcp2l1-regulated genes in mouse embryonic stem cells grown in 2i medium

city: Bethesda

first: Jing

last: Huang

institute: National Cancer Institute

summary: Mouse embryonic stem cells (ESCs) grown in the 2i (an ERK inhibitor, PD0325901, and a GSK-3b inhibitor, CHIR99021) mimic pluripotent epiblasts in preimplantation blastocysts. ESCs grown in FBS containing medium are more heterogenous in morphology and expression of stem cell factors. Tfcp2l1 is a transcription factor highly expressed in ESCs grown in the 2i medium, suggesting that it plays in important role in ESC biology. To search for the putative role(s) of Tfcp2l1 in ESCs, we plan to use an integrated genomic approach--combing RNA-seq and ChIP-seq--to identify the direct targets of Tfcp2l1 in ESCs. RNA-seq is used to identify the transcripts regulated by Tfcp2l1 in ESCs grown in the 2i medium.

overall_design: Four repeats for each of the three conditions: 1) Wild type ESCs grown in 2i; 2) Tfcp2l1 knockout ESCs grown in 2i; 3) Wild type ESCs grown in FBS. To identify transcripts regulated by Tfcp2l1 in the 2i medium, compared 1) to 2). To perform GSEA of 2i versus FBS, compare 1) to 3).

first: Hualong

last: Yan


title: Expression data from Inflammatory breast cancer (IBC) cells

city: Philadelphia

first: Christoforos

last: Thomas

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary:
ERβ expression is associated with less metastasis in patients with IBC tumors. We investigated this association in preclinical models of IBC by knocking out ERβ in cells. Ablation of ERβ promotes migration and invasion of IBC cells and increases the metastatic potential of IBC tumors in vivo.
We used microarrays to detail the global programme of gene expression underlying the increased migration of ERβ knockout cells and identified distinct classes of up-regulated genes during this process.

overall_design: Inflammatory breast cancer KPL4 cells with CRISPR/CAS9-mediated knockout of ERβ were used for RNA extraction and hybridization on Affymetrix microarrays

first: Thomas

last: Christoforos


title: Strand-specific ChIP-seq at DNA breaks distinguishes single versus doubled stranded DNA binding and refutes single stranded nucleosomes

city: Planegg-Martinsried

first: Martina

last: Peritore

state: Bayern

address: Am Klopferspitz 18

institute: MPIB

summary: In a first step of DNA double-strand break (DSB) repair by homologous recombination, DNA ends are resected such that single-stranded DNA (ssDNA) overhangs are generated. ssDNA is specifically bound by RPA and other factors, which constitutes a ssDNA-compartment on damaged chromatin. The molecular organization of this ssDNA- as well as the adjacent dsDNA-compartment is crucial during DSB signaling and repair. However, data  regarding the association of the most basic chromatin components – the nucleosomes – have been discrepant. Here, we use site-specific induction of DSBs and chromatin-immunoprecipitation followed by strand-specific sequencing to analyse in vivo binding of key DSB repair and signalling proteins to either the ssDNA- or dsDNA-compartment. In case of nucleosomes, we show that recently proposed ssDNA-nucleosomes are not a major, persistent species, but that nucleosomes eviction and  DNA end resection are intrinsically coupled. These results support a model of separated dsDNA-nucleosome- and ssDNA-RPA-compartments during DSB signaling and repair.

overall_design: Strand-specific ChIP-seq of histones at HO and AsiSI induced double strand breaks in S. cerevisiae, in WT, fun30∆ rad9∆ cells, arp8∆ cells, Sth1-3AID-9myc Snf2-3AID-9myc cells with n ≥ 2 replicates

first: Karl-Uwe

last: Reusswig

first: Susanne

middle: C

last: Bantele

first: Tobias

last: Straub

first: Boris

last: Pfander


title: Mouse PanCancer Immune Panel on WT and SCID mT3-2D KPC Tumors

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

summary: To comprehensively assess the immune milieu of WT and SCID mT3-2D tumors, we employed NanoString nCounter immune profiling. The two groups of samples exhibited distinct immune profiles and indicated greater upregulation of immune-related genes in mT3-2D WT tumors than in SCID tumors.

overall_design: We utilized NanoString transcript profiling to evaluate broad changes in the transcriptome of 5 WT and 5 SCID mT3-2D whole tumors

first: Reham

last: Ajina

first: Zoe

middle: X

last: Malchiodi

first: Allison

last: Fitzgerald

first: Annie

last: Zuo

first: Shangzi

last: Wang

first: Maha

last: Moussa

first: Connor

last: Cooper

first: Yue

last: Shen

first: Quentin

middle: R

last: Johnson

first: Jerry

last: Parks

first: Jeremy

last: Smith

first: Marta

last: Catalfamo

first: Sandra

last: Jablonski

last: Weiner


title: Genome-wide enhancer maps link disease variants to genes and cell types

city: Stanford

first: Jesse

last: Engreitz

address: 450 Serra Mall

department: Genetics

institute: Stanford University

summary: We generated ATAC-seq and H3K27ac ChIP-seq data in immortalized immune cancer cell lines to predict enhancer-gene regulation using the ABC model.

first: Joseph

last: Nasser

first: Tung

last: Nguyen

first: John

last: Ray

first: Charles

last: Epstein

first: Nir

last: Hacohen

first: Eric

last: Lander


title: Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [day56 RNA-Seq]

city: Kishibe-Shinmachi,Suita

first: Takeshi

last: Masaki

state: Osaka

department: Vascular Physiology

country: Japan

institute: National Cerebral and Cardiovascular Center

summary: Pulmonary arterial hypertension (PAH) is a devastating disease characterized by arteriopathy in the small to medium-sized distal pulmonary arteries, often accompanied by infiltration of inflammatory cells. Aryl hydrocarbon receptor (AHR), a nuclear receptor/transcription factor, detoxifies xenobiotics and regulates the differentiation and function of various immune cells. However, the role of AHR in the pathogenesis of PAH is largely unknown. Here, we explore the role of AHR in the pathogenesis of PAH. AHR agonistic activity in serum was significantly higher in PAH patients than in healthy volunteer and was associated with poor prognosis of PAH. Sprague-Dawley (SD) rats treated with the potent endogenous AHR agonist, 6-formylindolo[3,2-b]carbazole in combination with hypoxia develop severe pulmonary hypertension (PH) with plexiform-like lesions, whereas SD rats treated with the potent vascular endothelial growth factor receptor 2  inhibitors did not. Ahr-knockout (Ahr-/-) rats generated using the CRISPR/Cas9 system did not develop PH in the SU5416/hypoxia model. A diet containing Qing-Dai, a Chinese herbal drug, in combination with hypoxia led to development of PH in Ahr+/+ rats, but not in Ahr-/- rats. RNA-seq analysis, ChIP-seq analysis, immunohistochemical analysis, and bone marrow transplantation experiments shows that activation of several inflammatory signaling pathways were upregulated in endothelial cells and peripheral blood mononuclear cells, which led to infiltration of CD4+ IL-21+ T cells and MRC1+ macrophages into vascular lesions in an AHR-dependent manner. Taken together, AHR plays crucial roles in the development and progression of PAH and the AHR signaling pathway represents a promising novel therapeutic target for PAH

overall_design: mRNA profiles of total lung tissue at day 56 of wild type (WT) and Ahr-/- SuHx rats

first: Makoto

last: Okazawa

first: Tadakatsu

last: Inagaki

first: Tomohiko

last: Ishibashi

first: Manabu

last: Shirai

first: Yoshikazu

last: Nakaoka


title: Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [PBMC]

overall_design: mRNA profiles of peripheral blood mononuclear cells (PBMCs) at day 0, 28 and 56 of  SuHx rats


title: 40S ribosome profiling reveals distinct roles for Tma20/Tma22 (MCT-1/DENR) and Tma64 (eIF2D) in 40S subunit recycling

first: Nicholas

last: Guydosh

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

summary: The recycling of ribosomes at stop codons for use in further rounds of translation is critical for efficient protein synthesis. Removal of the 60S subunit is catalyzed by the ATPase Rli1 (ABCE1) while removal of the 40S is thought to require Tma64 (eIF2D), Tma20 (MCT-1), and Tma22 (DENR). However, it remains unclear how these Tma proteins cause 40S removal and control reinitiation of downstream translation. Here we developed an enhanced 40S ribosome footprinting strategy to directly observe intermediate steps of ribosome recycling in cells. Deletion of the genes encoding these Tma proteins resulted in broad accumulation of unrecycled 40S subunits at stop codons, directly establishing their role in 40S recycling. Furthermore, the Tma20/Tma22 heterodimer was responsible for a majority of 40S recycling events while Tma64 played a minor role. Introduction of an autism-associated mutation into TMA22 resulted in a loss of 40S recycling activity, linking ribosome recycling and neurological disease.

overall_design:
40S ribosome profiling of 12 biological samples with 11 replicates. 80S ribosome profiling of 4 biological samples with one replicate. Deletion strains and mutations affect either translation initiation (rpl11b) or ribosome recycling (tma64   /tma20   , tma64   /tma22   , tma20   , tma22   , tma64   , tma22    YCplac33, tma22    YCplac33-TMA22, tma22    YCplac33-DENR, tma22    YCplac33-tma22-C11Y, tma22    YCplac33-tma22-A105L) + WT.

**Please note that wig files composed of combination of two biological replicates (e.g. 26-45end5_DY134Ffx182Ffx_*.wig) are linked to the sample with the lower number (e.g. DY134Ffx sample for 26-45end5_DY134Ffx182Ffx_*.wig) as indicated in the corresponding sample description field.

first: David

last: Young

first: Sezen

last: Meydan


title: Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [day 4 RNA-Seq]

overall_design: mRNA profiles of total lung tissue and endothelial cells at day 0 and day 4 of wild type (WT) and Ahr-/- SuHx rats


title: Bone marrow endothelial cells regulate myelopoiesis in diabetes

city: Charlestown

first: Kamila

last: Naxerova

address: 149 13th Street

department: Center For Systems Biology

institute: Massachusetts General Hospital / Harvard Medical School

summary: Background—Diabetes is a prevalent public health problem that affects about one third of the U.S. population and leads to serious vascular complications with increased risk for coronary artery disease. How bone marrow hematopoiesis contributes to diabetes complications is incompletely understood. We thus investigated the role of bone marrow endothelial cells in diabetic regulation of inflammatory myeloid cell production.     Methods and Results—In three types of mouse diabetes, we observed enhanced proliferation of hematopoietic stem and progenitor cells (HSPC) leading to augmented circulating myeloid cell numbers. Analysis of bone marrow niche cells revealed that endothelial cells in diabetic mice expressed less Cxcl12, a retention factor promoting HSPC quiescence. Transcriptome-wide analysis of bone marrow endothelial cells demonstrated enrichment of genes involved in epithelial growth factor receptor (EGFR) signaling in mice with diet-induced diabetes. To explore whether endothelial EGFR plays a functional role in myelopoiesis, we generated mice with endothelial-specific deletion of EGFR (Cdh5Cre EGFRfl/fl). Unexpectedly, we found enhanced HSPC proliferation and increased myeloid cell production in Cdh5Cre EGFRfl/fl mice compared to wild type mice with diabetes. Disrupted EGFR signaling in endothelial cells decreased their expression of the HSPC retention factor angiopoietin-1. We tested the functional relevance of these findings for wound healing and atherosclerosis, both implicated in complications of diabetes. Inflammatory myeloid cells accumulated more in skin wounds of diabetic Cdh5Cre EGFRfl/fl mice, significantly delaying wound closure. Atherosclerosis accelerated in Cdh5Cre EGFRfl/fl mice, leading to larger and more inflamed atherosclerotic lesions in the aorta.    Conclusions—In diabetes, bone marrow endothelial cells participate in the dysregulation of bone marrow hematopoiesis and promote cardiovascular complications via leukocyte overproduction. Specifically, diabetes reduces endothelial production of Cxcl12, a quiescence-promoting niche factor that reduces stem cell proliferation. We also describe a previously unknown counter-regulatory pathway, in which protective endothelial EGFR signaling curbs HSPC proliferation and myeloid cell production via angiopoietin-1.

overall_design: Bone marrow endothelial cells were isolate from mice with and without high fat diet-induced diabetes in triplicate.

first: Felix

last: Hoyer

first: Partha

last: Dutta

first: Matthias

last: Nahrendorf


title: WES for WT and SCID mT3-2D KPC Tumors and mT3-2D cell line

first: Elana

last: Fertig

type: Genome variation profiling by high throughput sequencing

summary: To determine the influence of in vivo tumor growth and antitumor immune responses on the generation of tumor neoepitopes, we performed whole exome sequencing (WES) on the mT3-2D cell line, WT tumors and SCID tumors

overall_design: DNA was extracted from the whole tumor tissue of the 5 WT mT3-2D subcutaneous tumors, the 5 SCID mT3-2D subcutaneous tumors and the mT3-2D cell line, and then WES was performed

first: Reham

last: Ajina

first: Zoe

last: Malchiodi

first: Allison

last: Fitzgerald

first: Annie

last: Zuo

first: Shangzi

last: Wang

first: Maha

last: Moussa

first: Connor

last: Cooper

first: Yue

last: Shen

first: Quentin

last: Johnson

first: Jerry

last: Parks

first: Jeremy

last: Smith

first: Marta

last: Catalfamo

first: Sandra

last: Jablonski

first: Louis

last: Weiner


title: Genome wide transcriptomics analyses of livers reveal induction of N-glycosylation upon loss of nuclear receptors FXR and SHP

status: Public on Mar 09 2021

city: Urbana

first: Sayeepriyadarshini

last: Anakk

address: 506 S. Mathews

department: Molecular and Integrative Physiology

institute: University of Illinois at Urbana Champaign

summary: We performed high-throughput RNA-sequencing on livers from hepatocyte specific Fxr-/- Shp-/- double knockout mice, and identified upregulation of N-glycan protein modification machinery. This correlated positively with Golgi structural defects and alterations in the hepatic secretome. This study identifies a new role for hepatic FXR-SHP axis in Golgi dynamics and N-glycosylation, apart from its traditional function in nutrient metabolism.

overall_design: Hepatic mRNA expression profiles of adult fl/fl Fxr fl/fl Shp and hepatocyte specific Fxr-/- Shp-/- (n=3) male mice.

first: Bhoomika

last: Mathur

first: Waqar

last: Arif

first: Auinash

last: Kalsotra


title: Aryl hydrocarbon receptor is essential for the pathogenesis of pulmonary arterial hypertension [ChIP-Seq]

first: Takeshi

last: Masaki

overall_design: Examination of 3 different histone modifications in rat total lung tissue. ChIP-seq was conducted using pooled  lung samples from SuHx rats at day4 , SuHx rats at 8weeks or normoxia control rats(day0) (3rats per group)

first: Makoto

last: Okazawa

first: Tadakatsu

last: Inagaki

first: Tomohiko

last: Ishibashi

first: Yoshikazu

last: Nakaoka


title: Cellular pyrimdine imbalance triggers mitochondrial DNA-dependent innate immunity [Scr_vs_Yme1l-si_RNA-seq]

city: Cologne

first: Thomas

last: MacVicar

address: Joseph-Stelzmann Str 9B

institute: Max Planck Institute for Biology of Ageing

summary: Cytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP–AMP syn- thase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS–STING–TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflamma- tion in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS–STING–TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.

overall_design: Transcript profiles of wildtype (WT) mouse embryonic fibroblasts (MEFs) treated with Scrambled (Scr) or Yme1l siRNA. The dataset includes three independent cultures for each condition (6 samples in total)

first: Hans-Georg

last: Sprenger

first: Janine

last: Altmüller


title: Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity [WT_vs_Yme1lKO_MEF_RNA-seq]

overall_design: Transcript profiles of wildtype (WT) and Yme1l-/-  mouse embryonic fibroblasts (MEFs). The dataset includes three independent cultures for each cell type (6 samples in total)


title: Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity [A33_OE_RNA-seq]

overall_design: Transcript profiles of wildtype (WT) or Slc25a33-MycFlag overexpressing HeLa cells treated with 40 µM 2',3' dideoxycytidine (ddC) for 72 h.


title: A specific RIP3+ subpopulation of microglia promotes retinopathy through a hypoxia-triggered necroptotic mechanism

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

summary: To elucidate the classification and function of microglia subsets in the angiogenic retina, we used single-cell RNA sequencing on isolated retinal microglia. We identified a novel subpopulation of microglia named sMG2, which highly expressed necroptosis-related genes Rip3 and Mlkl.

overall_design: Single cell profiling of retinal microglia from normal and oxygen-induced retinopathy mice, using 10X genomic platform.

first: Chang

last: He

first: Xialin

last: Liu


title: Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity [HeLa_CAD_RNA-seq]

overall_design: Transcript profiles of HeLa cells treated with esiRNA targeting Gfp (control) or CAD in the presence and absence of 2',3' dideoxycytidine (ddC)

first: Amir

last: Bahat


title: cAMP dependent gene expression in mouse hippocampal neurons

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Florida

summary: To identify cAMP-dependent lncRNAs, we treated DIV16 primary hippocampal neurons with 50uM Forskolin or equal volume DMSO for 30 minutes prior to RNA isolation using Trizol and Total RNA sequencing. We submitted samples to Scripps Florida Genomics Core for library preparation and sequencing.

overall_design: DIV16 primary hippocampal neurons treated with 50uM Forskolin or equal volume DMSO for 30 minutes

first: Eddie

last: Grinman


title: RNA-seq for WT and SCID mT3-2D KPC Tumors and mT3-2D cell lines

first: Elana

last: Fertig

summary: To investigate how pancreatic malignant epithelial cells responded to anti-tumor T-cell immune responses in vivo, RNA-seq was used to examine the gene expression profiles of the mT3-2D-GFP cell line and FACS sorted mT3-2D-GFP cancer cells isolated from  WT and SCID tumors.

overall_design: RNA was extracted from 6 WT tumors GFP+ sorted cells, 5 SCID tumors GFP+ sorted cells, and the mT3-2D-GFP cell line. Equal amounts of RNA from each corresponding group were combined as one sample (1 WT sample, 1 SCID sample, and 1 cell line). Then, RNA-seq was used to examine the gene expression profiles of these samples

first: Reham

last: Ajina

first: Zoe

last: Malchiodi

first: Allison

middle: A

last: Fitzgerald

first: Annie

last: Zuo

first: Shangzi

last: Wang

first: Maha

last: Moussa

first: Connor

last: Cooper

first: Yue

last: Shen

first: Quentin

last: Johnson

first: Jerry

last: Parks

first: Jeremy

last: Smith

first: Marta

last: Catalfamo

first: Sandra

last: Jablonski

first: Louis

last: Weiner


title: RNA-seq analysis of Ahr-knockout rats of SuHx model.

first: Takeshi

last: Masaki

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

overall_design: Refer to individual Series


title: Cellular pyrimidine imbalance triggers mitochondrial DNA-dependent innate immunity

first: Thomas

last: MacVicar

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: HAND2 is a novel obesity-linked adipogenic transcription factor regulated by glucocorticoid signaling

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

summary:
Aims: Adipocytes are critical cornerstones of energy metabolism. While obesity-induced adipocyte dysfunction is associated with insulin resistance and systemic metabolic disturbances, adipogenesis, the formation of new adipocytes and healthy adipose tissue expansion are associated with metabolic benefits. Understanding the molecular mechanisms governing adipogenesis is of great clinical potential to efficiently restore metabolic health in obesity. Here we investigate the role of Heart and neural crest derivatives-expressed protein 2 (HAND2) in adipogenesis.
Methods: Human white adipose tissue (WAT) were collected in a cross-sectional study of 318 individuals. In vitro, for mechanistic experiments we used primary adipocytes from human and mice as well as human multipotent adipose derived stem (hMADS) cells. Gene silencing was performed using siRNA or genetic inactivation in primary adipocytes from LoxP mouse models with Cre-encoding mRNA. Adipogenesis efficiency was measured by OilRedO staining, qPCR and microarray. A combinatorial RNASeq approach was used to identify gene clusters regulated by HAND2. In vivo, we created a conditional adipocyte Hand2 deletion mouse model using Cre under control of the Adipoq promoter (HAND2AdipoqCRE).
Results: We found that HAND2 is an obesity-linked white adipocyte transcription factor regulated by glucocorticoids that was required but insufficient for adipocyte differentiation in vitro. In a large cohort of humans with obesity, WAT HAND2 expression was correlated to body-mass-index (BMI). The HAND2 gene was enriched in white adipocytes compared to brown, induced early in differentiation and responded to DEX, a typical glucocorticoid receptor (GR, encoded by NR3C1) agonist. Silencing of NR3C1 in hMADS or deletion of GR in a transgenic conditional mouse model results in diminished HAND2 expression, establishing that adipocyte HAND2 is regulated by GCs via GR in vitro and in vivo. Furthermore, we identified gene clusters indirectly regulated by the GR-HAND2 pathway. Interestingly, silencing of HAND2 impaired adipocyte differentiation in hMADS and primary mouse adipocytes. However, a conditional adipocyte Hand2 deletion mouse model using Cre under control of the Adipoq promoter did not mirror these effects on adipose tissue differentiation, indicating that Hand2 was required at stages prior to Adipoq expression.
Conclusion: In summary, our study identifies HAND2 as a novel obesity-linked adipocyte transcription factor, highlighting new mechanisms of GR-dependent adipogenesis in human and mice.

overall_design: We performed gene expression microarray analysis in human multipotent adipose-derived stem (hMADS) cells treated with siRNA for HAND2 or controls

first: Maude

last: Giroud

first: Foivos-Filippos

last: Tsokanos

first: Giorgio

last: Caratti

first: Sajjad

last: Khani

first: Elena

middle: S

last: Vogl

first: Martin

last: Irmler

first: Christina

last: Glantschnig

first: Manuel

middle: G

last: Lozano

first: Daniela

last: Hass

first: Asrar

last: Ali Khan

first: Marcos

last: Rios Garcia

first: Frits

last: Mattijssen

first: Adriano

last: Maida

first: Daniel

last: Tews

first: Annette

last: Feuchtinger

first: Kirsi

last: Virtanen

last: Wabitsch

first: Matthias

last: Blüher

first: Jan

last: Tuckerman

first: Marcel

last: Scheideler

first: Alexander

last: Bartelt

first: Stephan

last: Herzig


title: FOXO and HSF1 rejuvenate immunity via positive feedback regulation of insulin/IGF-1 signaling

city: Daejeon

first: Seung-Jae

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

institute: KAIST

summary: A hallmark of aging is immunosenescence, a decline in immune function that appeared to be inevitable. Surprisingly, here we show that genetic inhibition of DAF-2/insulin/IGF-1 receptor drastically delays immunosenescence and even rejuvenates immunity in C. elegans. We find that p38 mitogen activated protein kinase (PMK-1), a key determinant of immunosenescence in wild-type, is dispensable for this rejuvenated immunity. Instead, we demonstrate that longevity-promoting DAF-16/FOXO and heat-shock transcription factor 1 (HSF-1) increase immunocompetence in old daf-2(-) animals. The up-regulation of DAF-16/FOXO and HSF-1 decreases the expression of zip-10/bZip transcription factor, which in turn down-regulates ins-7, an agonistic insulin-like peptide, for further reduction in insulin/IGF-1 signaling (IIS). Thus, reduced IIS bypasses immunosenescence and rejuvenates immunity via up-regulating anti-aging transcription factors that regulate an endocrine insulin-like peptide through a positive feedback mechanism. Because many functions of IIS are conserved across phyla, our study may lead to developing strategies for immune rejuvenation in humans.

overall_design: The investigation of the changes of gene expression in wild-type (WT) and daf-2(-) animals at day 1 (young) and day 9 (old) adulthood

first: Yujin

first: Dae-Eun

last: Jeong

first: Wooseon

last: Hwang

first: Seokjin

last: Ham

first: Hae-Eun

last: Park

first: Sujeong

last: Kwon

first: Yoonji

last: Jung


title: Hypothalamic Rax+ tanycytes contribute to tissue repair and tumorigenesis upon oncogene activation

city: Beijing

first: Xi

middle: ze

last: Guo

state: Beijing

address: No. 1 Courtyard, Beichen West Road, Chaoyang District

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Science

summary: We reveal that hypothalamic stem cells (HySCs) are physiologically quiescent but display regenerative and tumorigenic potential under pathological conditions.

overall_design: Single cell sequencing of adult mouse median eminance (aME) in 10x Genomics platform and bulk RNA-seq

first: Wenhui

last: Mu

first: Si

last: Li

first: Jingkai

last: Xu

first: Xize

first: Rakia

last: Manzoor

first: Gisela

last: Helfer

first: Falong

last: Lu

first: Chong

last: Liu

first: Qing

middle: F

last: Wu


title: Whole transcriptional analysis of induced cardiomyocytes from MICFs

status: Public on Feb 25 2021

first: Yang

last: Zhao

address: No. 5 Yiheyuan Road Haidian District

institute: Peking University

summary: We report that Sall4 and Myocd empower direct cardiac reprogramming from adult cardiac fibroblasts after myocardial infarction (MICFs). To examine the gene expression of induced cardiomyocytes (iCMs) on the genome-wide scale, we performed RNA-sequencing of MICFs and iCMs induced by GMTMS (our cocktails) or GMTMM (cocktails reported by Weda et al). We found significant changes in the global gene expression profiles of MICFs after GMTMS or GMTMM overexpression. Compared to MICFs, 1318 genes were significantly up-regulated and 1302 genes were significantly down-regulated in GMTMS-induced iCMs, in which high expression of many cardiac genes and concomitant suppression of fibroblast genes were observed. Go analysis revealed that many cardiac-related clusters were enriched in iCMs as well. These results demonstrate a cardiac-like phenotype reprogrammed from MICFs by GMTMS.

overall_design: Myh6-mCherry+ iCMs from GMTMS- and GMTMM-transduced MICFs were collected by FACS after a four-week induction. Due to low percent of mCherry+ iCMs (< 5%), five samples in each group were mixed together after FACS for the next RNA extraction and sequencing. MICFs without virus infection were also dissociated after the same culture time.

first: Hong

first: Qiushi

last: Sun


title: Genetic interaction network has a very limited impact on the evolutionary trajectories in continuous culture-grown populations of yeast

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: Background: The impact of genetic interaction networks on evolution is a fundamental issue. Previous studies have demonstrated that the topology of the network is determined by the properties of the cellular machinery. Functionally related genes frequently interact with one another, and they establish modules, e.g., modules of protein complexes and biochemical pathways. In this study, we experimentally tested the hypothesis that compensatory evolutionary modifications, such as mutations and transcriptional changes, occur frequently in genes from perturbed modules of genetically interacting genes. Results: Using haploid strains of Saccharomyces cerevisiae deletion mutants as a model, we investigated two modules lacking COG7 or NUP133, which are evolutionarily conserved genes with many compensatory interactions. We performed laboratory evolution experiments with strains bearing these mutations in two genetic backgrounds (with or without additional deletion of MSH2), subjecting them to continuous culture in a non-limiting minimal medium. Next, the evolved yeast populations were characterized through whole-genome sequencing and transcriptome analyses. No obvious compensatory changes resulting from inactivation of genes already included in modules were identified. The supposedly compensatory inactivation of genes in the evolved strains was only rarely observed to be in accordance with the established fitness effect of the genetic interaction network. In fact, a substantial majority of the gene inactivations were predicted to be neutral. Similarly, transcriptome changes during continuous culture mostly signified adaptation to growth conditions rather than compensation of the absence of COG7, NUP133 or MSH2 genes. Conclusions: Our findings demonstrate that the genetic interactions and modular structure of the network described in other studies have very limited effects on the evolutionary trajectory observed on the genomic and transcriptomic levels, following gene deletion of module elements and upon our experimental conditions. This observation indicates that the modular structure of the cellular machinery has no impact on compensatory evolution in the short term.

overall_design: Comparison of transcriptomes of  cell populations of Saccharomyces cerevisiae W303 wild type (WT) haploid strain and its single deletion derivatives  cog7delta, nup133delta, msh2delta and dual deletion derivatives cog7msh2delta and nup133msh2delta. Transcriptomes of populations grown for 35 generations in continuous culture were compared to transcriptomes of populations of the same strains grown in the same conditions for 200 or 350 generations. For each strain three biological replicates of continuous cultures were performed. Each biological replicate had two technical replicates with dye swapping. ,

first: Joanna

last: Klim

first: Urszula

last: Zielenkiewicz

first: Adrianna

last: Skoneczna

first: Anna

last: Kurlandzka

first: Szymon

last: Kaczanowski


title: Human ESC-based modeling of H3.3G34R-mutant high grade glioma

city: New York

first: Viviane

last: Tabar

state: New York

address: 1275 York Avenue

department: Department of Neurosurgery

institute: Memorial Sloan-Kettering Cancer Center

summary: H3.3G34R-mutant gliomas are lethal tumors of the cerebral hemispheres, with unknown mechanisms of topographic specificity and tumorigenicity. We developed a human embryonic stem cell (hESC)-based model of H3.3G34R-mutant glioma that recapitulates the anatomical and genetic characteristics of the patient tumors.

overall_design: A series of engineered hESC lines, which harbor p53 and/or ATRX mutations and express wild type or G34R-mutant histone H3.3 variant under HES5 promoter, were differentiated into ventral forebrain neural progenitor cells (NPCs) as well as ventral hindbrain NPCs and maintained in neural differentiation condition as 3D spheroids. At day 46 of differentiation, HES5-positive NPCs were isolated and expression profiles were obtained by RNA-sequencing.

first: Kosuke

last: Funato


title: microarray Analysis of MKN-45 cell lines after 48 hours post-transfection of miR-125b mimic (50nM) and mimic control.

city: Tianjin

first: ben

last: liu

address: Huanhuxi Road

department: Department of Epidemiology and Biostatistics

institute: Tianjin Medical University Cancer Institute and Hospital

summary: We demonstrate that miR-125b, a key node in this microRNA regulatory network, is upregulated in gastric cancer (GC) and associated with poor overall survival through an integrated analysis of microRNA and mRNA profiling of GC revealed a mRNA-regulatory network.So we have employed whole genome microarray expression profiling as a discovery platform to compare the transcriptome profiling of human gastric cells (MKN-45)  after 48 hours post-transfection of miR-125b mimic (50nM) and mimic control.Pathway analysis shows that the predicted targets of miR-125b are highly involved in apoptosis/program death pathway，and the robust apoptosis genes, BIK and CASP6 are validated as the directed targets of miR-125b.

overall_design: Gene expression profiling was examined by the Agilent platform (AgilentG3-_GX_1color) with MKN-45 cells and analysis with One-Color Microarray-Based Gene Expression Analysis protocol (Agilent). At 48 hours post-transfection of miR-125b mimic and mimic control, total RNAs were isolated from cells by Trizol reagents. The integrity of total RNAs was evaluated by an Agilent 2100 Bioanalyzer (Agilent). Cy3-labeled target cRNA was prepared by Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions. Labeled cRNAs were hybridized with a SurePrint G3 Human GE 8×60K Microarrays (Agilent).

first: Ben


title: Generation of a humanized Aβ expressing mouse demonstrating aspects of Alzheimer’s disease-like pathology

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

summary: We generated knock-in mice that express wildtype human Aβ under control of the mouse App locus. Remarkably, changing 3 amino acids in the mouse Aβ sequence to its wild-type human counterpart leads to age-dependent impairments in cognition and synaptic plasticity, brain volumetric changes, inflammatory alterations, the appearance of Periodic Acid-Schiff (PAS) granules and changes in gene expression.

overall_design: knock-in mouse model that expresses human non-mutated Aβ in the natural context of the endogenous mouse APP gene

first: David

last: Baglietto-Vargas

first: Stefania

last: Forner

first: Lena

last: Cai

first: Alessandra

last: Martini

first: Laura

last: Trujillo-Estrada

first: Vivek

last: Swarup

first: Marie Minh Thu

last: Nguyen

first: Kelly Do

last: Huynh

first: Dominic

middle: I

last: Javonillo

first: Kristine Minh

last: Tran

first: Jimmy

last: Phan

first: Enikö

last: Kramár

first: Cristina

last: Nuñez-Diaz

first: Gabriela

last: Balderrama-Gutierrez

first: Franklin

last: Garcia

first: Jessica

last: Childs

first: Carlos

middle: J

last: Rodriguez-Ortiz

first: Juan Antonio

last: Garcia-Leon

first: Masashi

last: Kitazawa

first: Mohammad

last: Shahnawaz

first: Dina

last: Matheos

first: Xinyi

last: Ma

first: Celia Da

last: Cunha

first: Ken

last: Walls

first: Rahasson

last: Ager

first: Claudio

last: Soto

first: Antonia

last: Gutierrez

first: Ines

last: Moreno-Gonzalez

first: Ali

last: Mortazavi

first: Andrea

last: Tenner

first: Grant

last: MacGregor

first: Marcelo

last: Wood

first: Kim

middle: N

last: Green

first: Frank

last: LaFerla


title: Systematic discovery and functional interrogation of SARS-CoV-2 viral RNA-host protein interactions during infection

status: Public on Feb 24 2021

first: Julia

last: Belk

state: California

sample_organism:
Homo sapiens
Chlorocebus sabaeus

platform_organism:
Homo sapiens
Chlorocebus sabaeus


title: RNA-seq and CUT&Tag analysis of mouse cDC1 and cDC2 populations upon DC-SCRIPT depletion

city: Parkville

first: Gordon

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

institute: Walter and Eliza Hall Institute of Medical Research

summary:
The functional diversification of dendritic cells (DCs) is a key step in establishing protective immune responses. Despite the importance of this lineage diversity, its genetic basis is not fully understood. DC-SCRIPT (Zfp366) is a poorly known transcription factor expressed in conventional DCs (cDCs) and their committed bone marrow progenitors but not in plasmacytoid DCs (pDCs). We show that mice lacking DC-SCRIPT displayed substantially impaired development of IRF8-dependent conventional DC1 (cDC1), while cDC2 differentiated normally. The residual DC-SCRIPT-deficient cDC1s had impaired CD8+ T-cell cross-priming, which could be in part explained by the direct control of DC-SCRIPT on IL-12p40 production. Genome-wide mapping of DC-SCRIPT binding and gene expression analyses revealed a key role for DC-SCRIPT in maintaining cDC1 identity via the direct regulation of cDC1 signature genes, including Irf8. Our study reveals DC-SCRIPT to be a critical component of the gene regulatory program shaping the functional attributes of cDC1s.
This SuperSeries is composed of the SubSeries listed below.

overall_design:
cDC1s and cDC2s were sorted from the spleens of WT or Zfp366-/- mice. RNA was extracted and profiled using RNA-seq and nuclei were isolated for Cut&Tag profiling of DC-SCRIPT binding.
Refer to individual Series


title: RNA-seq analysis of mouse cDC1 and cDC2 populations upon DC-SCRIPT depletion

summary: The functional diversification of dendritic cells (DCs) is a key step in establishing protective immune responses. Despite the importance of this lineage diversity, its genetic basis is not fully understood. DC-SCRIPT (Zfp366) is a poorly known transcription factor expressed in conventional DCs (cDCs) and their committed bone marrow progenitors but not in plasmacytoid DCs (pDCs). We show that mice lacking DC-SCRIPT displayed substantially impaired development of IRF8-dependent conventional DC1 (cDC1), while cDC2 differentiated normally. The residual DC-SCRIPT-deficient cDC1s had impaired CD8+ T-cell cross-priming, which could be in part explained by the direct control of DC-SCRIPT on IL-12p40 production. Genome-wide mapping of DC-SCRIPT binding and gene expression analyses revealed a key role for DC-SCRIPT in maintaining cDC1 identity via the direct regulation of cDC1 signature genes, including Irf8. Our study reveals DC-SCRIPT to be a critical component of the gene regulatory program shaping the functional attributes of cDC1s.

overall_design: cDC1s and cDC2s were sorted from the spleens of WT and Zfp366-/- mice. RNA was extracted and profiled using RNA-seq. Biological triplicates were prepared for each genotype to produce twelve samples in total.

first: Hannah

middle: D

last: Coughlan


title: CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) of WT and RAS mutant specimens from acute myeloid leukemia (AML) patients.

city: Aurora

first: Brett

last: Stevens

state: CO

institute: University of Colorado

summary: To understand the role of RAS mutations in AML, we performed CITE-seq on diagnosis specimens from WT and RAS mutant AML patients.

overall_design: Cells were harvested from AML patients at diagnosis and subjected to CITE-seq analysis.

first: Austin

last: Gillen

first: Craig

last: Jordan


title: Structure-function analysis of fission yeast cleavage and polyadenylation factor (CPF) subunit Ppn1 and its interactions with Dis2 and Swd22

first: Angad

last: Garg

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

summary: This RNA-Seq analysis compares gene expression of the deletion mutants of the cleavage and polyadenylation factor subunits – Ppn1, Swd22 and Dis2, contrasting to the WT strain in the fission yeast S. pombe

overall_design: 3 test samples and 1 parental control sample was processed (each sample had 3 biological replicate experiments)

first: Beate

last: Schwer

first: Stewart

last: Shuman


title: Activation of endogenous retroviruses during brain development causes neuroinflammation

city: Lund

first: Johan

last: Jakobsson

address: Sölvegatan 17

department: Wallenberg Neuroscience Center

institute: Lund University

summary: Endogenous retroviruses (ERVs) make up a large fraction of mammalian genome and are thought to contribute to human disease, including brain disorders. Aberrant activation of ERVs constitute a potential trigger for neuroinflammation, but mechanistic insight into this phenomenon remains unclear. Using CRISPR/Cas9-based gene disruption of the epigenetic co-repressor protein Trim28, we found a dynamic H3K9me3-dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo disruption of Trim28 in cortical NPCs during brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain of mice. Neuronal ERV expression was linked to inflammation, including activated microglia, and aggregates of ERV-derived proteins. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in neuroinflammation.

overall_design: In vitro CRISPR Trim28-KO in mouse neural progentiro cells (NPCs) with 3 guide RNAs (guide 3, 4 and 13 targeting exon 3, 4 and 13 of Trim28) where each guide has two duplicates. Two controls (where guide RNA towards LacZ were used). In vivo CRISPR Trim28-KO (cas knockin mice): five Cas9-GFP knock in mice (referred as Cas in this document) where injected with guide RNAs 3 or 4 or 13 (targeting exon 3, 4 and 13), or all three guide RNA combined, plus one control (guideRNA towards LacZ). All guideRNAs were co-injected with AAV vectors expressing Cre. In vivo CRISPR Trim28-KO (Stop-Cas knockin mice): five stop-Cas9-GFP knock in mice (referred as StopCas in this document) where injected with AAV vectors expressing guide RNAs 3 or 4 or 13 (targeting exon 3, 4 and 13), or all three guide RNA combined, plus one control (guideRNA towards LacZ). All guideRNAs were co-injected with AAV vectors expressing Cre. In vivo Trim28-KO (Trim28-fl mice): AAV.Cre injections into Trim28-fl animals (+/- and +/+):  4 KO samples and 4 controls. In vivo Trim28-KO during development: Emx1-Cre/Trim28-fl animals. Three KOs (homozygote for Trim28-fl) and three control (heterozygote for Trim28-fl). H3K9me3 cut and run: One sample in NPCs and its respective IgGs. Trim28-KO Single cell sequencing: Two KO and two controls from the Emx mice were sequenced in single cell.

first: Raquel

last: Garza


title: Exon Level Expression Profiling: a Novel Unbiased Transcriptome (Mouse)

status: Public on Feb 23 2021

city: Houston

first: vanaja

last: konduri

state: Texas

address: One Baylor Plaza

department: Pathology&Immunology

institute: Baylor College of Medicine

summary: Transcriptome analysis of RNA samples from flow cytometry sorted cells

overall_design: Splenocytes from three groups of five mice each from treatment groups were harvested, pooled and activated with PDAC antigen-loaded autologous DC overnight.

first: V

last: Konduri

first: Y

last: Baig

first: W

middle: K

last: Decker


title: SCID mT3-2D KPC Tumors and mT3-2D cell lines

city: Baltimore

first: Elana

last: Fertig

state: MD

address: 670 W. Baltimore Street, 3rd floor

institute: University of Maryland, Baltimore


title: Sperm modulate uterine immune parameters relevant to embryo implantation and reproductive success

city: Adelaide

first: John

last: Schjenken

state: South Australia

address: The Robinson Research Institute and School of Paediatrics and Reproductive Health. Level 6. Medical School North. Frome Road

institute: The University of Adelaide

summary:
Seminal fluid factors modulate the female immune response at conception to facilitate embryo implantation and reproductive success. Whether sperm affect this response has not been clear. We evaluated global gene expression by microarray in the mouse uterus after mating with intact or vasectomized males. Intact males induced greater changes in gene transcription, prominently affecting pro-inflammatory cytokine and immune regulatory genes, with TLR4 signaling identified as a top-ranked upstream driver. Recruitment of neutrophils and expansion of peripheral regulatory T cells were elevated by seminal fluid of intact males. In vitro, epididymal sperm induced IL6, CXCL2, and CSF3 in uterine epithelial cells of wild-type, but not Tlr4 null females. Collectively these experiments show that sperm assist in promoting female immune tolerance by eliciting uterine cytokine expression through TLR4-dependent signaling. The findings indicate a biological role for sperm beyond oocyte fertilization, in modulating immune mechanisms involved in female control of reproductive investment.
We used microarrays to detail the global programme of gene expression in mice following exposure to different components of seminal fluid

overall_design: CBAF1 females mated with intact or vasectomized BALB/c males were euthanized at 8 h post mating, or at 2000 h on the day of pro-estrus for unmated controls, and uterine tissue was harvested. Uterine endometrium was recovered and processed for microarray. Endometrial RNA from n=16 females was pooled into four independent biological replicates per treatment group (4 x control, 4 x intact, 4 x vasectomized) and analyzed using Affymetrix Mouse Gene 1.0 ST Arrays (Affymetrix, Santa Clara CA)

first: Sarah

last: Robertson


title: Bruceantin targets HSP90 to overcome resistance to hormone therapy in castration-resistant prostate cancer

city: Seoul

first: Jeong

middle: Hoon

last: Kim

address: Irwon-dong Gangnam-gu

institute: Sungkyunkwan University

summary: Here we report the identification of bruceantin as a highly potent inhibitor of HSP90. RNA-seq analysis demonstrated bruceantin inhibits the transcriptional activity of androgen receptor and androgen receptor variant 7 and downregulates their target genes in castration-resistant prostate cancer cells.

overall_design: mRNA profiles of 22RV1 cells treated with DMSO or 10 nM bruceantin for 24 hr were generated by deep sequencing, in triplicate, using Illumina HiSeq2500.

first: Sue

last: Moon

middle: H


title: Transcriptome of MV4;11 cells treated with ASH1L inhibitor AS-99

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

summary: This study describes the transcriptome profiling of MV4;11 human leukemia cells treated for 6 days with: 1) DMSO; 2) 3 µM of AS-99 ASH1L inhibitor.

overall_design: RNA-Seq profiling on MV4;11 human leukemia cells upon treatment with inhibitor of ASH1L activity. Biological replicates of each sample are labeled as 1/2/3.

first: Tomasz

last: Cierpicki


title: Studies on Trim71 in mouse embryonic stem cells

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

institute: Mayo Clinic

type: Non-coding RNA profiling by high throughput sequencing

summary: We studies on Trim71 regulates mouse embryonic stem cells by identifying the transcriptome-wide RNA targets of Trim71. Moreover, through inhibiting specific Trim71:mRNA interactions, we determined how Trim71 modulate miRNA activity in mouse embryonis cell cells

overall_design: Transcriptome-wide Trim71 target mRNAs were identified through CLIPseq, and the functional significance of target Trim71:mRNA interactions were determined through RNA-seq and smallRNA-seq in the WT and mutant mouse embryonic stem cells.

first: Q

last: Liu

first: H

last: Zhang

first: X

last: Chen

first: S


title: single nuclei RNAseq data from Atlantic salmon (Salmo salar) gill

status: Public on Feb 22 2021

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

summary: An snRNAseq analysis of the Atlantic salmon gill to characterise its cellular complexity and development.

overall_design: Atlantic salmon parr (>14cm) were raised on constant light, ad libitum food in freshwater. Smoltification was induced by photoperiod manipulation (8 weeks under short photoperiod 8h Light:16h Dark; 8 weeks back under constant light. Fish were collected at four timepoints (T1-4; n=2). T1 was parr fish under constant light at the beginning of the experiment. T2 were collected at the end of the 8 week exposure to short photoperiod. T3 were collected after 8 week return to constant light. T4 was collected after a subgroup of T3 were exposed to full strength seawater for 24h. Gill tissue were snap frozen until processing.

middle: C

first: Yasutaka

last: Mizoro

first: Shona

last: Wood

first: Louise

middle: M

last: Ince

first: Marianne

last: Iversen

first: Even

last: Jørgensen

first: Torfinn

last: Nome

first: Simen

last: Sandve

first: Sam

last: Martin

first: Andrew

last: Loudon

first: David

last: Hazlerigg