title: Ctcf Haploinsufficiency Mediates Intron Retention in A Tissue-specific Manner

city: Sydney

first: Charles

last: Bailey

state: NSW

address: Missenden Rd, Building 93

country: Australia

institute: Centenary Institute

summary: CCCTC binding-factor (CTCF) is a master regulator of gene transcription and chromatin organization with occupancy at tens of thousands of DNA target sites genome-wide. CTCF is essential for embryonic development and somatic cell viability and has been well-characterized as a haploinsufficient tumor suppressor. Increasing evidence demonstrates CTCF as a key player in several alternative splicing (AS) regulatory mechanisms, including transcription elongation, transcriptional regulation of splicing factors, DNA methylation, histone modification and chromatin architecture. However, the genome-wide impact of Ctcf haploinsufficiency on AS has not been investigated. We performed a transcriptomic analysis on multiple tissues from a Ctcf hemizygous (Ctcf+/-) mouse model to examine the effect of Ctcf haploinsufficiency on gene expression and AS. Distinct tissue-specific differences in gene expression were observed in Ctcf+/- mice compared to wildtype mice. While exon skipping was the most abundant form of AS in all tissues, we observed a surprisingly large number of increased intron retention (IR) events in Ctcf+/- liver and kidney. Increased IR in liver affected genes involved in cytoskeletal organization, splicing- and metabolic-related processes. This study provides further evidence for Ctcf dose-dependent and tissue-specific regulation of gene expression and AS. Our data provide a strong foundation for elucidating the mechanistic role of CTCF in AS regulation and its biological consequences.

overall_design: Transcriptomic analyses were performed on five tissues (brain, kidney, liver, muscle and spleen) from three wild type (C57BL/6) and three Ctcf haploinsufficient (Ctcf+/-) mice

first: Adel

last: Alharbi

first: Ulf

last: Schmitz

first: Amy

last: Marshall

first: Darya

last: Vanichkina

first: Rajini

last: Nagarajah

first: Melissa

last: Vellozzi

first: Justin

last: Wong

middle: G

first: John

last: Rasko


title: Transcriptional Profile of Col1a1GFP+ CNS cells in health and EAE

status: Public on Nov 11 2020

city: La Jolla

first: Cayce

last: Dorrier

address: 9500 Gilman Drive

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: Bulk RNA Sequencing of Col1a1GFP+ cells from the spinal cords of healthy Col1a1GFP mice and mice 5 or 10 days after EAE symptom onset compared to bulk RNA sequencing of whole spinal cord homogenate

overall_design: Spinal cords from Col1a1GFP+ mice in health, 5 days after symptom onset and 10 days after symptom onset were dissociated into a single cell suspension and GFP+ cells were enriched using FACS sorting, sequenced and compared to the transcriptome of whole spinal cord homogenate. Gene expression profiles of 3 biological replicates each consisting of 2-3 spinal cords were sequenced per condition except for the whole spinal cord homogenate samples, each of which consisted of 1 full spinal cord.

first: Richard

last: Daneman


title: Utilizing ex vivo generated double negative T cells prevents the development and progression of nonalcoholic steatohepatitis

city: Beijing

first: Guangyong

last: Sun

address: Yongan Street 95, Xicheng District

country: China

institute: Beijing Friendship Hospital

summary:
Methods: The DNT cells incubation with CD3/CD28 antibodies were stimulated with IL-10 (50 ng/ml) for 24 hours, then transcriptome sequencing studies were performed on DNT cells RNA.

Results: The distributions of up- (107) and downregulated (114) genes (≥ 1.5-fold difference, padj < 0.05) compared with without IL-10-treated DNT were depicted in a volcano plot. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that changed genes from IL-10-stimulated monocytes were involved in the immune response; inflammatory response; regulation of apoptotic and proliferation; cytolysis; cytokine-cytokine receptor interaction; and T cell receptor signaling pathway, among others. Compared with control DNT cells, IL-10-treated DNT exhibited downregulated levels of cell survival and activation genes (Bcl-xl, Cytc, Epcam, and Spi1), cell cytotoxicity genes (Nkp46, Klrg1, Slamf6, Cd107a, Cd161, and Cd226), immune responses genes (Lta, Cd127, H2-Oa, and H2-Dma), and upregulated cell exhaustion genes (Pd-1, Ctla4, and Tim3).In this study, we found IL-10 stimulated DNT cells highly expressed PI3K-AKT signaling genes, such as Jak3, Pik3ap1, Pik3cb, and Sgk1, and MAPK pathway genes, such as Stmn1, Fos, Kras, Nras, and Map3k5, which indicated that IL-10 upregulated NKG2A expression in DNT cells may through these pathways.

overall_design: The DNT cells stimulated with or without IL-10 were generated by deep sequencing in duplicate, using Illumina HiSeq.

first: Dong

last: Zhang


title: Genome-wide maps of chromatin state(ATAC-seq) and gene expression(RNA-seq) of cold exposed Dot1L-ablated mouse brown adipose tissue

status: Public on Nov 10 2020

city: Berkeley

first: Danielle

last: Yi

state: CA

address: 220 Morgan Hall

institute: UC Berkeley

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Using high throughput sequencing we report chromatin accessibility(ATAC-seq) and transcriptome profiling (RNA-seq)and in mouse brown adipose tissue (BAT) upon cold exposure in wildtype and Dot1L-BAT specific KO mice.

overall_design: Identification of genomic chromatin accessibility change profiling and gene expression induced by loss of Dot1L in mouse brown adipose tissue

first: Hei

middle: S

last: Sul


title: Targeted inhibition of cooperative mutation- and therapy-induced AKT activation in AML effectively enhances response to chemotherapy

city: Copenhagen

first: Kim

last: Theilgaard-Mönch

address: Ole Maaløes Vej 5

country: Denmark

institute: Rigshospitalet/National Univ. Hospital and Biotech Research and Innovation Centre

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Gene expression-based, mouse primary BC CML after knockdown of AMD1 gene.

city: Cheonan

first: Ita

middle: Novita

last: Sari

state: Chungcheongnam-do

address: Bongjeong-ro 25, Dongnam-gu

department: Soonchunhyang Institute of Medi-Bio Science

country: South Korea

institute: Soonchunhyang University

summary: We report the gene expression profiling of mouse BC CML model which were knockdown with either shControl or shAMD1 constructs. By obtaining RNA from primary BC CML cells from those mice (n: 3 for each shRNA),we find that thousands gene were dysregulated by AMD1 knockdown.

overall_design: Examination of gene expression profiling from 3 control BC CML mouse cells and 3 shRNA-mediated AMD1 knockdown in BC CML mouse cells

first: Hyog-Young

last: Kwon

middle: N


title: ATAC-seq analyses to study chromatin state after overexpression of BAZ2B in lineage-committed human hematopoietic progenitors

status: Public on Nov 12 2020

city: Barcelona

first: Karthik

last: Arumugam

state: Barcelona

address: C/Dr.Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

summary: We demonstrated that the overexpression of BAZ2B in human lineage-committed progenitors lead to an induction of reprogramming to a multipotent hematopoietic stem cell state. To understand the mechanism we overexpressed Luciferase or BAZ2B in lineage-committed progenitors for 14 days and performed the ATAC-seq experiments

overall_design: Human lineage-committed progenitors (Lin-CD34+CD38+) were transduced with doxycycline-indcible lentiviral vectors Luciferase or BAZ2B. The cells were cultured in vitro with media containing doxycycline for 14 days and then sorted for the transduced cells using the GFP reporter for further processing for the ATAC-seq analyses

first: Xiaochuan

last: Tu

first: Davide

last: Carnevali

first: Jordan

last: Kesner


title: Exon and Gene Level Expression Profiling of Islets in Gaz Knockout Mice on Control and High Fat Diets

status: Public on Nov 09 2020

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

summary:
Transcriptome analysis of  RNA samples from islets
To gain grater insight into the role and mechanisms behind the inhibitory G-Protein, Gaz we used global gene expression profiling.  In mice, transgenic loss of B-cell Gaz is protective against high fat diets. through increased insulin secretion. This mechansism is poorly understood and here, using global transcriptomics we attempt to understand the genetic impact of Gaz knockout on control and HFD diets in male mice.

overall_design: Raw probe cell intesity data was analyzed at both the gene- and exon-level using the Robust Multichip Analysis (RMA) algorithm within the Affymetrix Expression Console 1.3 software package

first: Michael

last: Schaid

first: Michelle

last: Kimple


title: A supernumerary designer chromosome for modular in vivo pathway assembly in Saccharomyces cerevisiae

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

summary: This study investigates the suitability of neochromosomes as orthogonal expression platforms for rewiring native cellular processes and implementing new functionalities.

overall_design: Comparison of gene expression between a strain with exclusive expression of glycolysis from a neochromosome (IMF17) and a strain with expression of glycolysis from the native genome (IMX2109).

first: Pascale

last: Daran-Lapujade

first: Marcel

last: van den Broek

first: Eline

last: Postma


title: Cardiac fibroblast proliferation rates and collagen expression mature early in life and do not change with advancing age

city: Vienna

first: Anela

last: Tosevska

address: Waehringer Guertel 18-20

department: Division of Rheumatology

country: Austria

institute: Medical Univrsity of Vienna


title: Transient Nodal signalling in left precursors coordinates opposed asymmetries shaping the heart loop

city: Paris

first: Audrey

last: Desgrange

address: 24 boulevard du Montparnasse

country: France

institute: Imagine - Institut Pasteur

summary: The secreted factor Nodal has been shown to be a major left determinant. Although it is associated with severe congenital heart defects, its role in heart morphogenesis has remained poorly understood. Here, we report that Nodal is transiently active in precursors of the mouse heart tube poles, before the morphological changes of heart looping. In conditional mutants, we show that Nodal is not required to initiate asymmetric morphogenesis. We provide evidence of a heart-specific random generator of asymmetry that is independent of Nodal. Using 3D quantifications and simulations, we demonstrate that Nodal functions as a bias of this mechanism: it is required to amplify and coordinate opposed left-right asymmetries at the heart tube poles, thus generating a robust helical shape. We identify downstream effectors of Nodal signalling, regulating asymmetries in cell proliferation, cell differentiation and extra-cellular matrix composition. Our work provides novel insight into how Nodal regulates asymmetric organogenesis.

overall_design: RNA-seq of wildtype or Nodal-deficient E8.5 embryonic microdissected cardiac region.

first: Sigolène

middle: M

last: Meilhac

first: Christine

last: Bole

first: Nicolas

last: Cagnard


title: Protein Fe-S centers as a molecular target of toxicity of a complex transition metal oxide nanomaterial with downstream impacts on metabolism and growth

status: Public on Nov 08 2020

city: Milwaukee

first: Rebecca

middle: D

last: Klaper

state: WI

address: 600 E Greenfield Ave

department: School of Freshwater Sciences

institute: University of Wisconsin Milwaukee

summary: We investigated the impacts of transition metal oxide (TMO) lithium-ion battery cathode nanomaterial, lithium cobalt oxide (LCO), on gene expression in the larvae of a model sediment invertebrate Chironomus riparius.

overall_design: Examination of increasing TMO/LCO exposure levels on gene transcription

first: Nicholas

middle: J

last: Niemuth

first: Yonqian

last: Zhang

first: Aurash

middle: A

last: Mohaimani

first: Angela

last: Schmoldt

first: Elizabeth

last: Laudadio

first: Robert

last: Hamers


title: Huntington’s disease as a lamin B1 nuclear envelopathy

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

summary: Lamins, the major structural proteins within the nuclear lamina, are crucial for the functionality of cellular nucleus and their alterations are involved in the so-called laminopathies. We previously found that Huntington’s disease (HD), a hereditary neurodegenerative disorder caused by an expansion of a CAG repeat in the huntingtin (htt) gene, courses with increased lamin B protein levels in specific brain regions in both mouse models and patients. We now show that these changes are mostly restricted to lamin B1, occur in striatal medium-sized spiny neurons and CA1 hippocampal neurons, and are accompanied by altered nuclear morphology, nucleocytoplasmic transport disruption and un-structuring of lamin-associated chromatin domains. Normalization of lamin B1 levels by betulinic acid administration in the R6/1 mouse model of HD results in beneficial restoring of nuclear lamina homeostasis and prevention of motor and cognitive dysfunction, opening a window for a new therapeutic approach for HD and other B1-type laminophaties.

overall_design: ChIP-seq (36 samples), RNA-seq (18 samples) and ATAC-seq (6 samples) of 30-week-old WT and R6/1 mice hippocampus. WT means Wild-type mice and R6/1 means R6/1 Huntington's disease transgenic mice (PubMed ID 8898202)

first: Rafael

last: Alcalá-Vida

first: Marta

last: Garcia-Forn

first: Esther

last: Pérez-Navarro


title: The CTD of EBF1 enhances Brg1 recruitment to chromatin

city: Freiburg

first: Nikolay

last: Zolotarev

address: Stübeweg, 51

department: Cellular and Molecular Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

summary: EBF1 binds lymphoid progenitor chromatin prior to the detection of chromatin accessibility, whereby a C-terminal domain (CTD) enables “pioneering” independently of cooperating transcription factors. The CTD of EBF1 includes a short prion-like domain (PLD) with an ability of liquid-liquid phase separation in vitro and in vivo. The PLD of EBF1 mediates the recruitment of the chromatin remodeler Brg1 (a subunit of SWI/SNF remodeling complex).

overall_design: 5 anti-Brg1 ChIP-seq samples in fetal liver EBF1 -/- c-kit+ lymphocyte progenitors transduced with different vectors (empty vector and different EBF1 versions wt, dC, d480-520, F-GATA3) and 1 input control. 2 anti-Brg1 ChIP-seq samples in Abelson murine leukemia virus (A-MuLV) transformed pro-B cells with EBF1 replacemnt (by EBF1 wt or dC) and 2 input controls. 2 anti-EBF1 ChIP-seq samples in Abelson murine leukemia virus (A-MuLV) transformed pro-B cells with EBF1 replacemnt (by EBF1 wt or dC) and 2 input controls.


title: Ultra-low dose aerosol infection provides an improved murine model of tuberculosis

status: Public on Nov 06 2020

city: Seattle

first: Kevin

last: Urdahl

state: Washington

address: 307 Westlake Ave N #500

department: Global Infectious Disease

institute: Seattle Children's Research Institute

summary: Tuberculosis (TB) is a heterogeneous disease manifesting in a subset of individuals infected with aerosolized Mycobacterium tuberculosis (Mtb). Unlike human TB, murine infection results in uniformly high lung bacterial burdens and poorly organized granulomas.  To develop a TB model that more closely resembles human disease, we infected mice with an ultra-low dose (ULD) of between 1-3 founding bacteria, reflecting a physiologic inoculum. ULD-infected mice exhibited highly heterogeneous bacterial burdens, well-circumscribed granulomas that shared features with human granulomas, and prolonged Mtb containment with unilateral pulmonary infection in some mice. We identified blood RNA signatures in mice infected with an ULD or a conventional Mtb dose (50-100 CFU) that correlated with lung bacterial burdens and predicted Mtb infection outcomes across species, including risk of progression to active TB in humans. Overall, these findings highlight the potential of the mouse TB model and show that ULD infection recapitulates key features of human TB.

overall_design: Whole-blood microarrays of BL6 mice measured 24 days after aerosol infection with M. tuberculosis and lung CFUs measured 26-97 days post infection, either ultra-low dose (ULD: 1-3 CFU) or conventional dose (CD: 50-100 CFU). Total 13 CD mice, 54 ULD mice and 7 unifected controls.

first: Fergal

last: Duffy

first: Courtney

last: Plumlee


title: Circulating microRNAs associated with liver fibrosis in chronic hepatitis C patients

city: Rio de Janeiro

first: Turan

middle: Peter

last: Urmenyi

address: Av Carlos Chagas Filho 373

country: Brazil

institute: Universidade Federal do Rio de Janeiro

type: Non-coding RNA profiling by high throughput sequencing

summary:
In this study, we compared circulating miRNAs identified in hepatitis C virus (HCV)-infected patients presenting two extremes of liver disease: mild/moderate fibrosis and cirrhosis. The patients in the cirrhosis group subsequently developed hepatocellular carcinoma (HCC).
Methods: Expression profile of miRNA were identify by semiconductor sequencing using Ion Proton High Power Sequencer. The sequences were exported in FASTQ format for further analysis using the CLC Genomics Workbench software version 8.5. The transcripts were trimmed  and then annotated by comparing sequence similarity to miRBASE. After identification of mature miRNAs, differential expression analysis of miRNAs between the mild fibrosis and cirrhosis groups was performed using Empirical Analysis of Differential Gene Expression (EDGE). To verify the potential target genes regulated by the differentially expressed miRNAs identified between the two groups studied, the miRnet tool version 2.0 was applied to identify the regulatory networks in which the miRNAs are involved.
Results: We identified 163 mature miRNAs in the mild/moderate fibrosis group and 171 in the cirrhosis group, with 144 in common to both groups. Differential expression analysis revealed 5 upregulated miRNAs and 2 downregulated miRNAs in the cirrhosis group relative to the mild/moderate fibrosis group. Functional analyses of regulatory networks (target gene and miRNA) identified gene categories involved in cell cycle biological processes and metabolic pathways related to cell cycle, cancer, and apoptosis.
Conclusion:These results suggest that the differentially expressed circulating miRNAs observed in this work (miR-215-5p, miR-483-5p, miR-193b-3p, miR-34a-5p, miR-885-5p, miR-26b-5p and miR -197-3p) may be candidates for biomarkers in the prognosis of liver disease.

overall_design: Serum miRNA profiles of chronic hepatitis C patients

first: B

middle: C

last: Cabral

first: L

last: Hoffmann

first: T

last: Bottaro

first: P

middle: F

last: Costa

first: A

middle: L

last: Ramos

first: H

last: Coelho

first: C

last: Villela-Nogueira

middle: P

last: Ürményi

first: D

last: Faffe

first: R

last: Silva


title: Translational adaptation to heat stress is mediated by 5-methylcytosine RNA modification in Caenorhabditis elegans

city: Heidelberg

first: Carine

last: Legrand

address: Im Neuenheimer Feld 580

institute: DKFZ

summary: In order to fulfil a wide range of cellular functions, RNA molecules contain, in addition to the four canonical bases, a large number of chemically modified structures. Among those, the methylation of carbon-5 of cytosines (m5C) is an abundant, widespread mark in different classes of RNAs. m5C is catalysed by DNMT2 and by seven members of the NSUN family of enzymes. While some m5C-methyltransferases have been studied individually and implicated in phenotypes observed in organisms ranging from yeast to humans, it remains unclear how the m5C methylome acts to sustain development in homeostasis and stress. Here, using Caenorhabditis elegans as a model organism, we developed the first organism devoid of detectable m5C in RNA, providing strong evidence that this modification and its derivatives are non-essential for the nematode’s development and fertility under standard laboratory conditions. We further used this genetic tool to determine the localisation of m5C sites in different RNA classes, and showed that NSUN-4 acts as a multisite-specific tRNA/rRNA methyltransferase in the mitochondria. In addition, we show that m5C is required for adaptation to temperature changes, as animals devoid of this modification present temperature-sensitive fertility defects. At the molecular level, we show that loss of m5C leads to increased ribosome pausing at triplets encoding for leucine and proline, the most frequently methylated tRNA isoacceptors in C. elegans. This is correlated with reduced translation efficiency of transcripts enriched in these amino acids. Finally, we found translation of Leu-UUG codons to be the most strongly affected upon heat shock, suggesting a role of m5C wobble methylation in the adaptation to heat stress.

overall_design: Whole-transcriptome bisulfite sequencing of  wild type and noNSUN (nsun-/-) strains were generated by deep sequencing, in triplicate, using Illumina

first: Isabela

last: Navarro

first: Francesca

last: Tuorto

first: Frank

last: Lyko

first: Eric

last: Miska


title: Anatomical diversity of dermis in homeostasis and wound repair

city: London

first: Tanya

last: Shaw

address: Guy's Campus, New Hunt's House, Great Maze Pond

department: Centre for Inflammation Biology & Cancer Immunology

country: United Kingdom

institute: King's College London

summary: Skin has distinct characteristics depending on the anatomical site; however, the cell and molecular differences, and their functional implications, have been little described. RNA-sequencing of healthy adult mouse skin from the abdomen, back, and face/cheek has revealed that dermis from different sites is distinct, and that this aligns with their diverse embryonic origins (abdominal dermis develops from lateral plate mesoderm, dorsal dermis  from paraxial mesoderm, and cheek dermis from neural crest). The functional implications for wound repair are evident from the differences in extracellular matrix and cell migration observed in tissue and dermal fibroblasts from these sites, and the histological and transcriptional variations during a wound response.

overall_design: 24 samples have been analysed by RNA-seq (total RNA): 4 mice for each of 3 anatomical sites (abdomen, back, cheek), and each mouse included a Day3 full-thickness 2mm punch-biopsy skin wound and an adjacent unwounded "paired" control.

first: Patrycja

last: Jaworska

first: Vasiliki

last: Sofra

first: Hanfei

last: Song

first: Malcolm

last: Logan

first: Anthony

last: Graham


title: RNA sequencing of single blastocyst-stage embryos (E3.5) from zygotes which were injected with sperm sRNAs from normal or depressive male mice.

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

institute: Nanjing University

summary: We demonstrated that sperm sRNAs contribute to paternal transmission of depression-like symptoms.To further investigated the mechanism by which sperm sRNAs contribute to depression inheritance. Since the early embryonic period represents a window of plasticity important for adult phenotypes, we injected sperm sRNAs from mice of normal(F0-Ctl) or stress induced depressive(F0-Dep)into zygotes and assessed transcriptional changes when the embryos developed to the E3.5 blastocyst stage (sRNA-Dep-E3.5 vs sRNA-Ctl-E3.5).

overall_design: sRNAs isolated from normal (F0-Ctl) or stress induced depressive (F0-Dep) mouse sperm with a concentration of 2 ng/μl were microinjected into zygotes of the C57Bl/6J background. The zygotes were then cultured in M16 medium at 37 °C in 5% CO2. On the second day, the 2-cell embryos were transferred to potassium-supplemented simplex optimized medium. Embryos at the blastocyst stage (E3.5) were collected at approximately 96 h after microinjection.A single blastocyst-stage embryo was suspended in RNA lysis reagents and frozen at −80 °C, ready for RNA-sequencing processing.

first: Yanbo

last: Wang


title: High-content screen identifies drugs that restrict tumor cell extravasation across the endothelial barrier

status: Public on Nov 05 2020

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Metastases, which largely rely on hematogenous dissemination of tumor cells via the vascular system, significantly limit prognosis of patients with solid tumors. To colonize distant sites, circulating tumor cells must destabilize the endothelial barrier and transmigrate across the vessel wall. Here we performed a high-content screen to identify drugs that block tumor cell extravasation by testing 3520 compounds on a transendothelial invasion co-culture assay. Hits were further characterized and validated using a series of in vitro assays, a zebrafish model enabling 3-D visualization of tumor cell extravasation, and mouse models of lung metastasis. The initial screen advanced 38 compounds as potential hits, of which 4 compounds enhanced endothelial barrier stability while concurrently suppressing tumor cell motility. Two compounds: niclosamide and forskolin, significantly reduced tumor cell extravasation in zebrafish and niclosamide drastically impaired metastasis in mice. Because niclosamide had not previously been linked with effects on barrier function, we performed single cell RNA sequencing to reveal mechanistic effects of the drug on both tumor and endothelial cells. Importantly, niclosamide affected homotypic and heterotypic signaling critical to intercellular junctions, cell-matrix interactions, and cytoskeletal regulation. Proteomic analysis indicated that niclosamide-treated mice also showed reduced levels of kininogen, the precursor to the permeability mediator bradykinin. Our findings designate niclosamide as an effective drug that restricts tumor cell extravasation through modulation of signaling pathways, chemokines, and tumor-endothelial cell interactions.

overall_design: Single cell RNA sequencing on cultured tumor and endothelial cells under different conditions.

first: Georg

last: Hilfenhaus

first: Matteo

last: Pellegrini

first: M

last: Iruela-Arispe


title: Uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles

city: Singapore

first: Vibhor

last: Kumar

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

summary: Representation of single cells in biologically meaningfull terms has potential to improve classical analysis steps as well as give rise to multiple new applications. We have developed UniPath for representation of single-cell expression and open-chromatin profile using pathway enrichment scores. UniPath can also perform pseudo-temporal ordering of single-cells using their pathway enrichment-scores. We analysed several datasets using UniPath. Analysis of atlas of mouse single-cell RNAseq profiles with UniPath revealed surprising but biologically-meaningful convergence of different cell-types from distant organs.

overall_design: We performed single cell RNA-seq for two types of cells from non-small cell lung cancer (NSCLC) cell-lines. Applying UniPath revealed the importance of enrichment and co-enrichment of several pathways in tumorogenicity of NSCLC.

first: Sudhagar

last: Samydurai


title: Integrated analysis of DNA methylation and gene expression profiles identified S100A9 as a potential biomarker in ulcerative colitis

city: Urumqi

first: Shasha

last: Su

state: Xinjiang

address: 116 Huanghe Road, Shayibake

department: Department of Diestive

institute: Traditional Chinese Medicine Hospital Affiliated to Xinjiang Miedcal University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: In this research,  90 differential expression mRNAs (DEMs), 72 differential expression lncRNAs (DELs) and biological functions and pathway were identified in ulcerative colitisby (UC) integrated analysis. Potential therapeutic target for treatment was preliminary verified by qRT-PCR experiment and bioinformatics analysis.

overall_design: Differential expression mRNAs (DEMs) and lncRNAs (DELs) in UC samples compared with healthy samples were identified, meanwhile, differential methylation promoters (DMPs) in UC samples compared with healthy controls were obtained. Besides, functional enrichment analyses, and construction of functional regulatory and interaction network were conducted. Finally, DEMs and DELs was verified by qRT-PCR experiment and potential therapeutic targets for the development of novel treatments was preliminary identified.

first: Hongmei

last: Guo


title: Differential plasma exosomal long non-coding RNAs expression profiles and their emerging role in E-cig users, cigarette, waterpipe and dual smokers

city: Rochester

first: Irfan

last: Rahman

state: NY

address: 601 elmwood ave

department: Environmental Medicine

institute: University of Rochester Medical Center

summary:
Long non-coding RNA (lncRNA) are the varied set of transcripts that are known to play a critical role in biological processes like gene regulation, transcription, post-transcriptional modification, and chromatin remodeling.
Recent studies have reported the presence of lncRNA in the exosomes and have proven their involvement in regulating cell-to-cell communication in lung pathologies including lung cancer, chronic obstructive pulmonary disease (COPD), asthma, and idiopathic pulmonary fibrosis (IPF).

overall_design: In this study, we compared the lncRNA profiles in the plasma-derived exosomes amongst non-smokers (NS), cigarette smokers (CS), E-cig users (E-cig), waterpipe smokers (WP) and dual smokers (CSWP) using GeneChip™ WT Pico kit for transcriptional profiling.

first: Gagandeep

last: Kaur

first: Kameshwar

last: Singh

first: Krishna

last: Maremanda

first: Dongmei

last: Li

first: Hitendra

last: Chand


title: Heat Shock Factor 1-dependent extracellular matrix remodeling mediates the transition from chronic intestinal inflammation to colon cancer

city: Rehovot

first: Ruth

last: Scherz-Shouval

address: Hertzel 234

department: Biomolecular sciences

country: Israel

institute: Weizmann institute of science

summary: Chronic inflammation underlies tumor initiation, progression, invasion, and metastasis. In the colon, long-term exposure to chronic inflammation drives colitis associated colon cancer (CAC) in patients with inflammatory bowel disease (IBD). While the causal and clinical links between chronic inflammation and CAC are well established, our molecular understanding of how chronic inflammation leads to the development of colon cancer is still lacking. Here we deconstruct the evolving microenvironment of CAC, by measuring proteomic changes and extracellular matrix (ECM) organization over time in a genetically modified mouse model of CAC. We detect early changes in ECM structure and composition, and report that the transcriptional regulator heat shock factor 1 (HSF1) plays a crucial role in orchestrating these events. Activated in stromal fibroblasts of the gut, HSF1 promotes ECM remodeling and inflammatory programs which lead to the development of CAC. Loss of HSF1 abrogates ECM assembly by colon fibroblasts in cell culture, prevents inflammation-induced ECM remodeling in mice and significantly inhibits progression to CAC. Establishing the relevance of our experimental findings to human disease, we find high activation of stromal HSF1 in CAC patients, and detect the HSF1-dependent proteomic ECM signature in human colorectal cancer. Thus, HSF1-dependent ECM remodeling plays a crucial role in mediating inflammation-driven colon cancer.

overall_design: Bulk RNA expression of 8 samples, in duplicate for each condition, from 9.5 week old HSF1-null and HSF1 WT mice treated and not treated(Control) with one cycle of AOM-DSS

first: Oshrat

last: Levi-Galibov

first: Hagar

last: Lavon

first: Rina

last: Wassermann-Dozorets

first: Meirav

last: Pevsner-Fischer

first: Shimrit

last: Mayer

first: Esther

last: Wershof

first: Yaniv

last: Stein

first: Lauren

last: Brown

first: Gil

last: Friedman

first: Reinat

last: Nevo

first: Ofra

last: Golani

first: Lior

last: Katz

first: Rona

last: Yaeger

first: Ido

last: Laish

first: John

last: Porco Jr

first: Erik

last: Sahai

first: Dror

last: Shouval

first: David

last: Kelsen


title: Genome-wide expression profiling of acute promyelocytic leukemia NB4 cells treated with all-trans-retinoic acid

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

summary: Acute promyelocytic leukemia (APL) is a hematological disease characterized by a balanced reciprocal translocation that leads to the synthesis of the oncogenic fusion protein PML-RARα. APL is mainly managed by a differentiation therapy based on the administration of all-trans retinoic acid (ATRA) and arsenic trioxide (ATO). However, therapy resistance, differentiation syndrome, and relapses require the development of new low-toxicity therapies based on the induction of blasts differentiation. Here, we performed a high-throughput gene expression profile of the maturation inducible APL cell line NB4 untreated or exposed to ATRA.

overall_design: We performed a whole mRNA transcriptome analysis by Affymetrix microarray of NB4 cells exposed to 1 µM ATRA for 120h or only to DMSO as control (Ctrl). Two biological replicates were performed for each condition.

first: Alessandra

last: Di Masi


title: Structural basis of virulence activation in Francisella tularensis

city: Boston

first: Simon

last: Dove

state: MA

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

summary: The bacterium, Francisella tularensis (Ft), is one of the most infectious agents known and classified as a category A bioweapon. Ft virulence is controlled by a unique set of transcription regulators, the MglA-SspA heterodimer, PigR, and the stress signal, ppGpp. These factors activate Francisella pathogenicity island (FPI) gene expression, which is required for virulence. MglA-SspA is expressed during infection and constitutively associates with the σ70 associated RNAP holoenzyme (RNAPσ70), indicating that RNAPσ70-(MglA-SspA) is a virulence specific polymerase. How virulence activation is mediated by these components, however, is unknown. Here we report cryo-EM structures of FtRNAPσ70, FtRNAPσ70-(MglA-SspA) and RNAPσ70-(MglA-SspA)-ppGpp-PigR complexes with promoter DNA. FtRNAPσ70-DNA and FtRNAPσ70-(MglA-SspA)-DNA structures and RT-PCR analyses show MglA-SspA stabilizes σ70 binding to DNA to regulate FPI-independent, virulence-enhancing genes. Strikingly, an Escherichia coli RNAPσ70 complex with EcSspA suggests this is a general mechanism for SspA-like regulation of bacterial RNAPσ70. Finally, our FtRNAP-σ70-(MglA-SspA)-ppGpp-PigR-DNA structure reveals that ppGpp binds to MglA-SspA to tether the DNA-binding activator, PigR, to FPI promoters. PigR in turn recruits FtRNAP CTDs to two DNA upstream (UP) elements, generating stable FPI transcription complexes. Thus, these studies unveil a novel paradigm for pathogenesis in Ft involving a virulence-specific RNAP that employs two (MglA-SspA)-based strategies to activate virulence genes.

overall_design: Comparision of transcript abundance in F. tularensis cells with and without MglA or PigR

first: Brady

last: Travis

first: Kathryn

last: Ramsey

first: Samantha

last: Prezioso

first: Thomas

last: Tallo

first: Jamie

last: Wandzilak

first: Allen

last: Hsu

first: Mario

last: Borgnia

first: Alberto

last: Bartesaghi

first: Richard

last: Brennan

first: Maria

last: Schumacher


title: CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

city: Saarbrücken

first: Tobias

last: Fehlmann

address: Campus E2 1

institute: Saarland University

summary: Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach relying on nucleotide labeling by re-usable antibodies, but whether it is applicable to scRNA-seq, has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS. To assess the quality and performance of converted libraries, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and, after conversion, on a DNBSEQ-400RS. CoolMPS-derived results were in very high agreement with the Illumina dataset, and we demonstrate how technical variance between both technologies is significantly lower when compared to biological variance. Indeed, CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.

overall_design: Single-nuclei RNA transcriptomes of hippocampus tissue extracted from 2 months (young) and 18 months (old) C57BL/6J male wild-type mice. Libraries were sequenced on an Illumina instrument and, after chemical conversion, on an MGI DNBSEQ-400RS using CoolMPS technology.

first: Oliver

last: Hahn

first: Hui

last: Zhang

first: Andreas

last: Keller

first: Tony

last: Wyss-Coray


title: Single cell transcriptomic heterogeneity in invasive ductal and lobular breast cancer cells

city: Pittsburgh

first: Fangyuan

last: Chen

state: PA

address: 204 Craft Avenue

institute: University of Pittsburgh

summary: Invasive lobular breast carcinoma (ILC), one of the major breast cancer histological subtypes, exhibits unique clinical and molecular features compared to the other well-studied ductal cancer subtype (IDC). The pathognomonic feature of ILC is loss of E-cadherin, mainly due to inactivating mutations within the CDH1 gene, but the extent of contribution of this genetic alteration to ILC-specific molecular characteristics remains largely understudied. To profile these features transcriptionally, we conducted single cell RNA sequencing on a panel of IDC and ILC cell lines, as well as an IDC cell line (T47D) with CRISPR-mediated knock out (KO) of CDH1. Inspection of intra-cell line heterogeneity illustrated genetically and transcriptionally distinct subpopulations in multiple cell lines and highlighted rare populations of cells with long latency and an apoptosis-related signature indicative of dormancy. Investigation of CDH1 KO-induced alterations showed transcriptomic membranous systems remodeling, elevated regulon activation resemblance of T47D CDH1 KO cells to ILCs, and suggests IRF1 as a major regulator of the pro-apoptotic and anti-proliferative feature of ILCs.

overall_design: scRNA-seq data of a mixture of 9 groups of cells of 8 cell lines: MCF7 (MCF7 wild type and MCF7 with ESR1 Y537S mutation), T47D wild type, T47D with CDH1 knock out (CRISPR), MDA-MB-134-VI, SUM44-PE, BCK4, MCF10A, and HEK293; using 10X Genomics 3' Chromium v3.0 and Illumina NovaSeq 6000 System.

first: Kai

last: Ding

first: Nolan

last: Priedigkeit

first: Ashuvinee

last: Elangovan

first: Steffi

last: Oesterreich

first: Adrian

middle: V

last: Lee


title: Fatostatin/Saracatinib drug treatment of mouse primary microglia cultures

first: Jessica

middle: Erin

last: Rexach

address: 2506 Gonda Bldg, 695 Charles E. Young Dr. South

department: Neurology

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

overall_design: Refer to individual Series


title: Fatostatin drug treatment of mouse primary microglia cultures

summary: To test the effect of fatostatin on gene expression patterns in microglia, we treated mouse (C57BL/6) primary microglial cultures with  fatostatin (5microM, 72h) versus DMSO-only control and quantified gene expression using 3' end labeling.  Sequencing libraries were prepared using the Lexogen QuantSeq 3'Forward kit and sequencing of single end reads (1 x 65) was performed on an Illumina HiSeq 4000 at 5M reads per sample.   For processed data, reads were aligned against GRCm38 using STAR. Transcripts were quantified and annotated against GencodeM11 using Rsubread.  Samples were normalized with CQN.

overall_design: Mouse primary cultures were treated with fatostatin versus DMSO vehicle control; and RNAseq performed using Lexogen QuantSeq 3' Forward kit.

first: Daniel

last: Geschwind


title: Next Generation Sequencing Facilitates Quantitative Analysis of SREBP transgenic and SREBP/Endotrophin Transcriptomes

city: dallas

first: Philipp

last: Scherer

address: 5323 harry hines

institute: UTsouthwestern

summary:
Purpose: The goals of this study are to compare NGS-derived liver transcriptome profiling (RNA-seq).
Methods: Alb-CRE/rosa26 rtTA/SREBP(S1a/Ctrl) vs Alb-CRE/rosa26 rtTA/SREBP/TRE-ETP (S1a/ETP) transgenic mice liver (RNAseq)
Results: an increase in the levels of markers that are important for immune responses and inflammation and initiating and promoting tumour growth . In addition, genes abundantly expressed in neutrophils (Elane, Mpo, Ngp, Prtn3, Chil3, Cd177, S100a8, S100a9, and Lcn-2) were up-regulated
Conclusions: Our data reveal that ETP can act as a “second hit” during NAFLD progression and can play an important role in the development of NASH and hepatocellular carcinoma (HCC).

overall_design: RNAseq experiment on livers from S1a/Ctrl and S1a/ETP mice . RNA from three mice(pooled) were used per group (doxycycline(200mg/kg) treatment for 10 months).

first: Scherer

last: Philipp


title: Gene expression data from lung 1 day after influenza infection with liraglutide

city: Akita

first: Takehiro

last: Sato

state: Akita

address: Hondo 1-1-1

department: Endocrinology, Diabetes, and Geriatric Medicine

country: Japan

institute: Akita University

summary: We found liraglutide ameliorates influenza virus infection in mice.Using a microarray, we identified a group of up-regulated  genes  that could explain influenza improvement.

overall_design: Mice were anesthetized and A/Puerto Rico/8/34 (H1N1; PR8) influenza virus (10 TCID50/50μl) was intratracheally administered to each mouse. Liraglutide(200 μg per kg body weight/0.2ml) or saline (0.2ml) are subcutaneously injected to each mice(n=each 3). One day after the infection, the lung was excised and the gene expressions were analyzed.

first: Yumiko

last: Imai

first: Yuichiro

last: Yamada


title: Expanding the transcriptomic sequence space in leukaemia by RUNX1/RUNX1T1-mediated alternative splicing

city: Newcastle Upon Tyne

first: Olaf

last: Heidenreich

address: Brewery Lane

department: Wolfson Childhood Cancer Research Centre

institute: Newcastle University

summary: The fusion oncogene RUNX1/RUNX1T1 encodes an aberrant transcription factor, which plays a key role in the initiation and maintenance of acute myeloid leukaemia. In this study we comprehensively identify and characterize splicing events associated with RUNX1/RUNX1T1. We show that this oncogene is a regulator of the alternative RNA splicing in leukaemic cells. We found two principal mechanisms underlying changes in the production of RNA isoforms: (i) RUNX1/RUNX1T1-mediated regulation of alternative transcription start sites selection, and (ii) direct or indirect control of the expression of the genes encoding splicing factors. The first mechanism leads to the expression of RNA isoforms with alternative structure of the 5’-UTR regions. The second mechanism generates alternative transcripts with new junctions between internal cassettes and constitutive exons. We also show that RUNX1/RUNX1T1-mediated differential splicing affects several functional groups of genes and produces proteins with unique conserved domain structures. In summary, this study reveals a novel layer of transcriptome re-organization in leukaemia by an aberrant transcriptional regulator.

overall_design: Nascent RNA-sequencing of t(8;21)-positive AML, Kasumi-1 cell line, with siRNA targeting the fusion site of the RUNX1/RUNX1T1 mRNA (siRR) and a mismatch siRNA (siMM) served as a control

first: Vasily

last: Grinev

first: Farnaz

last: Barneh

first: Ilya

last: Ilyushonak

first: Sirintra

last: Nakjang

first: Job

last: Smink

first: Anita

last: van Oort

first: Richard

last: Clough

first: Michael

last: Seyani

first: Hesta

last: McNeill

first: Mojgan

last: Reza

first: Natalia

last: Martinez-Soria

first: Salam

last: Assi

first: Tatsiana

last: Ramanouskaya

first: Constanze

last: Bonifer


title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer [single-cell RNA-seq tumor]

status: Public on Nov 04 2020

first: Sarah

middle: J.

last: Hill

address: 450 Brookline Avenue

department: Department of Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Immune therapies have had limited efficacy in high grade serous ovarian cancer (HGSC). The cellular targets and mechanism(s) of action of these agents in HGSC are unknown. Here we performed immune functional and single cell RNA sequencing transcriptional profiling on novel HGSC organoid/immune cell co-cultures treated with a variety of immune checkpoint blockade (ICB) antibodies compared to controls.

overall_design:
Single cell RNA seq on immune cells from organoid parent tumor from one patient.
>>>Raw data not available due to patient privacy concerns<<<

first: Changxin

last: Wan


title: Saracatinib drug treatment of mouse primary microglia cultures

first: Jessica

last: Rexach

summary: To test the effect of saracatinib on gene expression patterns in microglia, we treated mouse (C57BL/6) primary microglial cultures with saracatinib (1microM, 24h) versus DMSO vehicle control and quantified gene expression.  Sequencing libraries were prepared using the Lexogen QuantSeq 3'Forward kit with sequencing performed on an Illumina HiSeq 4000 (single end reads 1 x 65; 5M reads per sample).   For processed data, reads were aligned against GRCm38 and quantified using STAR.  Samples were normalized with CQN.  Batch correction was completed using ComBat from sva version 3.6.0.

overall_design: Mouse primary cultures were treated with saracatinib versus DMSO vehicle control; and RNAseq performed using Lexogen QuantSeq 3' Forward kit.

first: Daniel

last: Geschwind


title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer [single-cell RNA-seq organoid]

overall_design:
single cell RNA seq on immune cells from organoid co-cultures.

>>>Raw data not available due to patient privacy concerns<<<


title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer [bulk RNA-seq tumor]

overall_design:
Bulk RNA seq on 13 tumor samples

>>>Raw data not available due to patient privacy concerns<<<


title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer


title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer [ATAC-seq]

overall_design:
Case set, ATACseq on a treated NK cell line KHYG1

>>>Raw data not available due to patient privacy concerns<<<


title: Male fertility in plants requires active DNA demethylation of genes that control pollen tube funcion

city: Lyon

last: Bouyer

address: 46 Allée d'Italie

department: ENS-Lyon/RDP

institute: CNRS

type: Methylation profiling by high throughput sequencing

summary: We show that in model plant Arabidopsis thaliana, the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) of the model plant Arabidopsis thaliana act semi-redundantly in pollen for hypomethylation of the vegetative cell, required for the activation of key genes involved in pollen tube function

overall_design: Whole genome sequencing of bisulfite-converted genomic DNA was carried out on sperm cells and vegetative cells of Arabidopsis thaliana wild type (Col-0 accession), ros1, dme/+ and dme/+;ros1 mutants

first: Filipe

last: Borges


title: Enhanced efficacy of simultaneous PD-1 and PD-L1 immune checkpoint blockade in high grade serous ovarian cancer [bulk RNA-seq immune cells]

overall_design:
Case set,  bulk RNA seq on sorted T and NK cells from treated organoid co-cultures

>>>Raw data not available due to patient privacy concerns<<<


title: Determine in vivo the contribution of distal intestinal segments to calcium homeostasis and bone mineralization

city: Piscataway

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

summary: To explore this question, we will use three different male mouse models including VDR KO mice and transgenic mice with hVDR only expressed in the distal intestine (KO/VDR-Tg). All the mice which are C57BL6J background will be raised until 2-3 months old with standard chow diet (n=3 mice per genotype group). Compared to the KO/VDR-Tg mice without any injection, the same type of mice will be administered 1 ng/g bw 1,25(OH)2D3 at 48, 24 and 6 hours prior to termination to determine both early and late effects of 1,25(OH)2D3.

overall_design: Mouse data comprising RNA-Seq from 21 samples was obtained: 11 from the colon (4 VDR knockout replicates, 3 VDR uninjected replicates, 4 VDR vitamin D treated replicates) and 10 from the ileum (4 VDR knockout replicates, 3 VDR uninjected replicates, 3 VDR vitamin D treated replicates).

first: Puneet

last: Dhawan

first: Rohit

last: Aita

first: Shanshan

last: Li

first: Sylvia

last: Christakos


title: Gene expression profiling in myelodysplastic syndrome patients treated with deferasirox

city: Prague 2

first: Hana

last: Votavova

address: U Nemocnice 1

department: Genomics

country: Czech Republic

institute: Institute of Hematology and Blood Transfusion

summary: Deferasirox (DFX) is an oral iron chelator used to reduce iron overload caused by frequent red blood cell transfusions in anemic myelodysplastic syndrome (MDS) patients. To study molecular mechanisms by which DFX improves outcome in MDS, we analyzed  gene expression patterns in MDS patients before and after DFX therapy.

overall_design: Total RNA was isolated from bone marrow CD34+ cells obtained from MDS patients before and after DXF treatment. Gene expression profiles were assayed using Illumina Human HT-12 v. 4 microarrays and the data were validated by RT-qPCR.

first: Zuzana

last: Urbanova

first: Monika

last: Hruba

first: David

last: Kundrat

first: Michaela

last: Merkerova Dostalova

first: Anna

last: Jonasova

first: Jaroslav

last: Cermak

first: Vladimir

last: Divoky

last: Belickova


title: HDAC inhibition ameliorates cone survival in retinitis pigmentosa mice

city: Saclay

first: Jerome

middle: Eric

last: Roger

state: Please select

address: 151 Route de la Rotonde, Campus CEA Saclay - Bat 151

department: CERTO

institute: CNRS-Universite Paris Sud

summary: Cone photoreceptor cell death in inherited retinal diseases, such as Retinitis Pigmentosa (RP), leads to the loss of accurate and color vision and ultimately blindness. In RP, a vast number of mutations are affecting the structure and function of rod photoreceptors while cones remain mutation-free. Once majority of rods have degenerated cones are dying secondarily due to the increased oxidative stress, inflammation and loss of structural and nutritional support normally provided by rods. Here we demonstrated that secondary cone cell death in animal models for RP is governed by an increased activity of histone deacetylates (HDACs). A single intravitreal injection of an HDAC inhibitor at a late stage of the disease, when majority of rods have already degenerated, is sufficient to delay cone death and support long-term cone survival. Surviving cones are retaining functionality and are mediating light-driven ganglion cell responses. RNA-seq analysis of surviving cones demonstrated that HDAC inhibition affords multi-level protection trough regulation of different prosurvival pathways including MAPK, PI3K-AKT and autophagy. These study suggest a unique possibility for targeted pharmacological protection of both primary degenerating rods and mutation-free secondary dying cones and creates hope to maintain vision in RP patients independent of the disease stage.

overall_design: 2000 to 5000 frozen sorted-cells were lysed in approximatively 10µl of lysis buffer and cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit (catalog 634888, Takara Bio). First-strand cDNA synthesis was performed using 20 to 50% of the input and was followed by full-length double-strand cDNA amplification using 17 PCR cycles. Quality of the resulting cDNA was validated using Bioanalyzer and High Sensitivity DNA Kit (Agilent) as well as Qubit dsDNA HS fluorometric quantification (ThermoFisher Scientific). NGS libraries were prepared using 150 pg of cDNA input and the Nextera XT DNA Library Preparation Kit (catalog FC-131-1024, Illumina) with 11 cycles of PCR.

first: Marijana

last: Samardzija

first: Andrea

last: Corna

first: Raquel

last: Gomez-Sintes

first: Mohamed

last: Jarboui

first: Angela

last: Armento

middle: E

first: Eleni

last: Petridou

first: Wadood

last: Haq

first: Francois

last: Paquet-Durand

first: Eberhart

last: Zrenner

first: Günther

first: Christian

last: Grimm

first: Patricia

first: Marius

last: Ueffing

first: Dragana

last: Trifunović


title: The small RNAs PA2952.1 and prrH as regulators of virulence, motility and iron metabolism in Pseudomonas aeruginosa

city: Vancouver

first: Shannon

last: Coleman

state: BC

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

summary:
Purpose: Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that undergoes swarming motility in response to semisolid conditions with amino acids as a nitrogen source. With a genome encoding hundreds of potential intergenic small RNAs (sRNAs), P. aeruginosa can easily adapt to different conditions and stresses. We previously identified 20 sRNAs dysregulated under swarming conditions and here provide phenotypic characterization for these sRNAs.
Methods: Here, these sRNA were overexpressed in strain PAO1 and subjected to an array of phenotypic screens.
Results: Overexpression of prrH resulted in decreased swimming motility, while a ∆prrH mutant had decreased cytotoxicity and increased pyoverdine production. Overexpression of the previously uncharacterized PA2952.1 resulted in decreased swarming and swimming motility, increased gentamicin and tobramycin resistance under swarming conditions, and increased trimethoprim susceptibility. RNA-Seq and proteomics were performed on the wildtype overexpressing PA2952.1 cf. the empty vector control under swarming conditions, and revealed the differential expression of 784 genes and differential abundance of 445 proteins. Amongst these were found 82 transcriptional regulators, two-component systems, sigma and anti-sigma factors. Downstream effectors included downregulated pili, dysregulated flagellar genes, the upregulated efflux pump MexGHI-OpmD, the upregulated arn operon, and downregulated DNA synthesis genes. Genes involved in iron and zinc uptake were also dysregulated, and certain pyoverdine and phenazine genes were upregulated.
Conclusions: Overall, the sRNAs PA2952.1 and prrH appeared to be involved in regulating virulence-related programs in P. aeruginosa, including iron acquisition and motility.

overall_design: Five biological replicates of the wildtype strain overexpressing PA2952.1 were compared to five biological replicates of the wildtype with the empty vector as a control.

middle: R

first: Maren

last: Smith

first: Victor

last: Spicer

first: Ying

last: Lao

first: Patrick

last: Taylor

first: Neeloffer

last: Mookherjee

first: Robert

last: Hancock


title: Control of root thermomorphogenesis by systemic and local regulatory signals (4h RNA-seq)

city: Ghent

first: Thomas

last: Jacobs

address: Technologiepark-Zwijnaarde, 71

country: Belgium

institute: VIB Center for Plant Systems Biology

summary: Temperature is one of the most impactful environmental factors in response to which plants adjust their growth and development. While the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here we found that shoot and root growth responses to high ambient temperature are negatively correlated during early seedling development. A shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these responses and triggers long-distance signaling to control root growth and auxin levels in the root. In addition to the HY5/PIF dependent shoot module, a local regulatory axis composed of auxin biosynthesis and auxin perception factors mediates root responses to high ambient temperature. Together, our findings uncover that roots integrate long-distance signals with local hormonal inputs during thermomorphogenesis.

overall_design: Analysis of short-term (4hours) response to higher ambient temperature in wild type, hy5 and phyAB plants

first: Wolfgang

last: Busch

first: Christophe

last: Gaillochet


title: Control of root thermomorphogenesis by systemic and local regulatory signals (18h RNA-seq)

overall_design: Analysis of long-term (18hours) response to higher ambient temperature in wild type, hy5 and phyAB plants


title: Control of root thermomorphogenesis by systemic and local regulatory signals

overall_design: Refer to individual Series


title: Characterization of human non-hematopoietic bone marrow cells in non-fibrotic and fibrotic conditions

status: Public on Nov 03 2020

city: Aachen

first: Ronghui

last: Li

address: Pauwelsstr. 19

institute: RWTH Aachen

summary: We isolated non-hematopoietic cells from fibrotic and non-fibrotic human bone marrow and perfomed scRNAseq on them. We identified 3 different stromal populations and 2 populations of hematopoietic progenitors. Our analysis revealed mesenchymal stromal cells (MSC) as pro-fibrotic cells. MSCs were functionally reprogrammed with loss of their progenitor status and acquisition of a pro-fibrotic phenotype in the fibrotic bone marrow. Additionally, stromal cells exhibited an upregulation of pro-inflammatory mediators like S100A8/A9.

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to profile human non-fibrotic bone marrow as well as bone marrow with diagnosed myelofibrosis

first: Nils

middle: B

last: Leimkühler

first: Hélène

last: Gleitz

first: Rafael

last: Kramann

first: Ivan

middle: G

last: Costa

first: Rebekka

middle: K

last: Scheider


title: Dissecting the functional reprogramming and drug targets of the microenvironment in bone marrow fibrosis by single cell mapping


title: Tracking Epigenetic Modification-Mediated Genome Organization

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

country: China

institute: Tsinghua University

summary: Spatiotemporal control of chromatin structure and dynamics at sub-kilobase to megabase scales is essential for genome function. Epigenetic modification plays important roles in transcriptional regulation. How histone marks regulate genome organization at different scales remain unclear. Here we introduce an EpiGo (Epigenetic perturbation induced Genome organization) system to modify hundreds of genomic loci with H3K9me3 spanning megabases on human chromosome 19 and simultaneously track their changes of genome organization. EpiGo-mediated H3K9me3 spreads more extensively in transcriptionally inactive regions than active regions. H3K9 trimethylation of active regions trigger local chromatin compaction without substantial gene silencing. H3K9 trimethylated loci or regions associate with HP1a condensates and adjacent loci with H3K9me3 coalesce over time. H3K9 trimethylation of inactive regions reshape local genome compartmentalization. These results reveal that H3K9me3 mediates local chromatin compaction or genome compartmentalization upon distinct transcriptional states.

overall_design: We introduce an EpiGo (Epigenetic perturbation induced Genome organization) system to modify hundreds of genomic loci with H3K9me3 spanning megabases on human chromosome 19 and simultaneously track their changes of genome organization.

last: Feng

first: Yao

last: Wang

first: Hanhui

last: Ma


title: Development and validation of a NanoString BASE47 bladder cancer gene classifier

city: Chapel Hill

first: Kim Lab

last: UNC

state: NC

address: 450 West Drive, Room 21-209

country: USA

institute: UNC-CH LCCC

summary:
Purpose: We sought to develop and evaluate a diagnostic classifier of UC subtype with the goal of accurate classification from clinically available specimens.
Methods: Tumor samples from 52 patients with high-grade UC were profiled for BASE47 genes concurrently by RNAseq as well as NanoString. After design and technical validation of a BASE47 NanoString probeset, results from the RNAseq and NanoString were used to translate diagnostic criteria to the Nanostring platform. Evaluation of repeatability and accuracy was performed to derive a final Nanostring based classifier.  Diagnostic classification resulting from the NanoString BASE47 classifier was validated on an independent dataset (n=63). The training and validation datasets accurately classified 87% and 93% of samples, respectively.
Results: We have derived a NanoString-platform BASE47 classifier that accurately predicts basal-like and luminal-like subtypes in high grade urothelial cancer. We have further validated our new NanoString BASE47 classifier on an independent dataset and confirmed high accuracy when compared with our original Transcriptome BASE47 classifier.
Conclusions: The NanoString BASE47 classifier provides a faster turnaround time, a lower cost per sample to process, and maintains the accuracy of the original subtype classifier for better clinical implementation.

overall_design: RNASeq of macrodissected FFPE tumor samples from 52 muscle-invasive urothelial cancer patients

first: William

middle: Y

last: Kim

first: Jordan

last: Kardos

first: Tracy

last: Rose

first: Ujjawal

last: Manocha


title: Examination of gene expression in different populations of the embryonic thymus at E15.5 and E19.5 by bulk RNA-seq

city: Cambridge

first: Alastair

last: Crisp

address: Francis Crick Avenue

institute: MRC Laboratory of Molecular Biology

summary: ILC2 contribute to immune homeostasis, protective immunity and tissue repair.  However, an understanding of the microenvironmental factors and transcriptional circuits that support development of these innate lymphocytes within lymphoid organs, alongside their adaptive T and B cell relatives, is only starting to emerge.  Here we demonstrate that functional ILC2 arise in the embryonic thymus, from shared T cell precursors, and precede the emergence of CD4+CD8+ (double-positive) T cells.  Strikingly, RORa expression repressed T cell development, whilst promoting ILC2 in the thymus. Thymic ILC2 go on to contribute to the innate type-2 response at mucosal tissues with preferential colonisation of the intestinal lamina propria.  From RNAseq, ATACseq and ChIPseq data we propose a revised transcriptional circuit to explain the enigmatic co-development of T cells, ILC2 and NK cells from common progenitors in the thymus.  When Notch signalling is present, Bcl11b dampens Nfil3/Id2 expression, permitting E protein-directed T cell commitment.  However, concomitant expression of RORa overrides the Nfil3/Id2 repression, allowing Id2 to repress E proteins and promote ILC2 differentiation.  Thus, we demonstrate that RORa expression represents a critical checkpoint at the bifurcation of the T cell and ILC2 lineages in the embryonic thymus.

first: Ana

last: Ferreira

first: Jennifer

last: Walker

first: Paula

last: Clark

first: Jillian

last: Barlow

first: Morgan

last: Heycock

first: Sophie

last: Kitching

first: Alfred

last: Lim

first: Mayuri

last: Gogoi

first: Aydan

last: Szeto

first: Richard

last: Berks

first: Maria

last: Daly

first: Helen

last: Jolin

first: Andrew

middle: J

last: McKenzie


title: Single cell RNA-seq (10X Chromium 3') analysis of the DN1 population from E15.5 embryonic thymus of the 5x polychromILC mice

overall_design: Single cell RNA-seq analysis of the DN1 population from E15.5 embryonic thymus of the 5x polychromILC mice

middle: A


title: RORa expression is a critical checkpoint for the bifurcation of the T cell and ILC2 lineages in the embryonic thymus

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


title: Single cell RNA-seq (smartseq2) analysis of the ETP population from E15.5 embryonic thymus of the 5x polychromILC mice

overall_design: Single cell RNA-seq analysis of the ETP population from E15.5 embryonic thymus of the 5x polychromILC mice


title: Characterization of murine non-hematopoietic bone marrow cells in non-fibrotic, pre-fibrotic and fibrotic conditions

first: Ronghui

last: Li

summary: We isolated non-hematopoietic cells from fibrotic and non-fibrotic mouse bone marrow and perfomed scRNAseq on them. We identified 8 different stromal populations. Our analysis revealed two distinct mesenchymal stromal cells (MSC) subsets as pro-fibrotic cells. MSCs were functionally reprogrammed in a stagedependent manner with loss of their progenitor status and initiation of differentiation in the prefibrotic stage and acquisition of a pro-fibrotic and inflammatory phenotype in the fibrotic stage. In parallel, IL-33-expressing myelinating Schwann cell progenitors expanded, likely as a repair mechanism for the previously described neuropathy in MPN.

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to profile murine non-fibrotic bone marrow as well as bone marrow with Thrombopoietin- and JAK2V617F-induced myelofibrosis

first: Nils

last: Leimkühler

first: Hélène

last: Gleitz

first: Rafael

last: Kramann

first: Ivan

last: Costa

first: Rebekka

last: Scheider


title: LncRNAs Landscape in the patients of primary gout by Microarray Analysis

city: Nanchong City

first: daifei

last: dai

state: Sichuan Province

address: No. 234, Fujiang Road, Shunqing District

institute: North Sichuan Medical College

summary: To determine the expression profile and clinical significance of long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with primary gout and healthy control subjects. Human lncRNA microarrays were used to identify the differentially expressed lncRNAs and mRNAs in primary gout (n=6) and healthy subjects (n=6). Bioinformatics analyses were performed to predict the roles of differently expressed lncRNAs and mRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was applied to validate the results in 64 gout patients, and 32 healthy control subjects (HC). The microarray analysis identified 1479 differentially expressed lncRNAs (879 up-regulated and 600 down-regulated), 862 differentially expressed mRNAs (390 up-regulated and 472 down-regulated) in primary gout (fold change>2, P<0.05), respectively. The bioinformatic analysis indicated that the differentially expressed lncRNAs regulated the abnormally expressed mRNAs, which were involved in the pathogenesis of gout through several different pathways. Significant association was observed between these lncRNAs and the Clinical inflammation indicators and lipid metabolism indicators. Our results provide novel insight into the mechanisms of primary gout, and reveal that  ENST00000566457 and NR-026756 could effectively discriminate the gout group and the healthy control groups.

overall_design: Two-condition experiment：primary gout patients vs. healthy control subjects peripheral blood mononuclear cells. Biological replicates: 6 gout patients replicates，6 controls replicates.

first: Yufeng

last: Qing

first: Jianxiong

last: Zheng

first: Yiping

last: Tang

first: Fei

last: Dai

first: Zengrong

last: Dong

first: Quanbo

last: Zhang


title: Transcriptomic analysis of a symbiotic poxvirus in parasitoid wasps and fly hosts

city: Hilo

first: Kelsey

last: Coffman

state: HI

address: 64 Nowelo St

department: Tropical Pest Genetics and Molecular Biology Research Unit

institute: USDA-ARS

summary: Parasitoid wasps of the species Diachasmimorpha longicaudata are associated with a heritable poxvirus, known as DlEPV, that is stored in the venom gland of adult female wasps and transferred to tephritid fly hosts of the wasps during oviposition. We conducted a RNA-seq differential expression analysis to gain insight on how DlEPV can replicate in both wasps and their fly hosts but only cause pathogenic effects during replication in flies. Our analysis revealed that 91.2% (176 of 193) of DlEPV genes showed significant differential expression during peak virus replication in wasp venom glands compared to parasitized flies. Over 80% of DlEPV replication genes were significantly upregulated in wasps, while 79% of DlEPV putative virulence genes were significantly upregulated in fly hosts. These data therefore support a dichotomy of viral function, where virus replication is promoted in wasp tissue and virulence in host tissue. Such a division of viral activity could represent an important adaptation to maintain a stable symbiosis between this virus and its associated parasitoid.

overall_design: Two tissue types, wasp venom gland tissue and fly whole body tissue, were sequenced during peak virus replication, including 6 replicates each.

first: Gaelen

last: Burke


title: Genome-wide occupancy of Hes protein Deadpan in neural stem cells from Drosophila 3rd instar larvae

city: Linkoping

first: Srivathsa

last: Magadi

address: Campus US, Building 463 Cellbiologen, Entrance 64

department: Department of Biomedical and Clinical Sciences (BKV) Division of Molecular Medicine and Virology (MMV)

country: Sweden

institute: Linkoping University

summary: Excessive activation of Hes causes stem cell hyperplasia in larval CNS. Chromatin occupancy of Hes transcription factor Deadpan was analysed using Next genration sequencing ChIP-seq

overall_design: Using NGS genome-wide Deadpan occupancy was analysed

first: Christos

last: Delidakis


title: Transcriptome analysis of S. glabra in response to MeJA

city: Guangzhou

first: Niu

last: Yu

address: Number 682, Guangshan Yi Road, Longdong

institute: Research Institute of Tropical Forestry, Chinese Academy of Forestry

summary: We studied the MeJA response processes at four time points in Sindora glabra, which accumulates abundant sesquiterpenes in the tree trunk. Across the time course, differentially expressed genes involved in terpenoid backbone biosynthesis were significantly enriched, while JAZ genes involved in jasmonic acid pathway and TGA genes involved in salicylic acid pathway were significantly enriched at later time point after treatment.

overall_design: 12 samples were analyzed after MeJA treatment, each treatment contained three replicates

first: Zhaoli

last: Chen


title: Characterization of murine non-hematopoietic Gli1+ bone marrow cells in homeostasis

first: Ronghui

last: Li

summary: We performed fate tracing of Gli1+ cells in homeostasis. Sorted cells were subjected to scRNAseq and integrated with non-hematopoietic cells from mice with myelofibrosis induced by either ThPO- or JAK2V617F-overexpression. Gli1+tdTom+ cells largely overlap with pro-fibrotic adipogenic and osteogenic MSCs, which show a strong upregulation of ECM related transcripts. Additionally, a subgroup of Gli1+tdTom+ cells shows similarity with bone marrow SCPs.

overall_design: We used scRNA 3' RNA sequencing product from 10x Genomics to profile murine Gl1+tdTom+ non-hematopoietic bm cells in homeostasis.

first: Nils

last: Leimkühler

first: Hélène

last: Gleitz


title: Genome-wide Screens Identify Lineage- and Tumor-Specific Genes Modulating MHC-I- and MHC-II-Restricted Immunosurveillance of Human Lymphomas.

status: Public on Nov 02 2020

city: Bethesda

first: Devin

last: Dersh

state: MD

address: 33 North Drive

institute: NIH


title: Genome-wide Screens Identify Lineage- and Tumor-Specific Genes Modulating MHC-I- and MHC-II-Restricted Immunosurveillance of Human Lymphomas [DLBCL_GSK126]

summary: Tumors frequently subvert MHC class I (MHC-I) peptide presentation to evade CD8+ T cell immunosurveillance, though how this is accomplished is not always well-defined. To identify the global regulatory networks controlling antigen presentation, we employed genome-wide screening in human diffuse large B cell lymphomas (DLBCLs). This approach revealed dozens of genes that positively and negatively modulate MHC-I cell surface expression. Validated genes clustered in multiple pathways including cytokine signaling, mRNA processing, endosomal trafficking, and protein metabolism. Genes can exhibit lymphoma subtype- or tumor-specific MHC-I regulation, and a majority of primary DLBCL tumors displayed genetic alterations in multiple regulators. We established SUGT1 as a major positive regulator of both MHC-I and MHC-II cell surface expression. Further, pharmacological inhibition of two negative regulators of antigen presentation, EZH2 and thymidylate synthase, enhanced DLBCL MHC-I presentation. These and other genes represent potential targets for manipulating MHC-I immunosurveillance in cancers, infectious diseases, and autoimmunity.

overall_design: Paired-end RNAseq of mRNA isolated from patient-derived diffuse large B cell lymphoma cell lines treated with either DMSO or the EZH2 inhibitor GSK126 for 4 days. Conducted in triplicate

first: Jonathan

middle: W

last: Yewdell


title: Transcriptomic analysis of Diffuse Intrinsic Pontine Glioma (DIPG) identifies a targetable ALDH-positive subset of highly tumorigenic cancer stem-like cells

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

summary: Understanding the cancer stem-cell (CSC) landscape in diffuse intrinsic pontine glioma (DIPG) is desperately needed to address treatment resistance and identify novel therapeutic approaches. Patient derived DIPG cells demonstrated heterogeneous expression of aldehyde dehydrogenase (ALDH) and CD133 by flow cytometry. Transcriptome-level characterization identified elevated mRNA levels of MYC, E2F, DNA damage repair (DDR) genes, glycolytic metabolism and mTOR signaling in ALDH+ compared to ALDH- supporting a stem-like phenotype and indicating a druggable target. ALDH+ cells demonstrated increased proliferation and neurosphere formation and initiated tumors that resulted in decreased survival when orthotopically implanted. Pharmacological MAPK/PI3K/mTOR targeting downregulated MYC, E2F and DDR mRNAs and reduced glycolytic metabolism. In vivo PI3K/mTOR targeting inhibited tumor growth in both flank and an ALDH+ orthotopic tumor model likely by reducing cancer stemness. Characterization of DIPG CSCs coupled with targeting MAPK/PI3K/mTOR signaling provides an impetus for molecularly targeted therapy aimed at addressing the CSC phenotype in DIPG.

overall_design: Eight SU-DIPG-XIII samples were analyzed. Cells were maintained under normal cell culture conditions in T-75 flasks. At the time of treatments, each T-75 flask (at ~75% confluency there are 8x10^6 million cells) was centrifuged, conditioned media was saved, and cells were resuspended in 4 mL of the conditioned media and transfered to a new T-25 flask for treatment (one T-25 flask for every T-75 flask). Samples were treated with 100 nM of PD0325901 (PD-901), 100 nM of GSK2126458 (GSK-458), 50 nM PD-901 + 50 nM GSK-458 (combination) or equimolar DMSO for two hours prior to ALDEFLUOR Assay staining and FACS sorting into ALDH+ and ALDH- conditions. ALDH+ DMSO treated and ALDH- DMSO treated samples were used as controls for comparison.

first: Rachel

last: Surowiec

first: Sarah

last: Ferris

first: April

last: Apfelbaum

first: Carlos

last: Espinoza

first: Ranjit

last: Mehta

first: Karamoja

last: Monchamp

first: Veerin

last: Sirihorachai

first: Karan

last: Bedi

first: Stefanie

last: Galban


title: Examination of genomic accessibility in embryonic thymus cell populations by ATAC-seq

first: Alastair

last: Crisp

first: Ana

middle: C

last: Ferreira

first: Jennifer

last: Walker

first: Paula

last: Clark

first: Jillian

last: Barlow

first: Morgan

last: Heycock

first: Sophie

last: Kitching

first: Alfred

last: Lim

first: Mayuri

last: Gogoi

first: Aydan

last: Szeto

first: Richard

last: Berks

first: Maria

last: Daly

first: Helen

last: Jolin

first: Andrew

last: McKenzie


title: Alteration in the Culex pipiens transcriptome reveals the implication of the mosquito immune system during Rift Valley fever phlebovirus infection

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

country: Spain

institute: CNAG-CRG

summary: Rift valley fever (RVF) is an emerging zoonotic disease and it is caused by Rift valley fever phlebovirus (RVFV). This virus is commonly transmitted in endemic areas between wild ruminants and mosquitoes, mainly by mosquitoes of Culex and Aedes genus. Starting from 2000, several outbreaks have been reported outside the African continent, in countries facing the Mediterranean Sea, such as Saudi Arabia. The available vaccines for ruminants present limited efficacy or residual pathogenic effects. Consequently, new strategies are urgently required to limit the expansion of this zoonotic virus. The main objective of this work is to investigate the molecular responses of Culex pipiens to RVFV focusing mainly on genes implicated in the classical innate immunity pathways, RNAi mechanism and apoptosis process in order to elucidate the implicated genes in viral infection. The immune altered genes here described could be potential targets to control RVFV infection in mosquitoes. Some of the genes related to the immune defense response were previously described in others mosquito-arbovirus models, as also in Drosophila and human. To our knowledge, this study elucidates for the first time the Cx. pipiens-RVFV interaction in terms of defense infection-response, which was largely under studied and provides information to develop new approaches to prevent and control the expansion of the virus in the future.

overall_design: Examination of the virulent RVFV infection in Cx. pipiens mosquito interaction

middle: I

last: Nuñez

first: Jèssica

last: Gómez-Garrido

first: Marc

last: Dabad

first: Marco

last: Brustolin

first: Sandra

last: Talavera

first: Miguel

last: Berdugo

first: Tyler

last: Alioto

first: Albert

last: Bensaid

first: Núria

last: Busquets


title: Intravenous Nanoparticle Vaccination Generates Stem-Like TCF1+ Neoantigen-Specific CD8 T Cells

first: Robert

last: Seder

address: 40 Convent Dr

institute: Vaccine Research Center

summary:
Purpose: Single cell RNA sequencing technologies have dramatically increased the resolution at which cells can be characterized. The goal of this study was to characterize the expression differences between neoantigen (neoAg) specific CD8 T cells elicited by a TLR7/8 agonist nanoparticle vaccine delivered intravenously (IV) or subcutaneously (SC). Previous flow cytometry experiments had suggested that IV vaccination resulted in more TCF1+ cells as compared to the SC route.
Methods: Mice (n=5) were vaccinated twice, with a 2 week interval between vaccinations. Two weeks after the boost, mice were sacrificed and spleens collected, dissociated and stained with hashtag antibodies/flow cytometry antibodies. NeoAg-specific cells were labelled with a tetramer and sorted on a FACS Aria. Cells were processed through the 10X pipeline.
Results: We identified 12 clusters within our antigen specific CD8 T cells. The IV route elicited neoAg+ CD8 T cells with a predominantly stem-like gene signature whereas the SC route elicited more effector genes.

overall_design: Single cell RNA sequencing analysis of antigen specific CD8 T cells isolated from mouse spleens two weeks after prime boost vaccination with a synthetic peptide nanoparticle TLR-7/8 agonist vaccine.

first: Faezzah

last: Baharom

first: Ramiro

last: Ramirez-Valdez


title: Examination of RORa and GATA-3 binding sites in ILC2 by ChIP-seq

first: Alastair

last: Crisp

first: Ana

last: Ferreira

first: Jennifer

last: Walker

first: Paula

last: Clark

first: Jillian

middle: L

last: Barlow

first: Morgan

last: Heycock

first: Sophie

last: Kitching

first: Alfred

last: Lim

first: Mayuri

last: Gogoi

first: Aydan

last: Szeto

last: Berks


title: Synbiotic-Derived Metabolites Alleviate Stress-Induced Depression by Regulating Lymphocyte Activation through the Aryl Hydrocarbon Receptor

city: New York

first: Susan

last: Westfall

address: 1468 Madison Ave, 20-02

institute: Icahn School of Medicine at Mount Sinai

summary: Synbiotics are a combination of probiotics and prebiotics which can alter the composition of the gastrointestinal tract evoking beneficial effects throughout the body through the production of a battery of bioactive metabolites. In this study, a synbiotic was used to reduce the behavioral and biochemical symptoms of depression and this nanostring panel was used to decipher where along the gut-brain-axis the synbiotic-derived metabolites were invoking their beneficial effects on the immune system. The synbitoic was composed of two probiotic bacteria (Lactobacillus fermentum ATCC 793 and Bifidobacteria longum ATCC 15707 and a grape -derived prebiotic composed of grape seed polyphenol extract, resveratrol and a concord grape extract. Male mice (C57BL/6) were pretreatment with either nothing (control), BDPP, probiotic or synbiotic and underwent 28 days of chronic unpredicitable stress. After 28 days, animals' behavior reflected an increase in depressive- and anxiety-like behavior, rescued specifically by the synbiotic. This nanostring multiplex analysis reveals both tissue- and treatment-specific effects on immune modulators.

overall_design: 4 Tissues are included in this dataset: frontal cortex, hippocampus, ileum and liver. For each tissue, there are 5 treatment groups: (i) unstressed control, (ii) stressed control, (iii) stressed BDPP-treated, (iv) stressed-probiotic treated and (v) stressed-synbiotic treated. Each group has n = 3 replicates.

first: Giulio

middle: M

last: Pasinetti


title: Genome-wide Screens Identify Lineage- and Tumor-Specific Genes Modulating MHC-I- and MHC-II-Restricted Immunosurveillance of Human Lymphomas [DLBCL_RNAseq]

first: Devin

last: Dersh

overall_design: Paired-end RNAseq of mRNA isolated from patient-derived diffuse large B cell lymphoma cell lines; each cell line has two replicates.

first: Jaroslav

last: Holly

first: Jonathan

last: Yewdell


title: Hes protein Deadpan in neural stem cells from Drosophila 3rd instar larvae

first: Srivathsa

last: Magadi

overall_design: Refer to individual Series


title: Germline-driven replication repair-deficient high-grade gliomas exhibit unique hypomethylation patterns  hypomethylation patterns

city: Christchurch

first: Andrew

last: Dodgshun

address: 2 Riccarton Avenue

department: Children’s Haematology/Oncology Centre

country: New Zealand

institute: Christchurch Hospital

type: Methylation profiling by genome tiling array

summary: Replication repair deficiency (RRD) leading to hypermutation is an important driving mechanism of high grade glioma (HGG) occurring predominantly in the context of germline mutations in RRD-associated genes.  Although HGG present specific patterns of DNA methylation corresponding to oncogenic mutations, this has not been well studied in replication repair deficient tumors.  We analyzed 51 HGG arising in the background of gene mutations in RRD utilizing either 450k or 850k methylation arrays.  These were compared with HGG not known to be from patients with RRD. RRD HGG harboring secondary mutations in glioma genes such as IDH1 and H3F3A displayed a methylation pattern corresponding to these methylation subgroups. Strikingly, RRD HGG lacking these known secondary mutations clustered together with an incompletely described group of HGG previously labelled “Wild type-C” or “Paediatric RTK 1”. Independent analysis of two comparator HGG cohorts showed that other RRD/hypermutant tumors clustered within these subgroups suggesting that undiagnosed RRD may be driving some HGG clustering in this location. RRD HGG displayed a unique CpG Island Demethylator Phenotype in contrast to the CpG Island Methylator Phenotype described in other cancers.  Hypomethylation was enriched at gene promoters with prominent demethylation in genes and pathways critical to cellular survival including cell cycle, gene expression, cellular metabolism and organization.  These data suggest that methylation arrays may provide diagnostic information for the detection of RRD HGG. Furthermore, our findings highlight the unique natural selection pressures in these highly dysregulated, hypermutant cancers and provide novel impact of hypermutation and RRD on the cancer epigenome.

overall_design: 51 samples

first: Uri

last: Tabori


title: Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer

first: Robert

middle: S

last: Banh

address: 522 First Avenue, Smilow 907

department: Radiation Oncology

institute: New York University

summary: In this dataset, we included sequencing data of total and ribosome protected fragments obtained from PATU-8902 cell lines grown in DMEM (2.78mM glucose, 4mM glutamine, 1mM pyruvate) + 10%dialyzed FBS + 1% Pen/Strep with or without 400uM Ser and 400uM Gly for 24 hours.

overall_design: Ribosome profiling was performed in PATU-8902 cells grown with or without serine and glycine for 24hours.

first: Alec

last: Kimmelman


title: Comparison of the transcriptomic profiles of WT and complement C3-deficient mice with rhabdomyolysis-induced acute kidney injury

status: Public on Nov 01 2020

city: Paris

first: Anne

last: Grunenwald

state: Ile-de-France

address: 15 rue de l'Ecole de Médecine, Escalier E, 3ème étage

institute: INSERM UMRS1138 Cordeliers Research Center

summary: Rhabdomyolysis is a severe condition caused by skeletal muscle damage, leading to acute kidney injury (AKI). We demonstrate that complement has a direct pathogenic role in rhabdomyolysis-induced AKI. Deposition of C3d in the tubules of patients and mice correlated with rhabdomyolysis-induced AKI. Moreover, C3-defiient mice with rhabdomyolysis had preserved renal function. Mechanistically, C3-deficiency attenuated strongly inflammatory and apoptotic components of the renal transcriptome, perturbed by rhabdomyolysis. Complement was activated intrarenal by the lectin pathway via collectin-11. It proceeded in a C4-bypass manner and was amplified by heme-activated alternative pathway. Therefore, complement and heme are promising therapeutic targets for rhabdomyolysis-induced AKI.

overall_design: Comparison of the gene expression in kidney sections lysate of C56Bl/6 WT or C3-/- mice, injected or not with glycerol to induce rhabdomyolysis-associated acute kidney injury

first: Lubka

middle: T

last: Roumenina

first: Marie

middle: V

last: Daugan


title: Hes mediated transcriptomics in Drosophila larval CNS

summary:
Excessive activation of Hes causes stem cell hyperplasia in larval CNS. Transcriptomics of Notch induced hyperplasia and Hes induced hyperplasia were compared
Using affymetrix microarray, global gene expression analysis was performed.

overall_design:
RNA extracted from hand dissected 3rd instar larval CNS's obtained from control, Notch (data submitted in ArrayExpress E-MTAB-3561) and Hes induced hyperplasia using neural stem cell specific grhGAL4. affymetrix CEL files, CHP files generated by Transcription analysis console and matrix table containg Quantile normalised data using R for differential expression are provided.
Control and Notch (Quadruplicates) samples are deposited in  ArrayExpress  E-MTAB-3561

first: Christos

last: Delidakis


title: A histone H3.3K36M mutation in mice causes imbalance of histone modifications and defects in chondrocyte differentiation [RNA-seq]

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

institute: Kyushu University

summary: Histone lysine-to-methionine (K-to-M) mutations have been identified as driver mutations in human cancers. Interestingly, these ‘oncohistone’ mutations inhibit the activity of histone methyltransferases, and, therefore, they can potentially be used as versatile tools to investigate the roles of histone modifications. In this study, we created a conditional knock-in mouse line in which a H3.3K36M mutation can be induced in the endogenous H3.3 gene. Since the H3.3K36M mutation has been identified as a causative mutation of human chondroblastoma, we induced this mutation in the chondrocyte lineage in mouse embryonic limbs. We found that H3.3K36M causes global reduction of H3K36me2 and defects in chondrocyte differentiation. Importantly, the reduction of H3K36me2 was accompanied by a collapse of normal H3K27me3 distribution. Furthermore, the changes in H3K27me3, especially the loss of H3K27me3 at gene regulatory elements, were associated with misregulated expression of a set of genes important for limb development including HoxA cluster genes. Thus, taking advantage of the in vivo induction of H3.3K36M mutation, we reveal the importance of a counterbalance between H3K36me2 and H3K27me3 for chondrocyte differentiation and limb development.

overall_design: ChIP-seq for H3K36me2, H3K36me3, and H3K27me3 were performed in mouse E14.5 tibial midshafts. mRNA-seq was performed in mouse E14.5 tibial midshafts and ends.

first: Shusaku

last: Abe


title: Intravital imaging identifies long-term self-renewing stem cells in the adult mouse hippocampus

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

summary: Neural stem cells (NSCs) generate new neurons throughout life in the mammalian hippocampus. However, the potential for long-term self-renewal of individual NSCs within the adult brain remains unclear. We used chronic in vivo 2-photon microscopy and followed single NSCs that were genetically labeled through conditional recombination driven by the regulatory elements of the stem cell-expressed genes GLI Family Zinc Finger 1 (Gli1) or Achaete-scute homolog 1 (Ascl1). Through intravital imaging of NSCs and their progeny we identify a population of Gli1-targeted NSCs showing long-term self-renewal in the adult hippocampus. In contrast, once activated, Ascl1-targeted NSCs undergo limited proliferative activity before they becoming exhausted. Using protein expression profiling and single-cell RNA sequencing (scRNA-seq), we show that Gli1- and Ascl1-targeted cells have highly similar yet distinct transcriptional profiles, supporting the existence of heterogeneous NSC populations with diverse behavioral properties. Thus, we here provide the cellular framework for how functional diversity of NSCs enables the generation of new neurons in the adult hippocampus.

overall_design: Comparison between Gli1- and Ascl1-targeted tdTomato+ cells. 5 days or 12 weeks after tamoxifen injection, tdTomato+ cells were isolated from the dentate gyrus of 3 mice per group per timepoint. Single cells were FACS sorted into 384 -well plates. Seven 384-well plates were processed according to the SmartSeq2 protocol using a microliter pipetting robot and sequenced on an Illumina HiSeq2500 or HiSeq4000.

first: Sara

last: Bottes

first: Gregor-Alexander

last: Pilz

first: David

last: Jörg

first: John Darby

last: Cole

first: Merit

last: Kruse

first: Lachlan

last: Harris

first: Vladyslav

last: Korobeynyk

first: Izaskun

last: Mallona

first: Fritjof

last: Helmchen

first: Francois

last: Guillemot

first: Benjamin

middle: D

last: Simons

first: Sebastian

last: Jessberger


title: Space-time logic of liver gene expression

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

institute: Weizmann Institute

summary: We molecularly characterized thousands of liver hepatocytes cells at different time points around the circadian clock. This enable us to reconstruct mRNA expression profiles in space and time.

overall_design: mRNA profiles from single cells, Hepatocytes extracted from mouse liver were sequenced using the 10x single cell genomics platform

first: Colas

last: Droin

first: Jakob

last: El Kholtei

last: Halpern

first: Clémence

last: Hurni

first: Milena

last: Rozenberg

first: Sapir

last: Muvkadi

first: Shalev

last: Itzkovitz

first: Felix

last: Naef


title: Long non-coding RNA NEAT1 promotes sarcoma metastasis by regulating RNA splicing pathways

city: Durham

first: David

last: Kirsch

address: PO Box 96100

institute: Duke University

summary: To identify genes that are differentially expressed in lung metastases of sarcoma, we generated KrasLSL-G12D; Trp53Flox/Flox (KP) mice which develop autochthonous sarcomas in the muscle following injection of an adenovirus expressing Cre recombinase. Cre activates expression of mutant KrasG12D and deletes both alleles of Trp53. As each primary sarcoma reached the size of around 300 mm3, the leg bearing the tumor was amputated and the tumor stored for subsequent RNA sequencing. The amputated mice were followed for several months and 6 mice developed 14 lung metastases: two mice developed one lung metastases, two mice developed two lung metastases, and two mice developed four lung metastases respectively. RNA was then extracted from the 6 primary tumors and the 14 matched lung metastases. Therefore, a total of 20 RNA samples were sent for RNA sequencing

overall_design: a total of 20 RNA from the 6 primary tumors and the 14 matched lung metastases were sent for RNA sequencing

first: Jianguo

last: Huang

first: Mohit

last: Sachdeva

first: Dadong

last: Zhang

first: Xiaodi

last: Qin

first: Kouros

last: Owzar


title: CPSF controls PAS selection and epidermal differentiation

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

summary: Alternative polyadenylation (APA) is a regulatory mechanism that controls gene expression level and function through the usage of different transcription termination sites, but how APA is regulated to influence epidermal tissue differentiation remains under-characterized. Leveraging 3’READS+, we identified prevalent APA in keratinocytes. We further identified a high-confidence list of genes that alters their usages of polyadenylation site (PAS) during keratinocyte differentiation. To begin to understand the mechanisms that modulates PAS selection within a given gene, we identified that the expression of the Cleavage and Polyadenylation Specificity Factor (CPSF) complex is down regulated during keratinocyte differentiation. Suppression of CPSF using RNAi or CRISPRi strongly impaired epidermal regeneration with upregulation of terminal differentiation marker gene expression. Mechanistically, we identified that CPSF suppression decreased the usage of the GRHL3 proximal PAS and upregulated full-length GRHL3 mRNA production. Knockdown of GRHL3 in the context of CPSFi partially restored differentiation marker gene expression. We also found CPSF interacts with RNA-binding proteins to control PAS usage. Thus, our data suggest a model where CPSF binding preference and PAS choices regulate epidermal terminal differentiation.

overall_design: We examined alternative polyadenylation by 3’READS+ in undifferentiated and differentiated keratinocytes with two biological replicates each, as well as in CPSF1 siRNA knock down codition. To check gene expression in epidermal differentiation, we performed RNA-seq in undifferentiated and differentiated keratinocytes with three biological replicates each. To check whether the CPSF complex regulates keratinocyte gene expression, we further performed RNA-seq in control and CPSF1 siRNA knock down conditions with two replicates each, and RNA-seq in control and CPSF1 CRISPRi knock down conditions with two and three biologial replicats respectively.

first: Xin

last: Chen

first: Sarah

last: Lloyd

first: Junghun

last: Kweon

first: Giovanni

last: Gamalong