title: Tissue damage leads to a conserved stress response that initiates quiescent muscle stem cell activation

city: Créteil

first: Léo

last: Machado

state: Ile-De-France

address: 8 rue du Général Sarrail, Equipe 10 - Inserm U955

institute: INSERM

summary: In multicellular organisms, cells dynamically interact with the microenvironment, which determines their properties and gene-expression profile. Tissue damage, such as injury or experimental cell dissociation, leads to dramatic modifications of the niche, yet the early cellular responses in vivo remain ill-defined. We have generated single cell and nucleus atlases from intact, dissociated and injured muscle and liver, and identified a common stress response signature. This prevalent stress response was also detected in published datasets across tissues, demonstrating high conservation but also indicating a significant degree of data distortion in single-cell reference atlases. Using quiescent muscle stem cells as a paradigm of cell activation during tissue repair, we captured the kinetics of the early response to muscle injury. We show that an essential ERK1/2 primary proliferation signal precedes the initiation of the Notch-regulated myogenic program. Our study, therefore, defines the initial events priming cell activation following perturbations in tissue integrity in vivo and identifies a broadly conserved transcriptional stress response that acts in parallel to cell-specific adaptive alterations

overall_design: Study of tissue dissociation and  injury in mouse skeletal muscle stem cells, liver and muscle single-nuclei

first: Perla

last: Geara

first: Jordi

last: Camps

first: Matthieu

last: Dos Santos

first: Fatima

last: Teixeira-Clerc

first: Jens

last: Van Herck

first: Hugo

last: Varet

first: Jean-Michel

last: Pawlotsky

first: Rachel

last: Legendre

first: Maurilio

last: Sampaolesi

first: Thierry

last: Voet

first: Pascal

last: Maire

first: Frederic

last: Relaix

first: Philippos

last: Mourikis


title: miR-127-3p is an epigenetic activator of myofibroblast senescence situated within the miRNA enriched Dlk1-Dio3 imprinted domain on mouse chromosome 12 [mRNA array]

status: Public on Jan 31 2021

city: Cologne

first: Bent

last: Brachvogel

address: Joseph-Stelzmann Street 52

country: Germany

institute: University of Cologne

summary: During wound healing, fibroblasts differentiate into non-proliferative contractile myofibroblasts, contribute to skin repair, and eventually undergo apoptosis or become senescent. MicroRNAs (miR) are posttranscriptional regulators of gene expression networks that control cell fate and survival and may also regulate senescence. Here we determined regulated miRs in myofibroblasts isolated from wounds and analyzed their role in senescent myofibroblast formation. Transcriptome profiling showed that a 200 kbp region of the Dlk1-Dio3 imprinted domain on mouse chromosome 12 encodes for most of the upregulated miRs in the entire genome of mouse myofibroblasts. Among those, miR-127-3p induced a myofibroblast-like phenotype associated with a block in proliferation. Molecular analysis revealed that miR-127-3p induced a prolonged cell-cycle arrest with unique molecular features of senescence, including the activation of the senescence-associated ß-galactosidase, increase in p21 levels, inhibition of lamin B1, proliferation factors, and the production of senescence-associated inflammatory and extracellular matrix -remodeling components. Hence, miR-127-3p emerges as an epigenetic activator regulating the transition from repair to remodeling during skin wound healing, but may also induce age-related defects, pathological scarring and fibrosis, all linked to myofibroblast senescence.

overall_design: Dermal cells were isolated from skin of C57BL/6 newborn mice following dispase and collagenase type 1 digest as described (Etich et al., 2013) and cultured in DMEM (Gibco/ Thermo Fisher Scientific, Waltham, USA) with 10% FCS and 1% P/S. For transfection experiments 1x105 cells were cultured in a 12-well-plate and transfected with control or miR-127-3p mimic oligonucleotides. Phenol-chloroform extracted non-degraded RNA (100 ng) isolated from control or miR-127-3p transfected fibroblasts was amplified, labeled using the Low input Quick Amp Labeling kit and hybridized to a SurePrint G3 Mouse GE 8x60K Microarray (Agilent, Santa Clara, USA). After scanning and processing data were analyzed using Genespring14.9.1 Multi-Omic software and FunRich tool (Pathan et al., 2015).


title: Exposure to Gestational Diabetes Mellitus In Utero Alters DNA Methylation in Placenta and Fetal Cord Blood

city: Toronto

first: Zain

last: Awamleh

address: 686 Bay street

country: Canada

institute: Sickkids

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Sequential CRISPR gene editing in human iPSCs charts the clonal evolution of leukemia

city: New York

first: Eirini

last: Papapetrou

address: One Gustave L. Levy Place Box 1044A

country: USA

institute: Icahn School of Medicine

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Human cancers arise through an evolutionary process whereby cells acquire somatic mutations that drive them to outgrow normal cells and create successive clonal populations. “Bottom-up” human cancer evolution models could help illuminate this process, but their creation has faced significant challenges. Here we combined  human induced pluripotent stem cell (iPSC) and CRISPR/Cas9 technologies to develop a model of the clonal evolution of acute myeloid leukemia (AML). Through the sequential introduction of 3 disease-causing mutations (ASXL1 C-terminus truncation, SRSF2P95L and NRASG12D), we obtained single, double and triple mutant iPSC lines that, upon hematopoietic differentiation, exhibit progressive dysplasia with increasing number of mutations, capturing distinct premalignant stages, including clonal hematopoiesis, myelodysplastic syndrome, and culminating in a transplantable leukemia. iPSC-derived clonal hematopoietic stem/progenitor cells recapitulate transcriptional and chromatin accessibility signatures of normal and malignant hematopoiesis found in primary human cells. By mapping dynamic changes in transcriptomes and chromatin landscapes, we characterize transcriptional programs driving specific stage transitions and identify vulnerabilities for early therapeutic targeting. Such synthetic “de novo oncogenesis” models can empower the investigation of multiple facets of the malignant transformation of human cells.

overall_design: Chromatin accessibility (ATAC-seq) and gene expression (RNA-seq); 2-3 replicates per sample

first: Tiansu

last: Wang

first: Allison

last: Pine

first: Christina

last: Leslie


title: Exposure to Gestational Diabetes Mellitus In Utero Alters DNA Methylation in Placenta and Fetal Cord Blood  [Cord]

summary: Genome wide DNA Methylation in fetal cord blood and placenta from mother with GDM compared to mother with normal glucose tolerance

overall_design: Bisulphite converted 42 cord blood samples and used the Illumina 450K

first: Jill

last: Hamilton

first: Rosanna

last: Weksberg


title: Effect of bone marrow microenvironment on the sensitivity of breast cancer cells to antiestrogens

city: Boston

first: Eugen

last: Dhimolea

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Hormonal therapy (HT) inhibits the growth of hormone receptor-positive (HR+) breast (BrCa) and prostate (PrCa) cancers. HT resistance frequently develops within the complex metastatic microenvironment of the host-organ (often the bone), a setting poorly recapitulated in two-dimensional (2D) culture systems. To address this limitation, we cultured HR+ BrCa/PrCa spheroids and patient-derived organoids in 3D extracellular matrices (ECM) alone or together with bone marrow stromal cells (BMSCs). In 3D monocultures, antiestrogens/antiandrogens induced anoikis by abrogating the anchorage-independent growth of HR+ cancer cells but had only modest effect against tumor cells residing in the ECM niche. In contrast, BMSCs induced hormone-independent growth of BrCa/PrCa spheroids and restored lumen filling in the presence of HR-targeting agents. Molecular and functional characterization of the BMSC-induced hormone-independence and HT resistance in anchorage-independent cells revealed distinct, context-dependent, mechanisms. Cocultures of ZR75-1 and LNCaP with BMSCs exhibited paracrine IL-6-induced HT resistance via attenuation of HR protein expression, which was reversed by inhibition of IL-6 or JAK signaling. This paracrine IL-6/JAK/STAT3-mediated HT resistance was also confirmed in patient-derived organoids cocultured with BMSCs. Distinctly, MCF7 and T47D spheroids retained ER protein expression in cocultures, but also acquired redundant compensatory signals enabling anchorage independence via ERK and PI3K bypass cascades activated in non-IL-6-dependent manner. In summary, the acquisition of anchorage-independent growth in HR+ tumors is abrogated by HR blockade, but can be restored in the metastatic microenvironment through pleiotropic hormone-independent mechanisms. Combined analysis of tumor and microenvironmental biomarkers in metastatic biopsies of HT-resistant patients can help the refinement of treatment approaches.

overall_design: RNA profiles of breast cancer cells in 3D cultures in the presence vs. absence of immortalized bone marrow stromal cells HS5

first: Ricardo

last: de Matos Simoes

first: Constantine

last: Mitsiades


title: Transcriptional signature in microglia associated with Aβ plaque phagocytosis

city: Singapore

first: Gabriel

last: Chew

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

summary: The role of microglia cells in Alzheimer’s disease (AD) is well recognized,   however their molecular and functional diversity remain unclear. Here we   isolated amyloid plaque-containing (using labelling with methoxy–XO4, XO4+)   and non-containing (XO4-) microglia from an AD mouse model. Transcriptomics   analysis identified different transcriptional trajectories in ageing and AD mice.   XO4+ microglial transcriptomes demonstrated dysregulated expression of genes   associated with late onset AD. We further showed that the transcriptional program   associated with XO4+ microglia from mice is present in a subset of human microglia   isolated from brains of individuals with AD. XO4- microglia displayed transcriptional   signatures associated with accelerated ageing and contained more intracellular post-synaptic   material than XO4+ microglia, despite reduced active synaptosome phagocytosis.   We identified HIF1α as potentially regulating synaptosome phagocytosis in vitro   using primary human microglia, and BV2 mouse microglial cells. Together these findings   provide insight into molecular mechanisms underpinning the functional   diversity of microglia in AD.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-Seq and scRNA-seq


title: A first exon termination checkpoint that preferentially suppresses extragenic transcription [RNASEQ1_BMDM_4sU]

status: Public on Feb 01 2021

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

summary: Wdr82 and Zc3h4 repress transcription at extragenic sites.

overall_design: Transcriptome analysis to measure transcription in cells depleted of Wdr82, Zc3h4or other known termination factors.

first: Liv

middle: M

last: Austenaa

first: Marta

last: Russo

first: Elena

last: Prosperini

first: Sara

last: Polletti

first: Iros

last: Barozzi

first: Giuseppe

last: Diaferia

first: Gioacchino

last: Natoli


title: Exposure to Gestational Diabetes Mellitus In Utero Alters DNA Methylation in Placenta and Fetal Cord Blood [Placenta]

first: Zain

last: Awamleh

overall_design: Bisulphite converted 36 placenta samples and used the Illumina 450K


title: Changes in DNA methylation in Arabidopsis thaliana plants exposed over multiple generations to gamma radiation

city: Mol

first: Mohamed

last: Mysara

state: Belgium

address: Boeretang 200

country: Belgium

institute: Belgian nuclear research center (SCK-CEN)

type: Methylation profiling by high throughput sequencing

summary: Previous studies have shown that exposure to ionising radiation (IR) results in DNA methylation changes in plants. However, to the best of our knowledge, this phenomenon is yet to be studied across multiple generations. Furthermore, the exact role of these changes in the IR-induced plant response is still far from understood. Here, we study the effect of gamma radiation on DNA methylation and its effect across generations in young Arabidopsis plant.   A multigenerational set-up was used in which three generations of seven-day old Arabidopsis thaliana plants were exposed to either of the different radiation treatments (30 mGy h-1, 60 mGy h-1,  110 mGy h-1, or 430 mGy h-1) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS to measure whole genome methylation levels. Whole genome bisulphite sequencing (WGBS) was used to identify differentially methylated regions (DMRs), including their methylation context in the three generations in three different radiation conditions (control, 30 mGy/h, and 110 mGy/h). Both intra- and intergenerational comparisons of the genes and transposable elements (TEs) associated with the DMRs were made across the gamma radiation exposure conditions.   It was apparent that there was a higher number of changes in CpG methylation, whereas only limited changes in CHG methylation occurred and no changes in CHH methylation were observed.  A clear increase in IR-induced DMRs was seen over the three generations that were exposed to the lowest dose rate, where Gen 2 had a markedly higher number of DMRs than the previous two generations (Parent and Gen 1). Counterintuitively, we did not see significant differences in the plants exposed to the higher dose rate. In addition, a large number of DMRs associated with TEs were found, the majority of them being hyper methylated, likely leading to more genetic stability. Next to that, a significant number of DMRs were associated with genes (either in their promoter associated region or gene body). A functional analysis of these genes (not included in with this data) showed an enrichment for genes related to development as well as various stress responses, including DNA repair, RNA splicing, and (a)biotic stress responses. These observations indicate a role of DNA methylation in the regulation of these genes in response to IR exposure and shows a possible role for epigenetics in adaptation to IR in plants.

overall_design: A multigenerational set-up was used in which three generations of seven-day old Arabidopsis thaliana plants were exposed to either of the different radiation treatments (30 mGy h-1, 60 mGy h-1,  110 mGy h-1, or 430 mGy h-1) or to natural background radiation (control condition) for 14 days. The parental generation consisted of previously non-exposed plants, whereas generation 1 and generation 2 plants had already received a similar irradiation in the previous one or two generations, respectively. Directly after exposure the entire methylomes were analysed with UPLC-MS to measure whole genome methylation levels (duplicate analysis of samples was performed whenever possible) and with whole genome bisulphite sequencing (WGBS)(sequencing done twice to achieve sufficiently high coverage) to identify differentially methylated regions (DMRs), including their methylation context. Both intra- and intergenerational comparisons of the genes and transposable elements (TEs) associated with the DMRs were made across the gamma radiation exposure conditions. Of each condition 5 replicates were used.

first: Pol

middle: J

last: Laanen

first: Nele

last: Horemans

first: Eline

last: Saenen

first: Ann

last: Cuypers

first: Jorden

last: Van de Walle

first: May

last: Van Hees

first: Robin

last: Nauts

first: Filip

last: Van Niewerburgh

first: Stefan

last: Voorspoels

first: Griet

last: Jacobs


title: Macrophage contribution to follicular lymphoma pathogenesis: CSF-1R as a novel prognostic factor and therapeutic target

city: Barcelona

first: Patricia

last: Pérez-Galán

state: Barcelona

address: Centre Esther Koplowitz, Hemato-oncology dept, Rosello 149-153, 2nd floor

department: Hemato-oncology

country: Spain

institute: IDIBAPS

summary:
Follicular lymphoma (FL) patient samples from lymph node biopsies were in co-culture or not with M2 macrophages (generated from healthy donors) for 48h
We used microarrays to uncover the mechanisms underlying FL and macrophages crosstalk

overall_design: Global RNA expression  was done in CD20+ magnetically purified FL cells in monoculture or after macrophage coculture for 48h

first: Juan

middle: G

last: Valero

first: Alba

last: Céspedes

first: Martina

last: Hernández


title: Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [RNA-seq]

city: WuHan

first: Guan

middle: Peng

last: Peng

state: HuBei

address: shizishan street

department: college of informatics

country: China

institute: Huazhong Agricultural University

summary: We establish global maps of regulatory elements and chromatin states and their dynamics, for both the whole and subgenomes of four tissue types (young leaf, flower bud, silique, and root) of two B. napus lines. Approximately 52 % of the genome was annotated with different epigenomic signals. We also uncover a new bivalent chromatin state in B. napus and suggest its key roles in regulating tissue-specific gene expression. Furthermore, we observe that different types of duplicated genes have differential patterns of histone modifications, DNA methylation, and selection pressures. Together, we provide valuable epigenetic data resources of allopolyploid B. napus and reveal the central role of epigenomic information in understanding transcriptional regulation in polyploid plants.

overall_design:
Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues in B. napus.
RNA-seq: Total RNA was isolated from tissue using a QIAGEN RNeasy plant mini kit according to the manufacturer’s instructions. The RNA (2 ug) was used for library construction using an Illumina TruSeq RNA kit, according to the manufacturer’s recommendations. RNA sequencing was performed using an Illumina HiSeq X Ten platform.

first: Qing

last: Zhang

first: Pengpeng

last: Guan

first: Lun

last: Zhao


title: Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-reChIP]

overall_design: Here, we generated genome-wide profiling of five histone modifications and RNA polymerase II occupancy using an enhanced chromatin immunoprecipitation (eChIP) approach. By integrating DNA methylation, and transcriptome datasets, we constructed comprehensive epigenome landscapes across various tissues in B. napus.


title: RNA splicing and aggregate gene expression differences between lung squamous cell carcinoma from patients of West African and European ancestry

city: Durham

first: Jennifer

last: Freedman

address: 905 South Lasalle Street

institute: Duke Cancer Institute

summary: Study of genes that are differentially spliced and differentially expressed between African Americans and whites with lung squamous cell cancer.  Despite racial disparities in lung cancer, the molecular landscape of lung cancer in patients of African ancestry remains underexplored. Population-related differences in alternative RNA splicing have not been explored.  We identified differentially spliced genes and differentially expressed genes between lung squamous cell carcinoma from patients of West African and European ancestry.

overall_design: RNA extracted from 20 African American and 20 white resected lung tissue was run on Clariom D exon array.  Analysis to determine differences between population groups was performed using Transcriptome Analysis Console Software 4.0 (Affymetrix).

first: April

last: Deveaux

first: Tyler

last: Allen

first: Muthana

last: Al Abo

first: Dadong

first: Xiaodi

last: Qin

first: Brendon

last: Patierno

first: Lin

last: Gu

first: Jhanelle

last: Gray

first: Chad

last: Pecot

first: Holly

last: Dressman

first: Shannon

last: McCall

first: Rick

last: Kittles

first: Kouros

last: Owzar

first: Jeffrey

last: Crawford

first: Steven

last: Clarke


title: Gene expression program directed by an artificially evolved POU (ePOU)

city: Guangzhou

first: Chen

last: yanpu

state: guangdong

address: Kaiyuan No. 190, Luogang district

department: drug discovery pipelines

institute: Guangzhou Institute of Biomedicine and Health

summary: We generated Oct4 libraries by randomizing selected amino acids and by recombining domains of paralogous POU family genes. These libraries were subjected to iterative rounds of pooled screens to select variants that enhance pluripotency induction. We identified an artificially evolved POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of mouse embryonic fibrobast (MEF) reprogramming. We compared the transcriptomes of cells reprogramming under ePOU or Oct4 conditions at day 3 using RNA sequencing.

overall_design: mRNA profiles of 24 different reprogramming intermediate cells with ePOU/Oct4 in combination with Sox2/Sox17EK along with Klf4 and c-Myc, at day 0,2,3,4,6,and 13 of retrovirus system based

first: Yanpu

last: Chen

first: Ralf

last: Jauch

first: Vikas

last: Malik

first: Daisylyn Senna

last: Tan


title: miRNA expression in tracheal aspirates in mild/moderate and severe BPD

status: Public on Jan 30 2021

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

summary: Extreme preterm infants are a growing population in neonatal intensive care units who carry a high mortality and morbidity.  Multiple factors play a role in preterm birth, resulting in major impact on organogenesis leading to complications including bronchopulmonary dysplasia (BPD).  The goal of this study was to identify biomarker signatures associated with BPD severity.  We analyzed profiles in tracheal aspirates (TAs) from 25 extremely preterm infants receiving invasive mechanical ventilation.  Eight infants were diagnosed with mild/moderate BPD, and 17 were diagnosed with severe BPD, according to the NHLBI consensus conference classification . We found specific miRNA signatures in TAs that may serve as biomarkers for BPD severity.

overall_design:
We extracted RNA  from 0.5 mL of tracheal aspirates from premature neonates with BPD using the Plasma/Serum RNA Purification Kit. The expression of 1,066 human miRNAs was quantified using the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z). Results (Ct values) were normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
mild/moderate BPD: 5,17,25,68,79,82,85,97  severe BPD: 3,11,12,24,26,33,34,37,42,49,51,67,74,80,91,95,100

first: Roopa

last: Siddaiah

first: Christiana

last: Oji-Mmuo

first: Nathalie

last: Fuentes

first: Deborah

last: Montes


title: Integrative analysis of reference epigenomes in polyploid crop Brassica napus L.

first: Guan

last: Peng


title: The chromatin remodeler Lsh modulates genome-wide cytosine hydroxymethylation

city: Brussels

first: Maud

last: de Dieuleveult

address: Route de Lennik 808

institute: Free University of Brussels

summary: TET proteins convert 5-methylcytosine to 5-hydroxymethylcytosine, an emerging dynamic epigenetic state of DNA that can influence transcription. While Tet proteins have been associated to epigenetic repression or activation complexes, our understanding of the molecular mechanisms involved in Tet-mediated regulation of gene transcription remains limited. Here, we showed that Tet directly interact with lymphoid-specific helicase (Lsh), a chromatin remodelling factor belonging to the ISWI family. This specific interaction seems to regulate Tet enzymatic activity since Lsh knock-out leads to a substantial reduction of 5-hydroxymethylation global level in mouse embryonic fibroblasts (MEFs) and in embryonic stem cells (ES). Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh some regions of the genome gain while others loose 5hmC marks, with a weak correlation to gene expression changes . We further demonstrated that 5hmC modifications upon Lsh loss are not a direct consequence of 5mC decrease as DhMR (differentially hydroxymethylated regions) did not overlap with DMR (differentially methylated regions) underlying that these modifications occurred at different genomic loci. Altogether, our results suggest that DNA 5-hydroxymethylation and nucleosome folding are linked phenomena, highlighting novel means by which Tet proteins may influence gene regulation.

overall_design:
5hmC level in wild-type mouse or LSH KO embryonic stem cells and MEF cells using the hydroxymethyl collector kit (Active Motif). Genome: mm9.

Briefly, 1µg of genomic DNA was diluted in ultra-pure water to 35 ng/μL and then sonicated in cold water with a Bioruptor sonicator (Diagenode) to obtain fragments averaging 300 bp in size. The fragmented DNA was used in combination with the hydroxymethyl collector (Active Motif) following the manufacturer’s protocol. Briefly, a glucose moiety that contains a reactive azide group was enzymatically linked to hydroxymethylcytosine in DNA, creating glucosyl-hydroxymethylcytosine. Next, a biotin conjugate was chemically attached to the modified glucose via a “click reaction”, and magnetic streptavidin beads were used to capture the biotinylated-hmC DNA fragments. After extensive washing steps and chemical elution, the hydroxymethylated DNA fragments released from the beads were used in sequencing experiments.

first: Laurence

last: Colin

first: Matthieu

last: Defrance

first: Martin

last: Bizet

first: Emilie

last: Calonne

first: Rachel

last: Deplus

first: François

last: Fuks


title: miRNA profile in extracellular vesicles from human muscle progenitors

city: Tampa

first: Wanling

last: xuan

state: FL

address: 12901 Bruce B Down Blvd

department: DPS

institute: University of South Florida

summary: We investigated the enriched miRNAs in extracellular vesicles (EV)  from human myoblasts and givinostat induced muscle progenitor cells which are derived from human induced pluripotent stem cells

overall_design: Examination of global miRNA expression profile in extracellular vesicles  from human myoblasts and givinostat indcued muscle progenitor cells (n=3).

last: Xuan

first: Muhammad

last: Ashraf


title: Multi-cell type gene co-expression network analysis reveals coordinated interferon response and cross cell-type correlations in systemic lupus erythematosus

city: La Jolla

first: Ferhat

last: Ay

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

summary: Systemic lupus erythematosus (SLE) is an incurable autoimmune disease disproportionately affecting women. A major obstacle in finding targeted therapies for SLE is its remarkable heterogeneity in clinical manifestations as well as in the involvement of distinct cell types. To identify cell-specific targets as well as cross-correlation relationships among expression programs of different cell types, we here analyze six major circulating immune cell types from SLE patient blood. Our results show that the presence of interferon response signature stratifies patients into two distinct groups (IFNneg vs IFNpos). Comparing these two groups using differential gene expression and differential gene co-expression analysis, we prioritize a relatively small list of genes from classical monocytes including two known immune modulators: TNFSF13B/BAFF (target of belimumab, an approved therapeutic for SLE) and IL1RN (the basis of anakinra, a therapeutic for rheumatoid arthritis). We then develop a multi-cell type extension of the weighted gene co-expression analysis (WGCNA) framework, termed mWGCNA. Applying mWGCNA to RNA-seq data from six sorted immune cell populations (15 SLE, 10 healthy donors), we identify a co-expression module with interferon-stimulated genes (ISGs) among all cell types and a cross-cell type correlation linking expression of specific T helper cell markers to B cell response as well as to TNFSF13B expression from myeloid cells, all of which in turn correlates with disease severity of IFNpos patients. Our results demonstrate the power of a hypothesis-free and data-driven approach to discover drug targets and to reveal novel cross-correlation across cell types in SLE with implications for other autoimmune diseases.

overall_design: Assessment of the transcriptomic profiles of different immune cells in SLE

first: Bharat

last: Panwar

first: Benjamin

last: Schmiedel

first: Shu

last: Liang

first: Brandie

last: White

first: Enrique

last: Rodriguez

first: Kenneth

last: Kalunian

first: Andrew

last: McKnight

last: Soloff

first: Gregory

last: Seumois

first: Pandurangan

last: Vijayanand


title: Stilbenoid-mediated epigenetic activation of Semaphorin 3A in breast cancer cells involves changes in dynamic interactions of DNA with DNMT3A and NF1C transcription factor

city: Vancouver

first: Barbara

last: Stefanska

state: BC

address: 2205 East Mall

department: Land and Food Systems

institute: The University of British Columbia

summary: Genome wide DNA methylation profiling of lowly invasive MCF10CA1h  human breast cancer cell line treated with vehicle control (ethanol) and with 15uM RSV (resveratrol, 4-day treatment). The Illumina Infinium 450K Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs in the human cell line exposed to described treatments. Samples included biological triplicate of MCF10CA1h control (ethanol treated) and biological triplicate of MCF10CA1h treated with RSV.

overall_design: Bisulphite converted DNA from the 6 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip v1.2

first: Megan

last: Beetch

first: Kate

last: Shen

first: Sadaf

last: Harandi-Zadeh

first: Katarzyna

last: Lubecka

first: Kirsty

last: Flower

first: Matthew

last: Suderman

first: James

last: Flanagan


title: High-frequency head impacts cause chronic synaptic adaptations and long-term cognitive impairment [24h post-HFHI]

status: Public on Jan 29 2021

city: Washington

first: Bevan

last: Main

state: District of Columbia

address: 3970 Reservoir Rd NW

department: Neuroscience

institute: Georgetown University

summary: The goal of this study is to use bulk RNA-sequencing of to observe the effects of High Frequency Head Impacts contibuting to cognitive dysfunction in mice. Our results show HF-HI can alter brain function through synaptic adaptation. HF-HI mice develop chronic cognitive impairments in the absence of traditional brain trauma pathology, and transcriptomic profiling reveals that synapses are a primary target of this effect.

overall_design: Mice were subjected to HF-HI or a sham procedure. Bulk RNA sequencing was performed on Sham and HF-HI experimental groups at 24 hours post injury.

middle: S

first: Stephanie

last: Sloley

first: Charisse

middle: N

last: Winston

first: Alex

middle: C

last: Harvey

first: Alice

last: Kaganovich

first: Holly

middle: T

last: Korthas

first: Adam

middle: P

last: Caccavano

first: D

last: Zapple

first: Jian-Young

last: Wu

first: John

last: Partridge

first: Mark

middle: R

last: Cookson

first: Stefano

last: Vicini

last: Burns


title: Gene expression profiles in the colon epithelia of the humanized CYP1A (hCYP1A) mice treated with 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP)

first: xu

last: yang

address: jinsui road 9

institute: Guangzhou Women and Children's Medical Center

summary: Differentially expressed genes in the PBS or PhIP-treated hCYP1A mouse colon epithelia using the mouse exonic evidence based oligonucleotide (MEEBO) microarray.

overall_design: The study includes colon epithelia collected from 3 PBS (control)- and 5 PhIP-treated hCYP1A mice for the expression profile analyses in order to identify the differentially expresssed genes induced by dietary carcinogen PhIP.

first: Xu

last: Yang

first: Hong

last: Wang


title: High-frequency head impacts cause chronic synaptic adaptations and long-term cognitive impairment.

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

overall_design: Refer to individual Series


title: Integrative analysis of reference epigenomes in polyploid crop Brassica napus L. [ChIP-seq]

first: Guan

last: Peng

first: Qing

last: Zhang

first: Pengpeng

last: Guan

first: Lun

last: Zhao


title: Serine Metabolism Antagonizes Antiviral Innate Immunity Through Preventing ATP6V0d2-mediated YAP Lysosomal Degradation

city: Tianjin

first: Long

last: Shen

address: 22 Qixiangtai Road

institute: School of Basic Medical Sciences, Tianjin Medical University

summary: Here, we demonstrate that virus-infected macrophages display decreased expression of serine synthesis pathway (SSP) enzymes. Suppressing the SSP key enzyme phosphoglycerate dehydrogenase (PHGDH) by genetic approaches enhanced IFN-b-mediated antiviral innate immunity in vitro and in vivo. To further explore its mechanism, we used high-throughput sequencing technology (RNA-seq) to assess gene expression in PHGDH-deficiency BMDMs and RAW264.7 macrophages.

overall_design: Examination of differential expressive genes in bone marrow derived macrophages extracted from wild type and PHGDH knockout mice or RAW264.7 cells after PHGDH knockdown.

first: Qiujing

last: Yu


title: Genome-wide maps of QKI-5, SREBP2, and POL II in eye lens cells

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

summary: We found the genome-wide co-binding of QKI-5 and SREBP2. Notably, the genomic distribution analysis revealed that the co-binding events between QKI-5 and SREBP2 highly occurred at the regions of the promoter/transcription start site (TSS), where active transcription was taken place in a lens cell-specific manner, which was indicated by POL II binding events. Cellular pathway analysis of the genes whose promoters were co-bound by QKI-5, SREBP2, and POL II showed a significant enrichment of the SREBP2-medaited cholesterol biosynthesis pathway, and QKI depletion led to reduced co-occupancies of SREBP2 and POL II on the promoters of the genes involved in cholesterol biosynthesis. These data suggest QKI-5 as a potential transcription co-activator mediating SREBP2-dependent cholesterol biosynthesis in eye lens cells.

overall_design: We performed ChIP-seq of QKI-5, SREBP2 and Pol II in human lens epithelial (HLE-B3) cells and neural stem cell-derived lens progenitor-like cells of WT and QKI KO.

first: Seula

last: Shin

first: Jian

last: Hu

first: Fei

last: Lan


title: RNA-seq analysis of in vivo region-specific PDX (G144) tumour cell populations and in vitro SOX10 overexpression in G144 cells

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: For in vivo experiments GFP+ G144 human GBM cells were injected in the caudoputament of CD-1 nude mice. After tumour formation, GFP+ G144 cells were acultely purified from microdissected mouse brain regions (tumour bulk, corpus callosum, striatum) and sequenced to determine gene expression profiles of the different invasive populations. In vitro G144 cells engineered to express inducible SOX10 vector were exposed to Doxycyline for two days and sequenced to determine gene expression profiles following SOX10 overexpression.

overall_design: 3 independent biological repeats were sequenced for analysis

first: Simona

last: Parrinello

first: Samuel

last: Marguerat


title: L-lactate supplementation influences toxin production of Clostridioides difficile via energy metabolism

city: Braunschweig

first: Rebekka

last: Biedendieck

address: Rebenring 56

department: Institute of Microbiology

institute: Technische Universtität Braunschweig

summary: Metabolomic and transcriptomic analysis of changes in the exponential and stationary phase of Clostridioides difficile after cultivation in casamino acids medium (reference) and supplemented with L-lactate and the connection to toxin production.

overall_design: Clostridioides difficile 630∆erm (DSM28645) was grown in a casamino acids medium (reference) and supplemented with 0.5 g/L L-lactate (Lac). Samples were taken at exponential growth (1/2 ODmax) and at the beginning of the stationary phase (ODmax).

first: Julia

middle: D

last: Hofmann

first: Annika

last: Michel

first: Dieter

last: Jahn

first: Dietmar

last: Schomburg

first: Meina

last: Neumann-Schaal


title: Microglial activation protects from vascular degeneration in a rat model of inflammatory retinal vasoregression.

city: Mannheim

first: Matthias

last: Kolibabka

state: Baden-Wurttemberg

address: Theodor-Kutzer-Ufer 1-3

department: 5th Medical Department

institute: University Hospital Mannheim

summary: Microglial activation represents a hallmark of inflammatory retinal diseases like diabetic retinopathy. Anti-inflammatory and especially microglia modulating approaches have been proposed as therapies for these diseases. In this study, clodronate-coated liposomes were intravitreally injected to investigate the effects of increased microglial activation on vasoregression in a model of retinal degeneration. Clodronate-coated liposomes, injected twice over a period of 5 weeks to study the effects of long term clodronate treatment on microglial activation, vasoregression (acellular capillary formation and pericyte loss) and to identify the pathways mediating the observed effects.

overall_design: 9-weeks-old PKD rats receiving two intravitreal injections at 4 and 8 weeks of age with Clodronate-coated liposomes (PKD + Clodronate, 5 samples), Controlliposomes (PKD + Controlliposomes, 6 samples) or PBS (PKD + PBS, 5 samples), 9-weeks-old uninjected PKD rats (PKD, 6 samples), 9-weeks-old SD rats receiving two intravitreal injections at 4 and 8 weeks of age with Clodronate-coated liposomes (SD + Clodronate, 6 samples) were analyzed, 9-weeks-old uninjected SD rats served as control group (SD, 6 samples).

first: Sarah

last: Riemann

first: Paulus

last: Wohlfart

first: Hans-Peter

last: Hammes


title: Transcriptome dynamics in early in vivo developing and in vitro produced porcine embryos

city: Berlin

first: Vera

last: van der Weijden

address: Ihnestraße 63-73

department: Department of Genome Regulation

institute: Max Planck Institute for Molecular Genetics

summary:
Background: The transcriptional changes around the time of embryonic genome activation in pre-implantation embryos indicate that this process is highly dynamic. In vitro produced porcine blastocysts are known to be less competent than in vivo developed blastocysts. To understand the conditions that compromise developmental competence of in vitro embryos, it is crucial to evaluate the transcriptional profile of porcine embryos during pre-implantation stages. In this study, we investigated the transcriptome dynamics in in vivo developed and in vitro produced 4-cell embryos, morulae and hatched blastocysts.

Results: In vivo developed and in vitro produced embryos displayed largely similar transcriptome profiles during development. Enriched canonical pathways from the 4-cell to the morula transition that were shared between in vivo developed and in vitro produced embryos included oxidative phosphorylation and EIF2 signaling. The shared canonical pathways from the morula to the hatched blastocyst transition were 14-3-3-mediated signaling, xenobiotic metabolism general signaling pathway, and NRF2-mediated oxidative stress response. The in vivo developed and in vitro produced hatched blastocysts were compared to identify molecular signaling pathways indicative of lower developmental competence of in vitro produced hatched blastocysts. A higher metabolic rate and expression of the arginine transporter SLC7A1 were found in in vitro produced hatched blastocysts.

Conclusions: Our findings suggest that embryos with compromised developmental potential are arrested at an early stage of development, while embryos developing to the hatched blastocyst stage display largely similar transcriptome profiles, irrespective of the embryo source. The hatched blastocysts derived from the in vitro fertilization-pipeline showed an enrichment in molecular signaling pathways associated with lower developmental competence, compared to the in vivo developed embryos.

overall_design: The transcriptome profile of single in vivo developed and in vitro produced 4-cell embryos (n = 5), morulae (n = 10) and hatched blastocysts (n = 10) were analysed by RNA-sequencing. At the hatched blastocyst stage, in vivo developed and in vitro produced embryos were compared.

middle: A

first: Meret

last: Schmidhauser

first: Mayuko

last: Kurome

first: Johannes

last: Knubben

first: Veronika

middle: L

last: Flöter

first: Eckhard

last: Wolf

first: Susanne

middle: E

last: Ulbrich


title: Functional and structural basis of extreme conservation in vertebrate 5’ untranslated regions

city: Stanford

first: Gun Woo

last: Byeon

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University


title: Identification of LncRNA TRAF3IP2-AS1 as a key regulator of IL-17 signaling through the SRSF10-IRF1-Act1 axis in autoimmune diseases

city: Wuhan

first: Chenhui

last: Wang

state: Hubei

address: 1037 Luoyu Rd

institute: Huazhong University of Science and Technology

summary: Our study indicates that lncRNA TRAF3IP2-AS1 serving as a negative regulator of Act1 transcriptional expression and IL-17 signaling pathway activity,recruits SRSF10 to downregulate the transcription of IRF1, which is itself a transcriptional factor for Act1. And the psoriasis-susceptible variant A4165G of TRAF3IP2-AS1 is a gain-of-function mutant that binds more strongly than the wild-type form to SRSF10. It means that TRAF3IP2-AS1 or SRSF10 may be a good target for the treatment of human IL-17-related autoimmune diseases.

overall_design: The differentially expressed genes(DEGs) and alternative splicing events were analyzed in control and SRSF10-overexpression cells by  transcriptomic analysis.

first: Ruirui

last: He

first: Songfang

last: Wu

first: Ru

last: Gao


title: Nuclear IL-33/SMAD signaling axis promotes cancer development in chronic inflammation

status: Public on Jan 28 2021

city: Charlestown

first: Jongho

last: Park

address: Building 149 13th street

department: Cancer center immunology

institute: MGH


title: Analysis of transcriptional change by IL-33 [ChIP-seq]

summary:
To know target gene of IL-33 full-length, we generated IL-33 full length and IL-33 cytokine construct.
After overexpression each construct in cell line, we did ChIP assay and analyzed ChIP-seq. As a result,
we found different gene regulation by IL-33

overall_design: Analysis of finding target gene regulated by IL-33 in keratinocyte cell line

first: Shadmehr

last: Demehri


title: Transcriptomic Analysis of Wheat Seedling Responses to the Systemic Acquired Resistance Inducer N-Hydroxypipecolic Acid

first: Weihua

last: Tang

address: 300 Fenglin Rd

institute: Shanghai Inst. Plant Phys. & Eco.

summary: This experiment is to assess global changes of wheat gene expression in response to N-hydroxypipecolic acid (NHP), which is an inducer of plant systemic accquired resistance. Six plates (24 seeds per plate) of wheat (Triticum aestivum) cultivar Zhongyuan 98-68 were planted under 25ºC incubator. After three days, three plates of seedlings were treated with 1 μL 1 mM NHP per seedling, called as NHP-rep 1,2,3. The other three were treated with water and used as the control group (called as water-rep 1,2,3). The coleoptiles were collected after one day after the treatment. Each plate serves as a biological replicate for its treatment group for RNA sequencing.

overall_design: Three biological replicates of four-day-old wheat seedling at one day post water treatment were named water-rep 1, 2, 3, used as control. Three biological replicates of four-day-old wheat seedling at one day post NHP treatment (1 μL 1mM NHP per seedling) were named NHP-rep 1, 2, 3. Total RNA extracted from water-rep 1, 2, 3 and NHP-rep 1, 2, 3 were used for library preparation. The RNA sequencing was performed at Sinotech Genomics. The libraries for sequencing were prepared using SureSelect Strand-Specific RNA Component kit. RNA sequencing was performed using an Illumina NovaSeq 6000 machine to obtain 150 nt paired-end reads.

first: Eric

last: Zhang


title: Nanostring Wnt Pathway Panel of Metastatic Melanoma Patients Prior to Anti-PD-1 Treatment

city: Durham

first: Nicholas

last: DeVito

state: NC

address: 2301 Erwin Road

institute: Duke University

summary: FFPE tumor samples from metastatic melanoma patients were extracted and a Nanostring Wnt Pathway panel was performed

overall_design: Wnt pathway components with custom immune markers were selected to determine differences between responders and non-responders to anti-PD-1

first: Brent

last: Hanks


title: Cellular and molecular characterization of the dural sinuses as a neuroimmune interface [vasculature]

status: Public on Jan 27 2021

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

summary: Meningeal immunity is critical to appropriate CNS function. Here we perform single cell RNA-sequencing to investigate how brain and meningeal stromal populations regulate immune trafficking and retention in young and old mice.

overall_design: 15 young (2 months) and 15 old (24 months) mice were sacrificed with euthasol and brain and dural meninges were collected. Tissues were dissociated with collagenase 8 to obtain a single cell suspension and sorted by FACS based on the following phenotypes: endothelial DAPI-Singlets CD45-CD31+CD13- and mural DAPI-Singlets CD45-CD31-CD13+. Equal amounts of  endothelial and mural populations were pooled for single cell sequencing.

first: Justin

last: Rustenhoven

first: Taitea

last: Dykstra


title: High-frequency head impacts cause chronic synaptic adaptations and long-term cognitive impairment [Memantine study]

first: Bevan

last: Main

overall_design: Mice were subjected to an injection of Memantine or Saline i.p daily 1hr prior to HF-HI or a sham procedure. 24 hours after injury, RNA was isolated from brains. Bulk RNA sequencing was performed on 4 experimental groups with 4 samples per group (Saline+Sham, Saline+HFHI, Memantine+Sham, Memantine+HFHI)

first: Stephanie

last: Sloley

first: Charisse

last: Winston

first: Alex

last: Harvey

first: Alice

last: Kaganovich

first: Holly

last: Korthas

first: Adam

last: Caccavano

first: D

last: Zapple

first: Jian-Young

first: John

last: Partridge

first: Mark

last: Cookson

first: Stefano

last: Vicini

last: Burns


title: High-frequency head impacts cause chronic synaptic adaptations and long-term cognitive impairment [1m post-HFHI]

overall_design: Mice were subjected to HF-HI or a sham procedure. Bulk RNA sequencing was performed on Sham and HF-HI experimental groups at 1m post injury.

last: Wu


title: Single cell sequencing of whole eye organoids to identify ocular cell susceptible to infection with SARS-CoV2 and the viral response in infected cells

status: Public on Jan 26 2021

city: Kgs. Lyngby

first: Anne

middle: Zebitz

last: Eriksen

address: Produktions Torvet 423

department: Health Technology

country: Denmark

institute: Technical University of Denamrk

summary: We diffrenciated organoid cultures reprecenting ocular cell, from human pluipotent stem cells (hPSCs). The organoids were grown following a protocol for self-formed ectodermal autonomous multizone (SEAM) where the different orcular cells will form in concentric circles (zone) representing surface ectoderm, cornea, RPE, neural progenitors, dorsal optic cup and periocular mesenchyme.   We use this eye organoid to investigate whether the ocular surface is sucessable to infection with SARC-CoV-2. We show that a sup-group of cells get readerly infected after expositor to the virus through the media, at 1MOI for 24hours. We identify this cells population as limbal/corneal cells.  By anchoring the data from the infected SEAM culture to a not-infected SEAM culture we investigated the cellular response to infection. We find that both a NFkB and a interferon response is mounted, and interestingly the Interferon pathway genes are suppressed in the infected cells compared to the nearest neighbor clusters while the NFkB pathway is more highly expressed in the infected cell compared to neighbor cells.

overall_design: Single cell sequencing of a SEAM culture infected with SARS-CoV2 by exposure to the virus through the media at 1MOI for 24h and not-infected SEAM culture.

last: Zebitz Eriksen

first: Rasmus

last: Møller

first: Bar

last: Makovoz

first: Skyler

last: Uhl

first: Benjamin

last: tenOver

first: Timothy

last: Blenkinsop


title: Cellular and molecular characterization of the dural sinuses as a neuroimmune interface [Myeloid cells]

first: Jonathan

last: Kipnis

overall_design: At the age of 2 months, WT mice were subjected to one intracisternal injection of Ovalbumin coupled with an Alexa-647 (5ul), and, at the same time, to one intravenous injection of OVA coupled with an Alexa-488. Myeloid cells from the dura were sorted by FACS (CD45+CD11b+ Ly6g-) one hour after both injections. In total, 4 samples (double negative, OVA-488 positive only, OVA 647 positive only, double positive cells) were collected from 20 WT C57BL/6J mice.

first: Justin

last: Rustenhoven

first: Taitea

last: Dykstra


title: scRNAseq of MMTV-Neu primary site and lung cancer cells in early and late stage

city: New York

first: Julio

last: Aguirre-Ghiso

state: NY

address: 1468 Madison Avenue, A24-64e

institute: Icahn School of Medicine at Mount Sinai

summary:
Cancer cells can disseminate from early-evolved primary lesions. It is thought that a state of early disseminated cancer cell (early DCC) dormancy would precede genetic maturation of DCCs and metastasis initiation. Here we reveal at single cell resolution a previously unrecognized role of mesenchymal- and pluripotency-like programs in coordinating early cancer cell spread and a long-lived dormancy program in early DCCs. We identify in early lesions and early DCCs, the transcription factor ZFP281 as an inducer of mesenchymal- and primed pluripotency-like programs, which is absent in advanced primary tumors and overt metastasis. ZFP281 not only controls the early spread of cancer cells but also locks early DCCs in a prolonged dormancy state by preventing the acquisition of an epithelial-like proliferative program. Thus, ZFP281-driven dormancy of early DCCs may be a rate-limiting step in metastatic progression functioning as a first barrier that DCCs must overcome to then undergo genetic maturation.
This data set aims for a general characterization of the MMTV-Neu mouse model (primary site and lung DCCs) in early and late stages of cancer progression.

overall_design: Single cell RNA profile of early and late breast cancer cells of MMTV-neu mice in the primary site (early lesions, EL; primary tumors, PT) and lungs (early lung disseminated cancer cells, eL DCCs; late lung DCCs, LL DDCs)

first: Ephraim

last: Kenigsberg

first: Ana

last: Nobre


title: scRNAseq of MMTV-Neu lung cancer cells in early and late stage

summary:
Cancer cells can disseminate from early-evolved primary lesions. It is thought that a state of early disseminated cancer cell (early DCC) dormancy would precede genetic maturation of DCCs and metastasis initiation. Here we reveal at single cell resolution a previously unrecognized role of mesenchymal- and pluripotency-like programs in coordinating early cancer cell spread and a long-lived dormancy program in early DCCs. We identify in early lesions and early DCCs, the transcription factor ZFP281 as an inducer of mesenchymal- and primed pluripotency-like programs, which is absent in advanced primary tumors and overt metastasis. ZFP281 not only controls the early spread of cancer cells but also locks early DCCs in a prolonged dormancy state by preventing the acquisition of an epithelial-like proliferative program. Thus, ZFP281-driven dormancy of early DCCs may be a rate-limiting step in metastatic progression functioning as a first barrier that DCCs must overcome to then undergo genetic maturation.
This data set aims to characterize MMTV-Neu early and late lung disseminated cancer cells (DCCs).

overall_design: RNA profile of MMTV-Neu early and late lung disseminated cancer cells (DCCs)


title: ZFP281 ChIP-sequencing of MMTV-Neu early lesion (EL) and primary tumor (PT) spheres

summary:
Cancer cells can disseminate from early-evolved primary lesions. It is thought that a state of early disseminated cancer cell (early DCC) dormancy would precede genetic maturation of DCCs and metastasis initiation. Here we reveal at single cell resolution a previously unrecognized role of mesenchymal- and pluripotency-like programs in coordinating early cancer cell spread and a long-lived dormancy program in early DCCs. We identify in early lesions and early DCCs, the transcription factor ZFP281 as an inducer of mesenchymal- and primed pluripotency-like programs, which is absent in advanced primary tumors and overt metastasis. ZFP281 not only controls the early spread of cancer cells but also locks early DCCs in a prolonged dormancy state by preventing the acquisition of an epithelial-like proliferative program. Thus, ZFP281-driven dormancy of early DCCs may be a rate-limiting step in metastatic progression functioning as a first barrier that DCCs must overcome to then undergo genetic maturation.
This data set aims identify ZFP281 targets in MMTV-Neu early lesion (EL) and primary tumor (PT) cells

first: Xin

last: Huang

first: Jihong

last: Yang


title: Maternal Schistosomiasis CD45+

city: Salt Lake City

first: Keke

middle: Celeste

last: Fairfax

state: UT

address: 15 N Medical Drive East

department: Pathology

institute: University of Utah

summary: Maternal helminth infections are a global public health concern and correlate with altered infant immune responses to some childhood immunizations, but a mechanistic understanding of how maternal helminth infection alters the cellular immune responses of offspring is lacking. Here we establish a model of maternal Schistosoma mansoni infection in dual IL-4 reporter mice. We find that offspring born to mothers infected with S. mansoni have impaired production of IL-4 during homoeostasis, and following immunization with a Tetanus-Diphtheria vaccine. Single-cell RNASeq analysis of immunized offspring identified egg antigen-dependent reductions in B-cell cell cycle and proliferation-related genes.

overall_design: Offspring from S. mansoni patently infected, S. mansoni single-sex infected (adults only), and mock infected control mothers were immunized with 1/10th the human dose of a comercial tetanus/diphtheria vaccine. At Day 7 post immunization single-cell suspension form 6-8 draining lymph nodes per group were pooled and stained with Dapi (Sigma) and anti-CD45. Live CD45+ cells were sorted via BD FACSAria cell sorter and washed once in PBS containing 0.04% BSA. Samples were then processed for SCseq via a 10× platform (single cell 3'V2) according to the manufacturer’s instructions (10× Genomics). Paired-end RNASeq (125 cycles) was performed via an Agilent HiSeq next- generation sequencer. S

first: Diana

last: Cortes-Selva

first: Lisa

last: Gibbs

first: H

last: Ekiz


title: Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice

status: Public on Jan 17 2021

city: HANGZHOU

first: XIUWEN

last: TANG

address: YUHANGTONG ROAD

department: BIOCHEMISTRY AND GENETICS

institute: ZHEJIANG UNIVERSITY SCHOOL OF MEDICINE

summary: The nuclear phosphatase mitogen-activate protein kinase phosphatase-1 (MKP-1) is a key negative regulator of the innate immune response through the regulation of the biosynthesis of proinflammatory cytokines. In colorectal cancer (CRC), which is induced mainly by chronic inflammation, Mkp-1 overexpression was found in addition to disturbances in Mkp-1 functions, which may play a role in cancer development in different types of tumors. However, the potential molecular mechanisms by which Mkp-1 influences CRC development is not clear. Here, we performed global gene expression profiling of Mkp-1 KO mice using RNA sequencing (RNA-seq) to explore the role of Mkp-1 in CRC progression using transcriptome analysis.

overall_design: Two main categories including wild type that subdivided to three subgroups; wild type control (WT-C), wild type adenoma stage (WT-AS), wild type carcinoma stage (WT-CS), and Mkp-1 KO type that subdivided to three subgroups; Mkp-1 KO control (Mkp-1 KO C), Mkp-1 KO adenoma stage (Mkp-1 KO AS), Mkp-1 KO carcinoma stage  (Mkp-1 KO CS).

first: Xiuwen

last: Tang

first: Ahmed

last: Hammad


summary: Cancer cells can disseminate from early-evolved primary lesions. It is thought that a state of early disseminated cancer cell (early DCC) dormancy would precede genetic maturation of DCCs and metastasis initiation. Here we reveal at single cell resolution a previously unrecognized role of mesenchymal- and pluripotency-like programs in coordinating early cancer cell spread and a long-lived dormancy program in early DCCs. We identify in early lesions and early DCCs, the transcription factor ZFP281 as an inducer of mesenchymal- and primed pluripotency-like programs, which is absent in advanced primary tumors and overt metastasis. ZFP281 not only controls the early spread of cancer cells but also locks early DCCs in a prolonged dormancy state by preventing the acquisition of an epithelial-like proliferative program. Thus, ZFP281-driven dormancy of early DCCs may be a rate-limiting step in metastatic progression functioning as a first barrier that DCCs must overcome to then undergo genetic maturation.

overall_design: RNA sequencing of MMTV-Neu early lesion (EL) and primary tumor (PT) spheres, which recapitulate the in vivo behavior of EL and PT lesions


title: RNA-seq and Ribosome immunoprecipitation results from purified Drosophila male secondary cells

status: Public on Jan 20 2021

city: Geneva

first: Robert

last: Maeda

address: 30 Quai E. Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

summary: Even in well-characterized genomes, many transcripts are considered non-coding RNAs (ncRNAs) simply due to the absence of large Open Reading Frames (ORFs). However, it is now becoming clear that many small ORFs (smORFs) produce peptides with important biological functions. In the process of characterizing the ribosome-bound transcriptome of an important cell type of the seminal fluid producing accessory gland of Drosophila melanogaster, we detected an RNA, previously thought to be non-coding called, male specific abdominal (msa). Notably, msa is nested in the HOX gene cluster of the Bithorax complex and is known to contain a micro RNA within one of its introns. We find that this RNA encodes a novel “micropeptide“ (9 or 20 amino acids, MSAmiP) that is expressed exclusively in the secondary cells of the male accessory gland, where it seems to accumulate in nuclei. Importantly, loss of function of this micropeptide causes defects in sperm competition. In addition to bringing new insights into the biology of a rare cell type, this work underlines the importance of small peptides, a class of proteins now emerging as important actors in complex biological processes.

overall_design: Secondary cell samples transcripts from 4 experimental genotypes are included.  Wild type secondary cells (wt), iab-6 D1 mutant secomndary cells (D1), and mutants where the iab-8 micropeptide is removed (miP) are analyzed by RNA-seq from fluorescently sorted secondary cells.  The ribosome immunoprecipitation (RIP) samples are made from ribosomes immunoprecipitated from secondary cells.  3 biological replicates of each genotype are submitted.

first: Clément

last: Immarigeon

first: François

last: Karch


title: Transcriptional profiling of HIV dual reporter infected Jurkat T cells using CAGE.

status: Public on Jan 21 2021

city: Kyoto

first: Hiroyuki

last: Matsui

address: 54 Kawahara-cho, Shogoin, Sakyo-ku

department: Hematology and Oncology

country: Japan

institute: Kyoto University

summary: This study examine the transcriptional profiling of HIV dual reporter non-infected, latetnly infected and productively infected Jurkat T cells.

overall_design: HIV dual reporter non-infected, latetnly infected and productively infected Jurkat T cells were profiled by CAGE seq. Jurkat T cells not exposed to HIV dual reporter virus (non-exposed) were also profiled by CAGE seq.

first: K

last: Shirakawa

first: A

last: Takaori-Kondo

first: Y

last: Murakawa

first: S

last: Hirabayashi


title: Interception targets of Angelica Gigas Nakai root extract vs. pyranocoumarins in prostate early lesions and neuroendocrine carcinomas in TRAMP mice

status: Public on Jan 15 2021

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

summary: We reported efficacy of Angelica gigas Nakai (AGN) root ethanol extract and equimolar decursin (D)/decursinol angelate (DA) through daily gavage starting at 8 weeks of age (WOA) to male transgenic adenocarcinoma of mouse prostate (TRAMP) mice such that these modalities suppressed precancerous epithelial lesions in their dorsolateral prostate (DLP) to similar extent, but AGN extract was better than the D/DA mixture at promoting the survival of mice bearing prostate neuroendocrine carcinomas (NECa) to 28 WOA (Tang et al, Cancer Prev Res 2015). Here, we compared by microarray hybridization the mRNA levels in pooled DLP tissues and individual NECa to characterize potential molecular targets of AGN extract and D/DA. Clustering and principal component analyses supported distinct gene expression profiles of TRAMP DLP vs. NECa. Pathway Enrichment, Gene Ontology and Ingenuity Pathway Analyses of differential genes indicated that AGN and D/DA affected chiefly processes of lipid and mitochondrial energy metabolism and oxidation-reduction in TRAMP DLP, while AGN affected neuronal signaling, immune systems and cell cycling in NECa. Protein-Protein Interaction Network analysis predicted and reverse transcription-PCR verified multiple hub genes common in the DLP of AGN- and D/DA-treated TRAMP mice at 28 WOA and select hub genes attributable to the non-D/DA AGN components. The vast majority of hub genes in the AGN-treated NECa differed from those in TRAMP DLP. In summary, the transcriptomic approach illuminated vastly different signaling pathways and networks, cellular processes and hub genes of two TRAMP prostate malignancy lineages and their associations with the interception efficacy of AGN and D/DA.

overall_design: TRAMP mice treated with AGN and sacrificed at 16 and 28 WOA (AGN TRAMP DLP 16wk [n=10] or 28wk [n=14]); TRAMP mice treated with D/DA and sacrificed at 16 and 28 WOA (D/DA TRAMP DLP 16wk [n=11] or 28wk [n=13]). In addition, we selected 3 NECa each from vehicle-treated mice and AGN-treated mice and 2 WT whole prostates (24-28 WOA) for RNA isolation. RNA from the 16 samples was extracted by using the AllPrep DNA/RNA/Protein Mini kit (QIAGEN Inc., Valencia, CA) according to the manufacturer's protocol.

first: Su-Ni

first: Jinhui

last: Zhang

first: Cheng

first: Junxuan

last: Lü


title: A unique histone 3 lysine 14 chromatin signature underlies tissue-specific gene regulation

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

country: Australia

institute: John Curtin School of Medical Research, The Australian National University

summary: Organismal development and cell differentiation critically depend on chromatin state transitions. The in vivo functions of individual histone modifications, however, remain incompletely understood. Whereas acetylation of histone 3 lysines 9 and 27 (H3K9ac and H3K27ac) and methylation of H3K4 are common in transcriptionally active genes, certain developmentally regulated genes lack these modifications. Here, we show that a key set of genes lacking canonical histone marks are decorated with H3K14ac in Drosophila melanogaster. We created flies with a mutant histone H3 containing a lysine 14-to-arginine substitution, and demonstrate that H3K14 is essential for the expression of genes devoid of canonical histone modifications in the embryonic gut and in the larval wing imaginal disc. As a result, H3K14R mutant animals die as second instar larvae, and mutant mitotic clones cause defects in the wing margin of adult flies. We find that the bromodomain in Brahma (Brm), the catalytic subunit of the Drosophila SWI/SNF complex BAP, recognizes H3K14ac and that brm acts in the same genetic pathway as H3K14R. Our results show that acetylation of a single lysine is essential at genes devoid of canonical histone marks and uncover an important requirement for H3K14 in tissue-specific gene regulation.

overall_design: Analysis of gene expression from 3 different samples by RNA-seq (H3K14R mutant and controls), genomic distribution of H3K14ac in embryo and wing disc by ChIP-seq, chromatin accessibility in embryos (H3K14R mutant and controls) by ATAC-seq and RNA Polymerase II occupancy in wild-type and H3K14R embryos by CUT and TAG .

first: Isabel

last: Regadas

first: Roshan

last: Vaid

first: Sergey

last: Belikov

first: Gunjan

last: Dixit

first: Mattias

last: Mannervik


title: BROAD TRANSCRIPTIONAL FIRING REPRESSES BACTERICIDAL ACTIVITY IN HUMAN AIRWAY NEUTROPHILS

status: Public on Jan 22 2021

city: Atlanta

first: Diego

last: Moncada

state: Georgia

address: 201 Dowman Dr

department: Pediatrics

institute: Emory University

summary: Neutrophils are often considered terminally differentiated and poised for bacterial killing. In chronic diseases such as cystic fibrosis (CF), an unexplained paradox pits massive neutrophil presence against prolonged bacteria infections. Here, we show that neutrophils recruited to CF airways in vivo and in an in vitro transmigration model display rapid and broad transcriptional firing, leading to an upregulation of survival and anabolic genes, and a downregulation of antimicrobial genes. Newly transcribed RNAs are mirrored by the appearance of corresponding proteins, confirming active translation in these cells. Remarkably, treatment by the RNA polymerase II and III inhibitor alpha-amanitin restored expression of key antimicrobial genes, and increased bactericidal capacity of CF airway neutrophils in vitro and in short-term sputum cultures ex vivo. Broadly, our findings show that neutrophil plasticity is regulated at the terminal organ via RNA and protein synthesis, leading to adaptations that profoundly impact their canonical functions (i.e., bacterial clearance).

overall_design: Using an in vitro model, airway neutrophils were collected after 1, 2, 4 and 6 hour of transmigration towards CFASN

first: Camilla

last: Margaroli

last: Moncada Giraldo

first: Rabindra

last: Tirouvanziam


title: Dysregulated transcriptional responses to SARS-CoV-2 in the periphery support novel diagnostic approaches

status: Public on Jan 14 2021

first: Florica

last: Constantine

address: 304 Research Drive

summary: In order to elucidate novel aspects of the host response to SARS-CoV-2 we performed RNA sequencing on 77 peripheral blood samples across 46 subjects with COVID-19 and compared them to subjects with seasonal coronavirus, influenza, bacterial pneumonia, and healthy controls. The transcriptome in peripheral blood reveals unique aspects of the immune response in COVID-19 and provides for novel biomarker-based approaches to diagnosis.

overall_design: To define the host peripheral blood transcriptional response in subjects with SARS-CoV-2 infection, we performed RNA sequencing on samples from 46 individuals with PCR-positive, symptomatic SARS-CoV-2 infection, 14 of which were sampled at multiple timepoints. Subjects were enrolled when they presented for clinical care, and the time from symptom onset was recorded for each individual sample collected (range 1-35 days). Subjects with COVID-19 were divided based on disease severity and time from symptom onset (early ≤10 days, middle 11-21 days, late >21 days). As comparators, we profiled banked blood samples from patients presenting to the Emergency Department with acute respiratory infection (ARI) due to seasonal coronavirus (n=59), influenza (n=17) or bacterial pneumonia (n=20), and matched healthy controls (n=19).

first: Micah

last: McClain

first: Yiling

last: Liu

first: Thomas

last: Burke


title: Analysis of expression changes between IL-33 Knock out and WT mice in skin chronic inflammation

first: Jongho

last: Park

state: MA

summary:
To find differential expression gene between IL-33KO and WT mice, we collected skin epithelial RNA sample after all of mice were treated with DNFB for 22 days.  (allergen treat)
After RNA-seq analysis, we got 203 genes which showed different expression level between IL-33KO and WT mice after allergen treated.

overall_design: Analysis of differentially regulated genes in WT versus IL-33KO

first: Shadmehr

last: Demehri


title: Genome-wide gene expression profile of human medulloblastoma cell lines

status: Public on Jan 16 2021

city: Dallas

first: Lin

last: Xu

address: H106A,5323 Harry Hines Blvd.

department: Population & Data Sciences

institute: UT Southwestern Medical Center

summary: To study the effect of constitutive REST expression on DAOY, UW228 and UW426 cells, we generated low and high-REST (LR/HR) isogenic pairs of the three human medulloblastoma (MB) cell lines and performed RNA-Seq analysis. We also analyzed the expression profiles of D283 cells (Group3/4 MB cell line) with DAOY, UW228 and UW26 (SHH MB cell line ) to show the subgroup specific expression profiles.

overall_design: mRNA profiles of human medulloblastoma cell lines

first: Vidya

last: Gopalakrishnan


title: Transcription Factor Overexpression Drives Reliable Differentiation of Retinal Pigment Epithelium From Human Induced Pluripotent Stem Cells

status: Public on Jan 13 2021

city: San Francisco

first: Bruce

last: Conklin

address: 1650 Owens St

institute: Gladstone Institutes

summary: We report a robust, scalable method to generate iPSC-RPE using doxycycline-inducible expression of eye field transcription factors OTX2, PAX6 and MITF paired with RPE-permissive culture media. Doxycycline addition induces exogenous expression of these transcription factors in patient- and wildtype iPSCs to efficiently produce monolayers of RPE with characteristic morphology and gene expression. Further, these RPE monolayers display functionality features including light absorption via pigmentation, polarity-driven fluid transport, and phagocytosis. With this method, we achieve a highly efficient and easily scalable differentiation without the need for mechanical isolation or enrichment methods, generating RPE cultures applicable for in vitro studies.

overall_design: We analyzed samples from 3 different stages of the differentiation for each cell line, with 3 replicates each, resulting in 18 samples total.

first: Tessa

last: Dewell

first: Ketrin

last: Gjoni

first: Angela

middle: Z

first: Ashley

last: Libby

first: Anthony

last: Moore

first: Po-Lin

last: So


title: Cellular and extracellular vesicle miRNA profiles in GFP-PC3 and cavin-1-PC3 cell lines.

city: Herston

first: Harley

middle: Rose

last: Robinson

state: QLD

address: 300 Herston Road

institute: QIMRBerghofer

type: Non-coding RNA profiling by high throughput sequencing

summary: This study assessed exosomal and cellular miRNA profiles in GFP-PC3 cells and ectopically expressed cavin-1 PC3 cell lines. To understand the consequences of cavin-1 on extracellular vesicle (EV)-contained miRNAs, a small RNA-seq experiment was performed on cells and secreted EVs for GFP-PC3 and cavin-1-PC3 cells. Small RNA were selected for sequencing using the NEBNext Small RNA library Prep Kit. Libraries were size selected using a Perkin Elmer Labchip XT. Whole cell and EV libraries were multiplexed from three biological replicates and sequenced on an Illumina NextSeq500 mid-output run at a read depth of 1million reads per sample. While the raw data was mapped to the human miRNAome using RNA-STAR and miRBase (v21) as reference, 317 mature miRNAs were identified in EVs at varying abundances depending on cell of origin. The 317 miRNAs identified in both cell and EVs were further processed. After RUVseq normalization, DESeq2 analysis was used to identify differences between cellular miRNA profiles and EV miRNA profiles from the two different cell lines. This analysis ultimately defined the repertoire of selectively and passively exported exosomal miRNAs mediated by non-caveolar caveolin-1 and cavin-1 in a prostate cancer cell line. Aim: To assess exosomal miRNA compositional changes evoked by ectopic expression of cavin-1 in the PC3 advanced prostate cancer cell line. Objectives: 1. Determine differential expression of miRNAs in cells and 2. determine differential abundance of miRNAs in extracellular vesicles secreted from cavin-1 expressing or GFP expressing cells.

overall_design: miRNA profiles were sequenced from two different cell lines and corresponding extracellular vesicles, in triplicate, on an Illumina NextSeq500

first: Michelle

last: Hill

first: Alexandre

last: Cristino

first: Nicole

last: Cloonan


title: Efficient RNA polymerase II pause release requires U2 snRNP function

city: Göttingen

first: Sara

middle: Patricia

last: Monteiro Martins

address: Fassberg 11

department: Molecular Biology

institute: MPI for biophysical chemistry

summary: Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis in human cells. Multiomics analysis reveals that U2 snRNP inhibition increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity in the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires formation of functional spliceosomes, and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.

overall_design: Effect of U2 snRNP inhibition on transcription

first: Livia

last: Caizzi

last: Monteiro-Martins

first: Björn

last: Schwalb

first: Kseniia

last: Lysakovskaia

first: Jana

last: Schmitzova

first: Anna

last: Sawicka

first: Ying

last: Chen

first: Michael

last: Lidschreiber

first: Patrick

last: Cramer


title: Single-cell RNA sequencing of human nasal swab from COVID-19 patient

status: Public on Jan 12 2021

city: Daejeon

first: JUNGMO

last: KIM

state: -- None selected --

address: 291 Daehak-ro, Yuseong-gu

department: Center for Vascular Research

country: South Korea

institute: Institute for Basic Science

summary: Understanding on pathogenesis of COVID-19 is rapidly growing, but primary target cells of SARS-CoV-2 infection is still not known. Here, we performed single cell RNA sequencing on human nasal swab from COVID-19 patient to investigate the expression patterns of host cell entry factors of SARS-CoV-2.

overall_design: Single cells from COVID-19 patients' nasal swabs  were isolated and single-cell transcriptome libraries were generated

first: Gou

last: Koh

first: JungMo

last: Kim


title: Cellular and molecular characterization of the dural sinuses as a neuroimmune interface [T cells]

first: Jonathan

last: Kipnis

summary: Meningeal immunity is critical to appropriate CNS function. Here we perform single cell RNA-sequencing to investigate how brain and meningeal stromal populations regulate immune trafficking and retention in young and old mice.

overall_design: Single cell supspensions were prepared from the meninges of 3 and 22 month old mice. Single, live (Aqua-), CD45+, CD19-, F4/80-, NK1.1- TCRb+ T cells were FACS sorted using a BD Influx system. Each sample consists of T cells pooled from 4 individual mice.

first: Justin

last: Rustenhoven

first: Taitea

last: Dykstra


title: Next generation sequencing analysis of control and KSR1 knockdown CRC cell line translatomes.

status: Public on Jan 10 2021

city: Omaha

first: Chaitra

last: Rao

state: NE

address: 505 S 45th St

department: Eppley Institute

institute: University of Nebraska Medical Centre

summary: KSR1 signaling alters the translational landscape of human CRC cells to support their survival. To determine the effect of KSR1 on translatomes in colon cancer cells, we performed genome-wide polysome profiling. We stably expressed short hairpin RNA (shRNA) constructs targeting KSR1 or a non-targeting control in two K-Ras mutant CRC cell lines, HCT116 and HCT15. We isolated and quantified both total mRNA and efficiently translated mRNAs (associated with ≥ 3 ribosomes) using RNA sequencing. We used Anota2seq to calculate translation efficiency (TE) by comparing the differences in efficiently translated mRNAs to the total transcript of each mRNA.

overall_design: HCT116 and HCT15 control and KSR1 knockdown cells, total RNA and polysomal RNA was extracted using sucrose gradient fraction from three independent experiments for each condition.

first: Robert

last: Lewis

first: Siddesh

last: Southekal


title: Role of TLR7 and IFNAR1 in lacrimal gland autoimmunity in NOD mice

status: Public on Jan 04 2021

city: Iowa City

first: Scott

middle: Matthew

last: Lieberman

state: IA

address: 500 Newton Road, 2191A ML

institute: University of Iowa

summary: NOD mice spontaneously develop lacrimal gland inflammation. NOD mice that lack TLR7 or that lack IFNAR1 are protected from developing lacrimal gland inflammation. RNA sequencing studies were performed to compare gene expression profiles in lacrimal glands from wild-type (WT) vs Tlr7 knockout or Ifnar1 knockout nonobese diabetic (NOD) mice to determine disease-relevant gene and pathway profiles upregulated in WT lacrimal glands in either a TLR7- or IFNAR1-dependent manner.

overall_design: RNA-seq was performed using RNA isolated from lacrimal glands of male NOD mice including wild-type, Tlr7 knockout, and Ifnar1 knockout strains.

middle: M

first: Ivy

last: Debreceni

last: Chimenti

first: Merri-Grace

last: Allred


title: Spatiotemporal transcriptional dynamics of the cycling mouse oviduct

city: Austin

last: Battenhouse

address: 100 East 24th St., Stop A5000

department: Center for Biomedical Research Support

institute: The University of Texas at Austin

summary: Female fertility in mammals requires the iterative remodeling of the entire adult female reproductive tract across the menstrual/estrous cycle. Here we examine global transcriptional dynamics of the mouse oviduct along the anteroposterior axis and across the estrous cycle. Though we observed robust patterns of differential oviduct gene expression along the anteroposterior axis, we found surprisingly few changes in gene expression across the estrous cycle, in marked contrast to other mammals. We speculate that this is an evolutionarily derived state that may reflect the extremely rapid five-day mouse estrous cycle.

overall_design: Mouse oviducts from 7-9 week-old estrous-cycle-staged Swiss Webster female mice were linearized and dissected in duplicate for each of the four estrous stages across both anterior and posterior regions. RNA was extracted from the oviduct Anterior: stage Proestrus n=2, Estrus n=2, Metestrus n=2, Diestrus n=2. RNA was extracted from the oviduct  Posterior: stage Proestrus n=2, Estrus n=2, Metestrus n=2, Diestrus n=2.

first: Elle

last: Roberson

first: Riddhiman

middle: K

last: Garge

first: Ngan

last: Tran

first: Edward

last: Marcotte

first: John

middle: B

last: Wallingford


title: Gene expression profiling of CD44-CD133+ and CD44+CD133+ Caco2 population

status: Public on Jan 01 2021

city: SEOUL

first: JUNG

middle: HOON

last: KIM

state: MAPOGU

address: SOGANG R 1206

department: LIF SCIENCE

institute: SOGANG UNIV

overall_design: We confirmed gene expression profiling between two population through Agilent microchip data

first: J

middle: H

last: Kim


title: Single-cell transcriptomes of developing and adult olfactory receptor neurons in Drosophila

status: Public on Feb 01 2021

first: Hongjie

last: Li

address: one Baylor Plaza

summary: Recognition of environmental cues is essential for the survival of all organisms. Precise transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes of Drosophila olfactory receptor neurons (ORNs), thermosensory and hygrosensory neurons from the third antennal segment at an early developmental and adult stage. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using these receptors and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuronal types across multiple developmental stages. Cell-type-specific transcriptomes, in part, reflected axon trajectory choices in early development and sensory modality in adults. Our analysis also uncovered type specific and broadly expressed genes that could modulate adult sensory responses. Collectively, our data reveal important transcriptomic features of sensory neuron biology and provides a resource for future studies of their development and physiology.


title: Transcriptomic and Network Analysis of Minor Salivary Glands of Patients with Sjögren’s Syndrome

status: Public on Jan 06 2021

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

overall_design: Gene Expression analysis of minor salivary glands from Sjögren's and histologically normal patients

first: Akinsola

last: Oyelakin


title: Comparative transcriptomics for growth of engineered Pseudomonas putida strains when grown using ammonium or nitrate nitrogen sources

city: Richland

first: Joshua

last: Elmore

state: WA

address: 902 Battelle Blvd

institute: PNNL

summary: We report the transcriptomic profiles of 2 different Pseudomonas putida derivatives when they are grown in MME medium supplemented with either ammonium or nitrate as the sole nitrogen source. Expression of both heterologous and native genes are examined.

overall_design: Comparison of 2 P. putida strains when grown using nitrate or ammonium as sole nitrogen source.

first: Anne

last: Hatmaker

first: Adam

last: Guss


title: Spatially resolved single-cell RNA-sequencing reveals expression heterogeneity in tumor microenvironment

status: Public on Jan 08 2021

first: George

middle: Christopher

last: Hartoularos

state: CA

address: 513 Parnassus Ave S965F

department: Graduate Division

institute: University of California, San Francisco

summary: To better understand how individual cells function within an anatomical space, we developed XYZeq, a novel scRNA-seq workflow that uses combinatorial indexing in microwells to encode spatial metadata into scRNA-seq libraries. We used XYZeq to profile heterotopic mouse liver and spleen tumor models to capture transcriptomes from tens of thousands of cells across a total of eight tissue slices.

overall_design: Spatially resolved single-cell RNA-sequencing from eight tissue sections of MC38-injected liver and spleen organs (samples L30C and L30C8 are from the same slice). Additional experiments using cell lines and comparing to droplet-based single-cell RNA-seq.

first: Y

last: Lee

first: D

last: Bogdanoff

last: Wang

first: G

first: A

last: Marson

first: E

last: Chow

first: C

middle: J

last: Ye


title: Response to SARS-CoV-2 infection in cornea, limbus and sclera from human donors

status: Public on Dec 31 2020

city: New York

first: Rasmus

last: Moeller

address: 1 Gustave L. Levy Place

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

summary: Here we report the transcriptional response to SARS-CoV-2 in cornea, limbus and sclera from human cadaver donor tissue. All three tissues are characterized by an NFkB-mediated chemokine response to viral infection as well as type-I interferon stimulated genes.

overall_design: Cornea, limbus and sclera was isolated from human donor tissue and passaged in tissue culture. Cells were infected with SARS-CoV-2 for 24 hours in triplicate and the host response was compared to mock-infected samples.

last: Møller

first: Benjamin

middle: R

last: tenOever

first: Timothy

last: Blenkinsop


title: Feeding-induced resistance to acute lethal sepsis is dependent on hepatic BMAL1 and FXR signaling

city: Bethesda

first: Stephen

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

summary: Disruption of the circadian rhythm is associated with inflammatory diseases, metabolic syndrome and cancer. In mice, the time of day strongly influences lethality in response to LPS, with survival greatest at the beginning compared to the end of the light cycle (Halberg et al. 1960; Marpegan et al. 2009; Nguyen et al. 2013). Myeloid-cell intrinsic circadian clock components control inflammatory cytokine production (Gibbs et al. 2012; Curtis et al. 2015; Bellet et al. 2013), and metabolic inputs influence lethality in response to LPS (Wang et al. 2016; Weis et al. 2017; Traba et al. 2017), but the relative contributions of these inputs to daily changes in sepsis susceptibility are not known. Here we show that feeding, rather than light, controls time of day dependent LPS sensitivity. Mortality following LPS administration after 12 hours of food deprivation was associated with hypoglycemia, rather than inflammatory cytokine production, independent of the clock regulator BMAL1 expressed in myeloid cells. Deletion of BMAL1 in hepatocytes globally disrupted the transcriptional response to the feeding cycle in the liver and resulted in constitutively high LPS sensitivity. These results show that food, rather than light, is the ‘zeitgeber’ for acute mortality in response to LPS, with a critical role for the hepatocyte-intrinsic circadian clock in integrating nutritional cues to regulate survival in response to innate immune stimuli. Understanding the hepatic molecular programs operational in response to fasting versus fed cues could identify novel pathways that may be targeted to enhance resistance to endotoxemia.

overall_design: Mice were housed under stable 12 h dark 12 h light conditions and ad libitum feeding for at least a week before access to food was restricted to either the day-time (DF, food from ZT0 to ZT12) or the night-time (NF, food from ZT12 to ZT0). The amount of food was thereby not restricted and normal chow was fed. On day 5 of the time restricted feeding schedule, mice were euthanized at ZT0 or ZT12 and liver samples harvested for RNA isolation.

first: Sarah

middle: S

last: Geiger


title: Genome-wide maps of MRE11, NBS1 total RNAPII and phospho-Ser2-RNAPII in WT cells, upon shControl, shMRE11 or shNBS1 treatment, after treatment by DRB and after heat shock in HeLa cells

city: Montpellier

first: Rosemary

last: Kiernan

address: 141 rue de la cardonille

country: France

institute: UMR9002 CNRS-UM

summary: we used the technnology of ChIP-sequencing to sepcifically analyze the recruitment of the MRN Complex onto target genes in conjunction with RNAPII, investigating the effect of the depletion of MRN complex on RNAPII and active transcription

overall_design: HeLa were treated with shRNA or with DRB, or were heatshocked, and the different factors were ChIPed

first: Kader

last: Salifou

first: Callum

last: Burnard

first: Poornima

last: Basavarajaiah

first: Marion

last: Helsmoortel

first: Victor

last: Mac

first: David

last: Depierre

first: Celine

last: Franckhauser

first: Emmanuelle

last: Beyne

first: Xavier

last: Contreras

first: Jérôme

last: Dejardin

first: Sylvie

last: Rouquier

first: Olivier

last: Cuvier


title: Single-cell RNA sequencing reveals the induction of novel myeloid and myeloid-associated cell populations in visceral fat with long-term obesity

status: Public on Dec 24 2020

city: St Louis

first: Natalia

middle: Sara

last: Harasymowicz

address: Clayton Ave

department: Orthopaedic Surgert

institute: Washington University in St Louis

summary: Macrophages and other immune cells are important contributors to obesity-associated inflammation; however, the cellular identities of these specific populations remain unknown. In this study, we identified individual populations of myeloid cells found in mouse epididymal/visceral adipose tissue by single-cell RNA sequencing, immunofluorescence, and flow cytometry. Multiple canonical correlation analysis identified 11 unique myeloid and myeloid-associate cell populations. In obese mice, we detected an increased percentage of monocyte-derived pro-inflammatory cells expressing CD9 and TREM-2, as well as significantly decreased percentages of multiple cell populations, including tissue-resident cells expressing LYVE1, Mafb, and CD206. We have identified and validated a novel myeloid/macrophage population defined by Ly6a expression, exhibiting both myeloid and mesenchymal characteristics, with both hematopoietic and pro-fibrotic markers. Our mouse adipose tissue myeloid cell atlas provides an important resource to target obesity-associated inflammation and fibrosis.

overall_design: single cell RNA seuqnecing of the CD45posCD11bpos myeloid cells from mouse visceral adipose tissue

first: Farshid

last: Guilak


title: Single and double mutations in tomato ripening transcription factors have distinct effects on fruit development and quality traits

city: Davis

first: Barbara

last: Blanco-Ulate

address: 1 Shields Ave.

department: Plant Sciences

institute: University of California, Davis

summary: The study of climacteric fruit ripening in tomato has been facilitated by the spontaneous ripening mutants Colorless non-ripening (Cnr), non-ripening (nor), and ripening inhibitor (rin). These mutants effect the genes encoding ripening transcription factors (TFs) SPL-CNR, NAC-NOR, and MADS-RIN causing pleiotropic defects to the ripening program. Here, we demonstrate that some ripening processes occur in the mutant fruit but at later stages of development compared to the wild type. The rin and nor mutant fruit exhibit similar quality traits to wildtype at later stages of ripening and senescence and delayed expression of ripening-associated genes. In addition, we propose that the Cnr mutant has a broader range of effects to fruit development than just fruit ripening. Cnr fruit show distinct differences from wild type in ripening phenotypic traits and gene expression profiles prior to the initiation of ripening. We provide new evidence that some mutants can produce more ethylene than basal levels and demonstrate ABA accumulation is also affected by the mutations. Studies have examined the relationship between the CNR, RIN, and NOR TFs based on protein-protein interactions and transcriptional regulation during fruit ripening. We describe the genetic interactions affecting specific fruit traits by using homozygous double mutants. Cnr predominantly influences the phenotype of the Cnr/nor and Cnr/rin double mutants but additional defects beyond either single mutation is evident in the transcriptome of the Cnr/nor double mutant. Our reevaluation of the Cnr, nor, and rin mutants provides new insights the utilization of the mutants in breeding and studying fruit development.

overall_design: Examination of double ripening mutant fruit at two ripening stages

first: Jaclyn

middle: A

last: Adaskaveg

first: Christian

last: Silva

first: Peng

last: Huang


title: Neonatal T helper 17 responses are skewed towards an immunoregulatory interleukin-22 phenotype

city: Vancouver

first: Pascal

last: Lavoie

state: BRITISH COLUMBIA

address: 950 West 28th Avenue

institute: BC Children's Hospital

summary: We report broad developmental differences in gene expression profiles between neonatal (term) and adult naive CD4 T cells, resulting in non-stereotypic Th17 differentiation responses to TGF-beta.

overall_design: Total RNA obtained from naïve CD4 T cells (CD3+CD4+CD45RO-CCR7+CD25-) isolated by Fluorescent Activated Cell Sorted (FACS) from 12 neonates (cord blood) and 12 adults (peripheral blood) donors.

first: Hamid

last: Razzaghian

first: Fudan

last: Miao

first: Colin

last: Ross


title: Transgenic mice overexpressing the LH receptor in the female reproductive system spontaneously develop endometrial tumour masses

status: Public on Dec 19 2020

city: Firenze

first: Annarosa

last: Arcangeli

state: FI

address: Viale Morgagni 50

institute: University of Firenze

summary: We developed transgenic mice which overexpress the human LH-R transcript in the female reproductive tract, under the control of the oviduct-specific glycoprotein mouse promoter (mogp-1). The uteri of young TG mice showed signs of increased proliferation and trans-differentiation in the endometrial layer. A transcriptomic analysis,further confirmed by immunohistochemistry, showed that up regulated genes are mainly involved in cell cycle control, while down regulated genes are related to the immune system and the metabolism of xenobiotics. Aged TG females developed tumor masses resembling an EC:

overall_design: Gene expression profiling of primary masses and uteri from TG LH-R overexpressing animals. It has been compared with that of uteri from WT animals.

first: Tiziano

last: Lottini

first: Jessica

last: Iorio

first: Laura

last: Carraresi

first: Serena

last: Pillozzi

first: Elena

last: Lastraioli

first: Claudia

last: Duranti

first: Cesare

last: Sala

first: Miriam

last: Armenio

first: Ivo

last: Noci


title: Comparing lens epithelium gene expression profiles between highly myopic and emmetropic eyes

status: Public on Dec 22 2020

city: Shanghai

first: Yu

last: Du

address: 83 Fenyang Road

department: Ophthalmology

institute: Eye and Ear, Nose, and Throat Hospital of Fudan University

summary:
Clinical observations suggest increased size of lens in highly myopic subjects compared with emmetropic subjects. The layer of anterior lens epithelial cell membrane, being the most metabolically active part of the lens, can be easily acquired during standard lens surgery and is an ideal sample to study the gene expression difference between lens of different populations.
In this study, to investigate the possible molecular mechanisms underlying different features of lens between highly myopic and emmetropic subjects, gene expression profiling of lens epithelia of corresponding population was conducted.

overall_design: Comparative microarray analysis of lens epithelia from three human highly myopic eyes and three emmetropic control eyes acquired during lens surgery was performed using HG-U133 Plus 2.0 Array (Affymetrix, USA).

first: Xiangjia

last: Zhu

first: Dan

last: Li

first: Yi

last: Lu


title: CelFiE:  Comprehensive cell type decomposition of circulating cell-free DNA

city: Los Angeles

first: Noah

last: Zaitlen

address: 675 Charles E Young Dr S

department: Neurology

institute: UCLA

summary: Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising non-invasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not rely on CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from rare cell types composing less than 1% of the total mixture. In a positive control of cfDNA extracted from pregnant and non-pregnant women, CelFiE correctly estimates a large placenta component specifically in pregnant women (p = 4.5x10^-5). In cfDNA from ALS patients and age-matched controls, we observed increased cfDNA concentrations in ALS patients (p = 5.0x10^-3), and CelFiE identified a corresponding increased skeletal muscle component (p = 2.4x10^-3), consistent with muscle impairment characterizing ALS. Together these results show CelFiE may be a useful tool for biomarker discovery and monitoring of degenerative disease progression.

overall_design: 12 ALS and 12 age-matched controls were recruited from the UCSF ALS Center. cfDNA was extracted from 5mL of blood.

first: Christa

last: Caggiano

first: Barbara

last: Celona

first: Fleur

last: Garton

first: Joel

last: Mefford

first: Brian

middle: L

last: Black

first: Robert

last: Henderson

first: Catherine

last: Lomen-Hoerth

first: Andrew

last: Dahl