title: Suprachiasmatic VIP neurons are required for normal circadian rhythmicity with a subset expressing a molecularly distinct pacemaker profile

city: Charlottesville

first: John

middle: N

last: Campbell

state: VA

address: 485 MCCORMICK RD, GILMER HALL ROOM 229 PO BOX 400328

department: Biology

institute: University of Virginia

summary: The hypothalamic suprachiasmatic (SCN) clock contains several neurochemically defined cell groups that contribute to the genesis of circadian rhythms. Using cell specific and genetically-targeted approaches we have confirmed an indispensable role for vasoactive intestinal polypeptide expressing SCN (SCNVIP) neurons in generating the mammalian locomotor activity (LMA) circadian rhythm. Optogenetic-assisted circuit mapping revealed functional, di-synaptic connectivity between SCNVIP neurons and dorsomedial hypothalamic neurons, providing a circuit substrate by which SCNVIP neurons may regulate LMA rhythms. In vivo photometry revealed that while SCNVIP neurons are acutely responsive to light, their activity is otherwise behavioral state invariant. Single-nuclei RNA-sequencing revealed SCNVIP neurons comprise two transcriptionally distinct subtypes, including putative pacemaker and non-pacemaker populations. Given that SCNVIP neurons constitute ~10% of the total SCN population, and that other cell groups were unable to sustain coherent circadian LMA rhythms following SCNVIP disruption, our findings demonstrate a disproportionately large influence of the SCNVIP cell population on pacemaker function.

overall_design: Single-nuclei RNA-Seq (sNuc-Seq) analysis of 190 single-nuclei samples and 2 10-nuclei samples from SCN tissue of two 6wk old mice (pooled tissue) and one 10wk old mouse

first: William

last: Todd

first: Anne

last: Venner

first: Christelle

last: Anaclet

first: Rebecca

middle: Y

last: Broadhurst

first: Roberto

last: De Luca

first: Sathyajit

last: Bandaru

first: Lindsay

last: Issokson

first: Lauren

last: Hablitz

first: Olga

last: Cravetchi

first: Elda

last: Arrigoni

first: Charles

last: Allen

first: David

middle: P

last: Olson

first: Patrick

last: Fuller


title: Glutamine depletion regulates Slug to promote EMT and metastasis in pancreatic cancer [human]

status: Public on May 20 2020

city: San Diego

first: Brian

middle: Patrick

last: James

state: CA

address: 10901 North Torrey Pines Road

department: Genomics

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

type: Expression profiling by high throughput sequencing

summary: Tumor cells rely on glutamine to fulfill their metabolic demands and sustain proliferation. The elevated consumption of glutamine can lead to intratumoral nutrient depletion, causing metabolic stress that has the potential to impact tumor progression. Here, we show that nutrient stress caused by glutamine deprivation leads to the induction of epithelial-mesenchymal transition (EMT) in pancreatic ductal adenocarcinoma (PDAC) cells. Mechanistically, we demonstrate that glutamine deficiency regulates EMT through the upregulation of the EMT master regulator Slug, a process that is dependent on both MEK/ERK signaling and ATF4. We find that Slug is required in PDAC cells for glutamine deprivation-induced EMT, cell motility and nutrient stress survival. Importantly, we decipher that Slug is associated with nutrient stress in PDAC tumors and is required for metastasis. These results delineate a novel role for Slug in the nutrient stress response and provide insight into how nutrient depletion might influence PDAC progression.

overall_design: We performed RNA sequencing in AsPC-1 cells control or glutamine starved. Five replicates per group were evaluated.

first: Maria

middle: V

last: Recouvreux

first: Cosimo

last: Commisso


title: Expression data from adult mouse spleen

status: Public on May 19 2020

city: Incheon

first: Doyeun

last: Kim

address: 85 Songdogwahak-ro, Yeonsu-gu

country: South Korea

institute: Yonsei University

summary:
AIMP2-DX2 is known as a cancer-associated splicing variant of tumor suppressor, AIMP2, lacking exon 2 (shortly DX2 herein). However, it is not known whether its expression alone can drive tumorigenesis. Here we show that DX2 can induce the expansion of germinal center (GC) origin B lymphocytes and their infiltration into multi-organs in mouse model. In doxycycline-dependent inducible transgenic mice, monoclonal expansion of B cells with malignant transformation was developed in two out of seven cases. Induction of DX2 destabilized p53 and dysregulated cell cycle genes, leading to lymphomagenesis. Turning off DX2 induced the death of cancer cells, suggesting the significance of DX2 in the cancer cell growth. Consistently with the mouse phenotypes, higher expression of DX2 was observed in human Burkitt lymphoma and GCB diffuse large B cell lymphoma (DLBCL). Expression of DX2 was confirmed in a subset of GC origin lymphoma obtained from separate cohort using RNA silver in situ hybridization (SISH). In differentially expressed gene analysis, the high DX2 subset was well segregated in GCB lymphomas. High expression of transcription factor MEF2B and its target genes were observed in DX2-associated GCB DLBCL both at RNA and protein level, implying the pathological connection of DX2 with MEF2B in human lymphomagenesis. Functional significance of DX2 for cell viability was confirmed in human DLBCL cell line. In summary, our data suggest DX2 as a driver of lymphomagenesis and potential therapeutic target especially for GCB lymphomas
We used microarrays to detail the global programme of gene expression underlying lymphomagenesis induced by systemic overexpression of DX2

overall_design: Spleens were isolated from mouse overexpressing DX2 or control mouse. Total RNA was extracted from spleen using Trizol method and hybridized on Affimetrix microarrays.

first: Kim

last: Doyeun

last: Sunghoon


title: Trancriptional signatures of dexamethasone-treated sarcoidosis alveolar macrophages (AMs)

city: Detroit

first: Lobelia

last: Samavati

state: Michigan

address: 3990 John R#3 Hudson, Harper University Hospital

department: Internal Medicine (H0609)

institute: Dr.

summary: The goal of this study was to determine the effect of dexamethasone treatment on trancriptional signatures and pathways of sarcoidosis AMs.

overall_design: RNA-seq libraries were prepared using the NEBNext ultradirectional library preparation protocol (New England BioLabs, Ipswich, MA).

first: Jaya

last: Talreja


title: Investigation of the molecular effects of a dexpanthenol-containing ointment and liquid in the aftercare treatment of acute radiodermatitis and mucositis using newly developed 3D models for both skin conditions

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

country: Germany

institute: Uniklinik RWTH Aachen

summary: This study aimed to investigate the molecular effects of radiation and subsequent aftercare treatment with dexpanthenol-containing ointment and liquid on newly established full-thickness 3D skin models depicting acute radiodermatitis and mucositis. We established in vitro models of the non-keratinized mucous membrane as well as normal human skin models. To mimic radiomucositis and radiodermatitis, models were irradiated with 5 Gray. Afterwards, models were treated topically every second day with dexpanthenol-containing ointment or liquid in comparison to placebo and untreated controls.

overall_design: Six samples were analyzed: 5Gy-treated radiodermatitis model vs. control radiodermatitis; 5Gy-treated mucositis vs. control mucositis;  5Gy-treated + dexpanthenol-containing ointment radiodermatitis vs. 5Gy-treated radiodermatitis; 5Gy-treated + dexpanthenol-containing liquid mucositis vs.  5Gy-treated mucositis.

first: Yvonne

last: Marquardt

first: Laura

first: Laurenz

last: Schmitt

first: Kirsten

last: Prescher

first: Philipp

last: Winterhalder

first: Timm

last: Steiner

first: Frank

last: Hölzle

first: Michael

last: Eble

first: Jens

middle: M

last: Baron


title: Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis [Cynomolgus Macaque]

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

summary: Increased intraocular pressure (IOP) represents a major risk factor for glaucoma, a prevalent eye disease characterized by death of retinal ganglion cells that carry information from the eye to the brain; lowering IOP is the only proven treatment strategy to delay disease progression.  The main determinant of IOP is the equilibrium between production and drainage of aqueous humor, with compromised drainage generally viewed as the primary contributor to dangerous IOP elevations.  Drainage occurs through two pathways in the anterior segment of the eye, called conventional and uveoscleral.  To gain insights into the cell types that comprise these pathways, we used high-throughput single cell RNA sequencing (scRNA-seq). From ~24,000 single cell transcriptomes, we identified 19 cell types with molecular markers for each and used histological methods to localize each type. We then performed similar analyses on four organisms used for experimental studies of IOP dynamics and glaucoma: cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa) and mouse (Mus musculus). Many human cell types had counterparts in these models, but differences in cell types and gene expression were evident.  Finally, we identified the cell types that express genes implicated in glaucoma in all five species.  Together, our results provide foundations for investigating the pathogenesis of glaucoma, and for using model systems to assess mechanisms and potential interventions.

overall_design: In these experiments, we dissected the corneoscleral segments of the eye, and transcriptomically profiled the cells of trabecular meshwork and surrounding areas using single cell RNASeq. We studied samples from Human and four other commonly used animal models for glaucoma studies, cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa) and mouse (Mus musculus).

first: Tavé

last: van Zyl

first: Alexi

last: McAdams

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: Aviv

last: Regev

first: Dejan

last: Juric

first: Joshua

middle: R

last: Sanes


title: Humanized C3 Mouse: A Novel Accelerated Model of C3 Glomerulopathy

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

summary: We developed a novel, rapidly-progressing, severe murine model of C3G by replacing the mouse C3 gene with the human C3 homologue using Velocigene® technology. We conducted functional, histological, molecular and pharmacologic assays to characterize the presentation of renal disease and useful pharmacologic interventions in the humanized C3 (C3hu/hu) mice.

overall_design: 3 separate experiments are included. The first profiles livers from WT and humanized C3 (huC3) mice, N = 3 each. Experiment two replicated the experiment in kidneys (N = 3 for WT, N = 6 for huC3). Experiment three profiles kidneys from WT mice (N =5), huC3 mice treated with control antibody (N=3), and huC3 mice treated with an anti-C5 mAb (N = 4).

first: Kishor

last: Devalaraja-Narashimha

first: Karoline

last: Meagher

first: Yifan

last: Luo

first: Cong

last: Huang

first: Theodore

last: Kaplan

first: Sarah

last: Casanova

first: John

last: O’Brien

first: Rebecca

last: Peyser

last: McWhirter

first: Yu

last: Bai

first: Scott

last: MacDonnell

first: Ying

last: Hu

first: Adrianna

last: Latuszek

first: Srinivasa

last: Prasad

first: Tammy

first: William

last: Olson

first: Brian

last: Zambrowicz

first: Lynn

last: Macdonald

first: Andrew

last: Murphy

first: George

last: Yancopoulos

first: Lori

middle: G

last: Morton


title: Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis [Human]

first: Wenjun

last: Yan

first: Tavé

last: van Zyl

first: Alexi

last: McAdams

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: Aviv

last: Regev

first: Dejan

last: Juric

first: Joshua

last: Sanes


title: A rapid, sensitive, scalable method for Precision Run-On sequencing (PRO-seq)

city: Ithaca

first: Julius

last: Judd

state: NY

address: 417 Biotechnology Bldg; 215 Tower Road

department: Molecular Biology and Genetics

institute: Cornell University

summary: Tracking active transcription with the nuclear run-on (NRO) assays has been instrumental in uncovering mechanisms of gene regulation. The coupling of NROs with high-throughput sequencing has facilitated the discovery of previously unannotated or undetectable RNA classes genome-wide. Precision run-on sequencing (PRO-seq) is a run-on variant that maps polymerase active sites with nucleotide or near-nucleotide resolution. One main drawback to this and many other nascent RNA detection methods is the somewhat intimidating multi-day workflow associated with creating the libraries suitable for high-throughput sequencing. Here, we present an improved PRO-seq protocol where many of the enzymatic steps are carried out while the NRO RNA remains bound to magnetic beads. These adaptations reduce time, and we demonstrate that the resulting libraries are of the same quality as libraries generated using the original published protocol. The faster library preparation procedure decreases opportunity for sample loss and RNA degradation.

overall_design: Two replicate libraries of PRO-seq were generated using 1M K562 cells as input material with our new, quick PRO-seq protocol (qPRO-seq). As a comparison, we also generated two replicate libraries with identical input material (1M K562 cells) using published protocol (PMID: 27442863). We also demonstrated our new protocol is robust to low-input samples by generating two replicate libraries with the qPRO-seq protocol using 250k K562 cells as input.

first: Luke

middle: A

last: Wojenski

first: Lauren

last: Wainman

first: Nathaniel

middle: D

last: Tippens

first: Edward

middle: J

last: Rice

first: Alexis

last: Dziubek

first: Geno

last: Villafano

first: Erin

last: Wissink

first: Philip

last: Versluis

first: Lina

last: Bagepalli

first: Sagar

last: Shah

first: Dig

middle: B

last: Mahat

first: Jacob

last: Tome

first: Charles

last: Danko

first: John

middle: T

last: Lis

first: Leighton

last: Core


title: Mutation of the cytochrome P450 CYP360A8 gene increased sensitivity to herbicide paraquat in Daphnia magna

city: Suita

first: Hajime

last: Watanabe

address: Yamadaoka 2-1

country: Japan

institute: Osaka University

summary:
Purpose: To create a CYP gene mutant from D. magna as a model for xenobiotic metabolism study
Methods: We performed RNA-seq of wildtype 12 days old D. magna to find out the basal expression level of CYP genes. We picked up 5 highest expressed CYP genes and examined the temporal expression level from day 0 to day 12 by qPCR. We chose the highest expressed gene and performed mutagenesis to this gene by CRISPR/Cas9 to creat a mutant line.
Results: From RNA-seq result, we found that CYP360A8 is the highest expressed CYP in D. magna. qPCR result showed that CYP360A8 has developmental pattern where its expression is low in juvenile, increase 6 fold by maturation time and stay stable till day 12. Mutagenesis experiment of this gene resulted in the obtaning of a monoallelic mutant. Paraquat exposure to this mutant line showed more sensitivity of the mutant compared to wildtype (showed by 1.3 fold lower of EC50).
Conclusions: Our study showed the first mutant model of CYP in D. magna. This may be the start of creating a panel that list D. magna CYP gene with its inducing xenobiotics.

overall_design: mRNA profiles of 12 days old wild type D. magna

first: Pijar

last: Religia

first: Nhan

last: Nguyen

first: Quang

last: Nong

first: Tomoaki

last: Matsuura

first: Yasuhiko

last: Kato


title: Expression data from OMP52M51 resistant or acute treated leukemic mice

city: Padova

first: Valentina

last: Agnusdei

state: PD

address: Via Gattamelata, 64

country: Italy

institute: Istituto Oncologico Veneto

summary:
We recently demonstrated that a human Notch1-specific neutralizing antibody (OMP52M51) was very effective in T-ALL patient derived xenografts (PDX) bearing NOTCH1/FBW7 mutations. However, we observed development of acquired resistance following long-term administration of the antibody and used PDX models to investigate this phenomenon.
We analyzed expression profiles to identify genes and pathways modulated in mice treated until progression or acute treated with a neutralizing antibody against Notch1.

overall_design: Cells were recovered from spleens of control (Ctrl Ab), resistant (OMP52M51 resistant) or acute treated (acute) mice for RNA extraction and hybridization on Affymetrix microarrays. Each sample derived from a different mouse (3-5 mice/group).

first: Sonia

last: Minuzzo

first: Adriana Agnese

last: Amaro


title: Single-cell RNA-seq achieve the transcriptome module the SAN morphogenesis and the pacemaking cell fate determinant

city: New Orleans

first: YiPing

last: Chen

address: 6400 Freret Street

institute: Tulane University

summary: We analyze three (WT, Shox2-KO, Double-KO) different samples to segregate the transcriptional factors that modulate the SAN morphogenesis and the pacemaking cell fate determinants.

overall_design: Single-cell RNA-seq of E13.5  Shox2Cre/+;R26RmTmG, Shox2Cre/Cre;Nkx2-5F/F;R26RmTmG and Shox2Cre/Cre;R26RmTmG  SAN cells including atrial cells.

first: Hua

last: Li


title: Trancriptional signatures of dexamethasone-treated sarcoidosis monocytes.

first: Lobelia

last: Samavati

summary: The goal of this study was to determine the effect of dexamethasone treatment on trancriptional sigantures and pathways of sarcoidosis monocytes.

first: Jaya

last: Talreja


title: Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis [Mouse]

first: Wenjun

last: Yan

first: Tavé

last: van Zyl

first: Alexi

last: McAdams

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: Aviv

last: Regev

first: Dejan

last: Juric

first: Joshua

last: Sanes


title: The AP-1/JNK pathway is regulated by CD73 and gets dysregulated in aged hosts leading to defect in anti-pneumococcal function of neutrophils

city: Buffalo

first: Elsa

last: BouGhanem

address: 955 Main Street

department: Microbiology and Immunology

institute: University at Buffalo

summary: We used high through put RNA-sequencing to identify changes in the PMN transcriptome induced by S. pneumoniae infection in order to gain further insight into the signaling pathways that are required for host response and are dysregulated in older individuals. PMNs were isolated from bone marrow of young WT, old WT and CD73KO mice and challenged with S.pneumonia TIGR4 strain in-vitro. Analysis of differentially expressed genes revealed that genes in AP-1/JNK pathway were upregulated in PMNs from CD73KO and old mice but not in PMNs from young mice. Inhibition of AP-1 and JNK using inhibitors boosted the anti-microbial actiivity of neutrophils from old and CD73KO mice.

overall_design: Examination of age-related transcriptome changes in neutrophils isolated from young and old mice and challenged with S. pneumoniae

last: Ghanem

first: Manmeet

last: Bhalla

first: Brandon

last: Marzullo


title: Sorghum bicolor and Setaria viridis PARE-seq

city: Huntsville

first: Alex

last: Harkess

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

type: Non-coding RNA profiling by high throughput sequencing

summary: Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.

sample_organism:
Setaria viridis
Sorghum bicolor

platform_organism:
Setaria viridis
Sorghum bicolor

overall_design: For Sorghum bicolor, a variety of conditions were used to generate total RNA, including leaf and three stages of anther development. For Setaria viridis, single replicates of leaf, panicle, and two stages of spikelets were sampled.

first: Blake

middle: C

last: Meyers


title: Varenicline reduces ethanol consumption in male C57BL/6J mice: Potential gene expression mechanisms

city: State College

first: Aswathy

last: Sebastian

address: University Park

institute: PennState

summary: In recent years, varenicline has been shown to decrease ethanol consumption in adult rodents providing support as a therapeutic treatment for alcohol use disorder (AUD). Varenicline is a partial agonist at alpha4beta2 nicotinic acetylcholine receptors, but interacts with other receptors at high concentrations. In order to gain a greater understanding of the mechanisms by which varenicline decreases ethanol consumption, we performed RNA sequencing on striatal tissue from C57BL/6J mice treated with varenicline or saline prior to an ethanol Drinking-in-the-Dark (DID) session. Using classical tools to analyze RNA sequencing data, we found 809 differentially expressed genes with Cuffdiff and one significant co-expression network using WGCNA.

overall_design: Striatal gene expression from animals treated with saline or 2 mg/kg varenicline prior to ethanol Drinking-in-the-Dark

first: Helen

last: Kamens

first: John

last: Dziak

first: William

last: Horton

first: Constanza

last: Silva

first: Istvan

last: Albert

first: Runze

last: Li


title: PD-L1 Engagement on T cells Promotes Self-tolerance and  Suppression of Neighboring Macrophages and Effector T cells in Cancer

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: PD-1 ligation delimits immunogenic responses in T cells. However, the consequences of PD-L1 ligation in T cells are uncertain. We found that T cell expression of PD-L1 in cancer was regulated by tumor-antigen, microbial signals, and sterile inflammatory cues. PD-L1+ T cells exerted tumor-promoting tolerance via three distinct mechanisms: (i) Binding of PD-L1 induced STAT3-dependent back-signaling in CD4+ T cells preventing activation, reducing Th1-polarization, and directing Th17-differentiation. PD-L1 signaling also induced an anergic Tbet-IFNg- phenotype in CD8+ T cells and was equally suppressive compared to PD-1 signaling. (ii) PD-L1+ T cells restrained effector T cells via the canonical PD-L1-PD-1 axis and were sufficient to accelerate tumorigenesis even in the absence of endogenous PD-L1. (iii) PD-L1+ T cells engaged PD-1+ macrophages inducing an alternative M2-like program, which had crippling effects on adaptive anti-tumor immunity. Collectively, we demonstrate that PD-L1+ T cells have diverse tolerogenic effects on tumor immunity.

overall_design: For RNA-Seq experiments, mouse PDL1 knockout and wild-type T cells were stimulated in vitro using anti-CD3 and anti-CD28. Alternatively, CD45+ leukocytes were FACS-sorted from mouse pancreatic tumors 3 weeks after orthotopic implantation.

first: Berk

last: Aykut

first: George

last: Miller


title: Injury and apobec2-dependent regulation of zebrafish Muller glial cell gene expression

city: Ann Arbor

first: Daniel

last: Goldman

address: 109 Zina Pitcher Place

institute: University of Michigan

summary: In this work we identify genes differentially expressed in Muller glia form uninjured and injured retina with and without apobec2a knockdown

overall_design: duplicate samples of control, injured, and injured + apobec2 knockdown

first: Dan


title: Drosophila SWR1 and NuA4 complexes originate from DOMINO splice isoforms

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Genome-wide analysis of hemangiosarcoma tumor tissue using ChRO-seq finds ECM remodeling plays an important role in canine hemangiosarcoma pathogenesis.

first: Scott

last: Coonrod

address: 235 Hungerford Hill Road

department: Baker Institute for Animal Health

summary: Canine hemangiosarcoma (HSA) is an aggressive vascular tumor that arise from malignant endothelial cells.  To gain deeper understanding of HSA pathogenesis, we performed Chromatin-Run-On sequencing (ChRO-seq) experiment on 17 HSA tumor tissues and 4 normal tissue. ChRO-seq analysis revealed over a thousand differentially expressed genes in HSA tissue compared with normal splenic tissue (FDR <0.005). Interestingly the majority of genes overexpressed in HSA tumor tissue were associated with extracellular matrix (ECM) remodeling. This observation correlated well with our histological analysis, which found that HSA tumors contain a rich and complex collagen network. Additionally, we characterized the protein expression patterns of two highly overexpressed molecules identified in ChRO-seq analysis, podoplanin (PDPN) and laminin alpha 4 (LAMA4). We found that the expression of these two ECM-associated factors appeared to be largely limited to transformed endothelial cells within the HSA lesions. Outcomes from this study suggest that ECM remodeling has an important role in HSA pathogenesis.

overall_design: ChRO-seq was used to analyze canine splenic hemangiosarcoma tissues and normal splenic tissues.

first: Chinatsu

last: Mukai

first: Charles

last: Danko


title: Functional genomics of human colon organoids (RNA-Seq)

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

institute: Case Western Reserve Uni

summary: Organoids are a valuable 3D model to study the differentiated functions of the human intestinal epithelium. They are a particularly powerful tool to measure epithelial transport processs in health and disease. Though biological assays such as organoid swelling and intraluminal pH measurements are well established, their underlying functional genomics are not well characterized. Here we combine genome-wide analysis of open chromatin by ATAC-seq with transcriptome mapping by RNA-seq to define the genomic signature of human intestinal organoids (HIOs). These data provide an important tool for investigating key physiological and biochemical processes in the intestinal epithelium. We next compared the transcriptome and open chromatin profiles of HIOs with equivalent datasets from the Caco2 colorectal carcinoma line, which is an important 2D model of the intestinal epithelium. Our results define common features of the intestinal epithelium in HIO and Caco2 and further illustrate the cancer-associated program of the cell line. Generation of Caco2 organoids enabled interrogation of the molecular divergence of the 2D and 3D cultures. Over-represented motif analysis of open chromatin peaks identified   Caudal Type Homeobox 2 (CDX2) as a key activating transcription factor in HIO, but not in monolayer cultures of Caco2. However, the CDX2 motif becomes overrepresented in open chromatin from Caco2 organoids, reinforcing the importance of this factor in intestinal epithelial differentiation and function. Intersection of the HIO and Caco2 transcriptomes further showed functional overlap in pathways of ion transport and tight junction integrity among others. These data make an important contribution to understanding human intestinal organoid biology.

overall_design: Transcriptiome profiling of the human intestinal organoids in triple biological replicates from different donors

first: Shiyi

last: Yin

first: Michelle

last: Longworth


title: Functional genomics of human colon organoids (ATAC-Seq)

overall_design: IDR OMNI-ATAC-seq profiles of open chromatin were generated from 2 independent replicates of libraries for Caco2 cells and Human intestinal organoids

first: Shiy

first: Jenny

middle: L

last: Kerschner


title: Ribosome-quality control antagonizes the activation of integrated-stress response on colliding ribosomes

city: st louis

first: Liewei

middle: Leo

last: Yan

state: MO

address: 1 brookings dr.

institute: Washington University in St Louis

summary: Ribosome stalling occurring on aberrant mRNA activates quality control pathways to maintain proteostasis. Recently, ribosome stalling has also been linked to the activation of Gcn2 and the subsequent integrated-stress response (ISR). How the two processes are coordinated is not completely clear. Here we show that activation of ribosome-quality control by Hel2 suppresses that of Gcn2 in yeast. In the absence of Hel2, we observe a gene-expression signature indicative of ISR activation, suggesting that factor is used to suppress premature activation of Gcn2 in the absence of stress conditions. We further show that Hel2 and Gcn2 are activated by similar set of agents that cause ribosome stalling, with Hel2’s maximal activation occurring at lower frequency of stalling. Interestingly, inactivation of one pathway was found to result in the overactivation of the other, suggesting that both are activated by the same signal. Indeed, we provide evidence that suggests that, similar to Hel2, Gcn2 is activated by ribosome collisions. Collectively, our findings provide interesting details about how the multiple pathways that recognize stalled ribosomes coordinate to mount the appropriate response.

overall_design: Libraries were constructed from RNA collected from various S. cerevisiae strains treated with or without methyl methanesulfonate (MMS).

first: Hani

middle: S

last: Zaher


title: Drosophila SWR1 and NuA4 complexes originate from DOMINO splice isoforms [ChIP-seq]

summary: Histone acetylation and deposition of H2A.Z variant are integral aspects of active transcription. In Drosophila, the single DOMINO chromatin regulator complex is thought to combine both activities via an unknown mechanism. Here we show that two alternative splice isoforms of the DOMINO nucleosome remodeling ATPase, DOM-A and DOM-B, directly specify two distinct multi-subunit complexes. Both complexes are necessary for transcriptional regulation but through different mechanisms. The DOM-B complex incorporates H2A.V (the fly ortholog of H2A.Z) genome-wide in an ATP-dependent manner, like the yeast SWR1 complex. The DOM-A complex, instead, functions as an ATP-independent histone acetyltransferase complex similar to the yeast NuA4, targeting lysine 12 of histone H4. Our work provides an instructive example of how different evolutionary strategies lead to similar functional separation.

overall_design: ChIPseq experiment for H2A.V and H4K12ac upon control (GST/GFP), H2A.v, Domino-A, Domino-B and Tip60 RNAi.

first: Alessandro

last: Scacchetti

first: Peter

last: Becker


title: DNA methylation analysis of human peripheral blood mononuclear cell collected in the AIRWAVE study

city: London

first: Oliver

last: Robinson

state: London

address: St Mary's Campus, Norfolk Place

department: School of Public Health

country: United Kingdom

institute: IMPERIAL COLLEGE LONDON

type: Methylation profiling by genome tiling array

summary: Markers of biological ageing have potential utility in primary care and public health. We developed a model of age based on untargeted metabolic profiling across multiple platforms, including nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry in urine and serum, within a large sample (N=2,239) from the UK Airwave cohort. We validated a subset of model predictors in a Finnish cohort including repeat measurements from 2,144 individuals. DNA methylation age was assessed for 1,110 participants using the Infinium HumanMethylation EPIC BeadChip. We investigated the determinants of accelerated ageing, including lifestyle and psychological risk factors for premature mortality. The metabolomic age model was well correlated with chronological age (mean r=0.86 across independent test sets). Increased metabolomic age acceleration (mAA) was associated after false discovery rate (FDR) correction with overweight/obesity, diabetes, heavy alcohol use and depression. DNA methylation age acceleration measures were uncorrelated with mAA. Increased DNA methylation phenotypic age acceleration (N = 1,110) was associated after FDR correction with heavy alcohol use, hypertension and low income. In conclusion, metabolomics is a promising approach for the assessment of biological age and appears complementary to established epigenetic clocks.

overall_design: 1129 samples,including 14 replicates

first: Silvia

last: Polidoro

first: Giovanni

last: Fiorito

first: Paolo

last: Vineis

first: Paul

last: Elliott


title: Filamin B extensively regulates the transcription and alternative splicing and is associated with apoptosis in HeLa cells

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

summary: Post-transcriptional mechanisms is an important means for the body to fight against cancer, and it may also be hijacked by tumor cells to help them adapt to local microenvironment. Filamin B (FLNB), an actin-binding protein and providing crucial scaffolds for cell motility and signaling, was also identified as one of RNA binding proteins (RBPs). Recent works showed that FLNB might play important role not only in skeletal development but also in the regulation of tumorigenesis. However, the effects of dysregulated expression of FLNB at a molecular level are unclear. In this study, we used RNA-seq to analyze the global transcriptional level changes and alternative splicing between the knocked-down FLNB and the control in Hela cells. Reduced levels of FLNB led to a significant decrease in cell apoptosis, compared with control cells. FLNB knockdown extensively regulated the expression of genes in cell apoptosis, tumorigenesis, metastases, transmembrane transport, cartilage and nerve development. Moreover, FLNB regulated alternative splicing of a large number of genes enriched in cell death and apoptotic process. Meanwhile, some genes and alternative splicing related to skeletal development were enriched and regulated by FLNB. Quantitative RT-PCR confirmed the FLNB-regulated transcription and alternative splicing. This study provides the first transcriptome-wide analysis of FLNB. Our findings indicated that FLNB may play an important regulatory role in cancer cell apoptosis via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of FLNB mediated gene regulation.

overall_design: transcrptional analysis of FLNB knockdown and control in Hela cells

first: Hai-Rong

last: Ma

first: Chao

last: Cheng


title: Next Generation Sequencing identifies differential genes regulated by FTSJ1 overexpression

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

summary: We report the application of RNA-sequencing for high-throughput profiling of transcriptomes in PC9 cells transfected with stably expressed FTSJ1.

overall_design: Comparison of mRNA expression profiles between FTSJ1-overexpression PC9 cells  and control cells.

first: Qihan

last: He


title: Alternative splicing of LSD1+8a is mediated by SRRM4 in Neuroendocrine Prostate Cancer

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

summary: Neuroendocrine prostate cancer (NEPC) is the most virulent subtype. Currently, there is an urgent need to identify new biomarkers and therapeutic targets in NEPC. The splicing factor SRRM4 was previously demonstrated to be highly expressed in NEPC, to promote expression of genes linked to neuroendocrine differentiation and cancer progression, and to promote alternate splicing of genes, including REST. One of REST’s binding protein is lysine specific demethylase 1 (LSD1). Importantly,  a transcript variant of LSD1 called LSD1+8a is expressed in neuronal tissues and promotes neuronal gene expression.  However, there was no information about LSD1+8a’s importance in prostate cancer. Using adenocarcinoma and NEPC patient-derived xenografts and clinical specimens, we determined that LSD1+8a was expressed exclusively in NEPC. Furthermore, LSD1+8a  expression was significantly correlated with elevated mRNA expression of SRRM4.  Using SRRM4-overexpressing prostate cancer cell lines, we determined that alternative splicing of LSD1+8a is directly mediated by SRRM4 and that LSD1+8a and SRRM4 co-regulate a unique program of cancer-promoting genes that is not regulated by canonical LSD1. Our findings demonstrate that measurement of LSD1+8a expression is a promising NEPC biomarker and suggest that targeting LSD1+8a in NEPC may be a useful strategy to block expression of genes linked to cancer progression.

overall_design: We analyzed differential gene expression in LNCaP (clone FGC) cells transiently transfected with LSD1, LSD1+8a, SRRM4, and empty vector

first: Daniel

last: Coleman

first: David

last: Sampson

first: Archana

last: Sehrawat

first: Duanchen

last: Sun

first: Jacob

last: Schwartzman

first: Joshua

last: Urrutia

first: Ahn

last: Lee

first: Xuesen

last: Dong

first: Colm

last: Morrissey

first: Zheng

last: Xia


title: Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis [Pig]

city: Cambridge

first: Wenjun

last: Yan

address: 52 Oxford Street

institute: Harvard University

summary: Increased intraocular pressure (IOP) represents a major risk factor for glaucoma, a prevalent eye disease characterized by death of retinal ganglion cells that carry information from the eye to the brain; lowering IOP is the only proven treatment strategy to delay disease progression.  The main determinant of IOP is the equilibrium between production and drainage of aqueous humor, with compromised drainage generally viewed as the primary contributor to dangerous IOP elevations.  Drainage occurs through two pathways in the anterior segment of the eye, called conventional and uveoscleral.  To gain insights into the cell types that comprise these pathways, we used high-throughput single cell RNA sequencing (scRNA-seq). From ~24,000 single cell transcriptomes, we identified 19 cell types with molecular markers for each and used histological methods to localize each type. We then performed similar analyses on four organisms used for experimental studies of IOP dynamics and glaucoma: cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa) and mouse (Mus musculus). Many human cell types had counterparts in these models, but differences in cell types and gene expression were evident.  Finally, we identified the cell types that express genes implicated in glaucoma in all five species.  Together, our results provide foundations for investigating the pathogenesis of glaucoma, and for using model systems to assess mechanisms and potential interventions.

overall_design: In these experiments, we dissected the corneoscleral segments of the eye, and transcriptomically profiled the cells of trabecular meshwork and surrounding areas using single cell RNASeq. We studied samples from Human and four other commonly used animal models for glaucoma studies, cynomolgus macaque (Macaca fascicularis), rhesus macaque (Macaca mulatta), pig (Sus scrofa) and mouse (Mus musculus).

first: Tavé

last: van Zyl

first: Alexi

last: McAdams

first: Yi-Rong

last: Peng

first: Karthik

last: Shekhar

first: Aviv

last: Regev

first: Dejan

last: Juric

last: Sanes


title: Exome sequencing data analysis to characterize copy number variants involved in m.14487T>C mutation

city: Wenzhou

first: Zhao

last: Qiongya

address: Chashan Street

institute: Wenzhou Medical University

summary: In this study, we analyze DNA whole-exome sequencing (WES) data from 3 patients with m.14487T>C mutation to detect rare candidate SNVs.

overall_design: Examination of EDTA blood of each patient or their biological parents (trio) with m.14487T>C mutation by deep sequencing

first: Jianxin

last: Lu

first: Hezhi

last: Fang

first: Qiongya

last: Zhao


title: Transcriptome profiling and Exome sequencing data analysis on m.14487T>C mutation


title: Transcriptome profiling of cybrids cells with and without m.14487T>C mutation

summary: Transcriptome profiling is a sensitive strategy to uncover the change of mitochondrial to nucleus signaling due to the minor alternation of mitochondrial OXPHOS function. Therefore, we hypothesized that even a minor alternation of OXPHOS function can also remold transcriptome profiles in m.14487T>C mutant cybrid when compared with control cybrids. Our data suggest that a comparable mitochondrial OXPHOS function between m.14487T and m.14487C cybrids is not because of compensatory boost of mitochondrial biogenesis in m.14487C cybrids.

overall_design: Examination of cybrids cells with and without m.14487T>C mutation from three different patients by deep sequencing,in triplicate,using Illumina Hiseq 2000.


title: Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis

sample_organism:
Macaca fascicularis
Macaca mulatta
Homo sapiens
Sus scrofa
Mus musculus


title: Cell Atlas of Aqueous Humor Outflow Pathways in Eyes of Humans and Four Model Species Provides Insights into Glaucoma Pathogenesis [Rhesus Macaque]


title: Transcriptional profiling of HBV-naïve subjects after vaccination against Hepatitis A/B viruses, Diphtheria/Tetanus toxoids and Cholera.

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

summary: Mechanisms of poor responses to vaccines remain unknown. Hepatitis B virus-naïve elderly subjects received three vaccines, including a vaccine against hepatitis B virus (HBV). Transcriptomic profilling of blood collected pre-vaccination and post-vaccination was performed in order to identify candidate biomarkers of antibody response to the different vaccines.

overall_design:
One hundred and seventy four (174) generally healthy, Hepatitis B virus (HBV) naïve, adult residents of Québec were vaccinated with two doses of Twinrix® (HBsAg and Hepatitis A virus - Glaxo Smith-Kline), generic Tetanus-diphtheria booster (tetanus and diphtheria - Sanofi-Pasteur), and Dukoral (recombinant cholera toxin B subunit and whole killed Vibrios - Sanofi Pasteur) according to the respective product labels. Blood samples were taken seven (7) post vaccination. Blood samples were conserved in PAXgene tubes. RNA was extracted and hybridized to Affymetrix arrays. 2 technical replicates were included in the study.
technical replicate: EM131_1009_V3, EM131_1009_V3_rep1
technical replicate: EM131_2036_V3, EM131_2036_V3_rep1

first: Rafick-Pierre

last: Sékaly


title: Advancing the fathead minnow (Pimephales promelas) as a model for immunotoxicity testing/Consequences of early life stage thyroid suppression on long term immune function in the fathead minnow (Pimephales promelas)

city: Denton

first: Leah

middle: Marie

last: Thornton Hampton

state: Texas

address: 1155 Union Cir

institute: University of North Texas

summary: Characterization of the renal transcriptomic response to Yersinia ruckeri/Conseuqences of early life stage thyroid suppression on long-term immune function and the immune response in the fathead minnow (Pimephales promelas)

overall_design: Comparison of renal transcriptome in adult female fathead minnnows following intraperitoneal injection of Hank's Balanced Salt Solution (HBSS) (n=4) or Yersinia ruckeri (n = 4)/Comparison of renal transcriptome in adult female fathead minnnows following early life stage exposure (0-30 days post hatch) to propylthiouracil (PTU) and  intraperitoneal injection of Yersinia ruckeri (n = 4/group)

first: Miranda

last: Finch

first: Christopher

last: Martyniuk

first: Barney

last: Venables

first: Marlo

middle: K

last: Sellin Jeffries


title: Dopaminylation of Histone H3 in Ventral Tegmental Area Regulates Cocaine-seeking

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Vulnerability to relapse during periods of attempted abstinence from cocaine use is hypothesized to result from rewiring of brain reward circuitries, particularly ventral tegmental area (VTA) dopamine neurons. How cocaine exposures act on midbrain dopamine neurons to precipitate addiction-relevant changes in gene expression is unclear. We found that histone H3 glutamine 5 dopaminylation (H3Q5dop) plays a critical role in cocaine-induced transcriptional plasticity in midbrain. Rats undergoing withdrawal from cocaine showed an accumulation of H3Q5dop in VTA. By reducing H3Q5dop in VTA during withdrawal, we reversed cocaine-mediated gene expression changes, attenuated cue-induced dopamine release in nucleus accumbens and reduced cocaine-seeking behavior. These findings establish a neurotransmission-independent role for nuclear dopamine in relapse-related transcriptional plasticity in VTA.

overall_design: Following chronic cocaine vs. saline self administration (extended access), rats were infected intra-VTA with either empty vector (RFP) or H3.3 WT controls vs. H3.3Q5A viruses, followed by a 30 d period of forced abstinence

first: Ashley

middle: E

last: Lepack

first: Ian

last: Maze


title: lncRNA expression profiles from murine BALB/c macrophages at the extremes of the M(LPS+IFN-γ) and M(IL-4) polarized phenotypes

city: Wuhu

first: Xueqin

last: Li

address: 2 Western Zheshan Road

institute: wannan medical college

summary:
Macrophages possess the hallmark feature of plasticity, allowing them to undergo a dynamic transition between M(LPS+IFN-γ) and M(IL-4) polarized phenotypes. The aim of the present study was to screen for differentially lncRNAs that were associated with macrophage polarization.
The lncRNA profiles of three  M(LPS+IFN-γ) and three M(IL-4) samples were obtained using microarray analysis. Based on the threshold of fold-change >2.0 and a p-value < 0.05, we screened a total of 1,251 lncRNAs, of which 627 were upregulated and 624 downregulated in  M(LPS+IFN-γ) macrophages compared to that in M(IL-4) macrophages.This study provides new insights into the role of genes in macrophage differentiation and polarization.

overall_design: Total RNA was prepared from bone marrow-derived macrophages of wild-type BALB/c mice treated in M(LPS+IFN-γ) or M(IL-4) conditions (n=3 replicates per condition originating from different mice)

first: Kun

last: Lv


title: Drosophila SWR1 and NuA4 complexes originate from DOMINO splice isoforms [RNA-seq]

first: Tamas

last: Schauer

overall_design: RNAseq experiment of control (GST/GFP), H2A.v, Domino-A, Domino-B and Tip60 RNAi in 3 biological replicates.

first: Alessandro

last: Scacchetti

first: Peter

last: Becker


title: The omentum of obese girls harbors small adipocytes and browning transcrips

city: New Haven

first: Elena

last: Tarabra

state: Connecticut

address: 330 cedar street

department: Endocrinology/Pediatrics

institute: Yale University - School of Medicine

summary: Severe obesity (SO) affects about 6% of youth in US, augmenting the risks for cardiovascular disease and Type 2 diabetes. Herein, we obtained paired omental (omVAT) and abdominal subcutaneous (SAT) adipose tissue biopsies from obese girls with SO, undergoing sleeve gastrectomy (SG), to test whether differences in cellular and transcriptomic profiles between omVAT and SAT depots affect insulin sensitivity differentially. Following weight loss, these analyses were repeated in a subgroup of subjects having a second SAT biopsy. We found that omVAT displayed smaller adipocytes compared to SAT, increased lipolysis through adipose triglyceride lipase (ATGL) phosphorylation, reduced inflammation and increased expression of browning/beige markers. Contrary to omVAT, SAT adipocyte diameter correlated with insulin resistance. Following SG, both weight and insulin sensitivity improved markedly in all subjects. SAT adipocytes size became smaller showing an increased lipolysis through perilipin-1 phosphorylation, decreased inflammation and increased expression in browning/beige markers. In summary, in adolescent girls with SO, both omVAT and SAT depots showed distinct cellular and transcriptomic profiles. Following weight loss, the SAT depot changed its cellular morphology and transcriptomic profiles into a more favorable one. These changes in the SAT depot may play a fundamental role in the resolution of insulin resistance.

overall_design: Human Abdominal Subcutaneous (SAT) and omental (omVAT) Adipose tissue mRNA profiles of 10 severe obese subjects and SAT mRNA profile of 4 subjects returned after weight loss (sequencing using Illumina Hi-Seq4000)

first: Jessica

last: Nouws

first: Alla

last: Vash-Margita

first: Geoffrey

last: Nadzam

first: Rachel

last: Goldberg

first: Michelle

last: VanName

first: Bridget

last: Pierpont

first: James

last: Knight

first: Gerald

middle: I

last: Shulman

first: Sonia

last: Caprio


title: POKI-Seq in Primary Human T Cells

status: Public on May 18 2020

city: San Francisco

first: Eric

last: Shifrut

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

summary: We adapted pooled non-viral targeted knock-ins to allow for simultaneous readouts of pooled knock-in barcode as well as RNA transcriptomes at the single cell level in primary human T cells. We used a library of 36 potentially therapeutic knock-in constructs each knocked into the TRAC locus along with a new TCR specificity to explore transcriptional changes in therapeutically relvant in vitro and in vivo environments.

overall_design: Pooled CRISPR knock-in screen with single cell RNASeq readout (POKI-Seq) in primary human T cells. Dataset includes T cells from four donors, two donors each in two different experiemnts.  The first experiment in vitro comparing TCR stimulation in the presense or absense of exogenous TGFB.  The second experiment comparing in vivo TILs isolated from a solid tumor xenograft model against ex vivo expanded input cells.

first: Theodore

last: Roth

first: Cody

last: Mowery

first: Alexander

last: Marson


title: RNA profiles in serum and urine extracellular vesicles of patients with cholangiocarcinoma mimicking tumor expression: novel liquid biopsy approach

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

summary: Cholangiocarcinoma (CCA) represents a heterogeneous group of biliary cancers with poor prognosis. Although the aetiology is generally unknown, factors like Primary Sclerosing Cholangitis (PSC) predispose to its development. Simultaneously, around 80% of patients with PSC have concomitant Ulcerative Colitis (UC). As there are no specific and sensitive biomarkers for the non-invasive diagnosis of CCA, we aimed to analyse the RNA content of serum and urine extracellular vesicles (EVs) to find accurate biomarkers of CCA that could be reflecting tumor behaviour. The transcriptomic analysis of these EVs showed a differential profile of RNAs in patients with CCA compared to healthy individuals or patients with other diseases (PSC and UC), presenting some RNAs high diagnostic values to distinguish patients with CCA. Moreover, the differential abundance of several RNAs in serum and/or urine EVs correlated with the deregulated expression of those transcripts in CCA tissue compared to surrounding liver (TCGA and Copenhagen cohorts), in tumor (EGI1, TFK1) and normal cholangiocyte (NHC) cell lines as well as in EVs secreted by those cell lines; pinpointing the potential involvement of those RNAs not only as liquid biopsy biomarkers but also as potential mediators of CCA pathogenesis.

overall_design: Total RNA obtained from normal (NHC) and tumoral (EGI1 and TFK1) cholangiocyte cell lines and from extracellular vesicles (EVs) isolated from serum, urine and cholangiocyte cell line supernatant

first: Ainhoa

last: Lapitz

first: Ander

last: Arbelaiz

first: Jose

last: Lavin

first: Colm

last: O'Rourke

first: Adelaida

last: La Casta

first: Cesar

last: Ibarra

first: Juan

middle: P

last: Jimeno

first: Alvaro

last: Santos-Laso

first: Marcin

last: Krawczyk

first: Maria

last: Perugorria

first: Raul

last: Jimenez-Agüero

first: Alberto

last: Sanchez-Campos

first: Ioana

last: Riaño

first: Esperanza

last: Gonzalez

first: Frank

last: Lammert

first: Marco

last: Marzioni

first: Rocio

last: Macias

last: Marin

first: Tom

middle: H

last: Karlsen

first: Luis

last: Bujanda

last: Falcon-Perez

first: Jesper

last: Andersen

first: Pedro

last: Rodrigues

first: Jesus

last: Banales


title: RT-PCR analysis of long non-coding RNAs expression in adriamycin-resistant osteosarcoma cells

city: Shenyang

first: Yanfeng

last: Cheng

address: No. 36 Sanhao Street

institute: Shengjing Hospital of China Medical University

summary:
One of the major challenges for chemotherapy is appearance of resistance to compounds. Despite several singling pathways have been implicated in development of Adriamycin (ADM) resistance, mechanisms involved in ADM-resistant osteosarcoma progression remain largely unknown. The present study attempts to illustrate the role of long noncoding RNA ARSR in development of ADM-resistance. We found lncRNA ARSR overexpressed in the Adriamycin resistant cell lines U2OS/ADM and MG63/ADM, accompanied with acquired multidrug resistance against to paclitaxel and cisplatin. Overexpression of lncRNA ARSR triggered rhodamine 123 efflux and survival, as well as migration of ADM resistant cells. Conversely, depletion of ARSR promoted rhodamine 123 retention and apoptosis while reduced motility of ADM resistant cells. Further investigation revealed that upregulation of ARSR enhanced Akt phosphorylation on Ser473 and increment of multidrug resistance-associated protein-1, apoptosis inhibitor Survivin and matrix metalloproteinase-2. Reduction of ARSR overcame the resistance to ADM and magnified the suppression of Akt-mediated signaling pathways by MK-2206. The current study gained novel evidence for understanding the mechanisms underlying adaptive ADM resistance, and provided rational to improve Akt-targeted therapy towards refractory osteosarcoma.  Methods: The expression of lncRNA was analyzed by RT2 lncRNA PCR Arrays. The differential expressed lncRNAs were further verified by qRT-PCR. The relationship between lncRNA expression and clinical features was evaluated with Spearman correlation test. Cell proliferation was measured by MTT assay. Cell apoptosis percentage was detected by ANNEXIN V-PI analysis. The promoter activity was illustrated by Luciferase assay, and the change of microRNA and protein was detected by qRT-PCR and western blot, separately.  Results: The expression of HAND2-AS1 declined in bladder cancer and correlated with depth of invasion and grades negatively. Restoration of HAND2-AS1 hampered cell growth by provoking cell apoptosis. Furthermore, one of the HAND2-AS1 sponge, miR-146, was found overexpression in bladder cancer tissue and cell lines. Expression of miR-146 related to HAND2-AS1 expression negatively. One of the targeted genes of miR-146, retinoic acid receptor beta (RARB) was downregulated in bladder cancer. In addition, the expression of RARB related to miR-146 negatively. Lost-of-function and gain-of-function experiments were used to identify the mechanisms underlying association of lncRNA HAND2-AS1: miR-146: RARB. miR-146 targeted RARB directly and hindered RARB-mediate apoptosis. However, the hindrance was impaired by HAND2-AS1 notably.  Conclusion: HAND2-AS1 diminished miR-146 expression, thereby releasing the suppression of miR-146 on RARB-mediated apoptosis, promoting bladder cancer regression.
Long noncoding RNA  profiling by array

overall_design: Three clones of parental osteosarcoma cell U2OS and three adriamycin-resistant U2OS (U2OS/ADM) sublines were recruited in the present study. RT-PCR LncRNA expression profiles were obtained with Qiagen custom RT2 PCR Arrays.


title: Functional genomics of human colon organoids

first: Ann

last: Harris

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

overall_design: Refer to individual Series


title: Tumor genetic heterogeneity analysis of chronic sun-damaged melanomas

city: Lund

first: Göran

last: Jönsson

address: Medicon Village

country: Sweden

institute: Lund University

summary: Chronic sun-damaged (CSDhigh) melanoma represents 10-20% of cutaneous melanomas and is characterized by infrequent BRAF V600E mutations and high mutational load. However, the order of genetic events, or the extent of intra-tumor heterogeneity (ITH) in CSDhigh melanoma is still unknown. Ultra-deep targeted sequencing of 40 cancer-associated genes was performed in 73 in situ or invasive CMM, including 23 CSDhigh cases. In addition, we performed whole-exome and RNA sequencing on multiple regions of primary tumor and multiple in-transit metastases from one CSDhigh melanoma patient. We found no significant difference in mutation frequency in melanoma-related genes or in mutational load between in situ and invasive CSDhigh lesions while this difference was observed in CSDlow lesions. In addition, increased frequency of BRAF V600K, NF1 and TP53 mutations (P < 0.01, Fisher’s Exact Test) was found in CSDhigh melanomas. Sequencing of multiple specimens from one CSDhigh patient revealed strikingly limited ITH with > 95% shared mutations. Our results provide evidence that CSDhigh and CSDlow melanomas are distinct molecular entities that progress via different genetic routes.

overall_design:
Gene expression profiles of multi-region sampling from one melanoma patient, consisting of: 4 intra-tumor samples, 7 in-transit metastases samples, and 1 normal skin sample, generated by RNAseq using an Illumina NextSeq 500 instrument.
The authors state "due to Swedish law, the patient consent, and the risk that the sequencing data contains personally-identifiable information and hereditary mutations, we cannot deposit the short sequencing read data in a repository."

first: Katja

last: Harbst

first: Martin

last: Lauss


title: Microaerobic fermentation alters lactose metabolism in Escherichia coli

city: NEW DELHI

first: Anurag

middle: Singh

last: Rathore

state: DELHI

address: Lab no. 356, Block III

department: Chemical Engineering

country: India

institute: Indian Institute of Technology

summary: We report the effect of oxygenation state in lactose grown escherichia coli producing recombinant proteins. To shed more light on the mechanistic correlation between the uptake of lactose and dissolved oxygen, a comprehensive study has been undertaken with the E. coli BL21 (DE3) strain. Differences in consumption pattern of lactose, metabolites, biomass and product formation due to aerobiosis have been investigated. Transcriptomic profiling of metabolic changes due to aerobic process and microaerobic process during protein formation phase has been studied and the results provide a deeper understanding of protein production in E. coli BL21 (DE3) strains with lactose based promoter expression systems.This study also provides a scientific understanding of escherichia coli metabolism upon oxygen fluctuations.

overall_design: Analysing the transcriptome of Escherichia culture grown in presence of lactose and also in different oxygenation of culture

first: Ashish

last: Chauhan

first: Kathiresan

last: Pandi

first: Jaya

last: Gupta


title: NelfA (Whsc2) promoter occupancy is required for active gene transcription during cardiac hypertrophy

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

summary: We examineD the genomic oppucpany and role of negative elongation factor A (NelfA) aka, Wolf-Hirschhorn syndrome candidate 2 (Whsc2), a critical component of the negative elongation complex in hearts undergoing pressure-overload induced cardiac hypertrophy. Alignment of high resolution genome wide occupancy data of NelfA, RNA Pol II, TFIIB and H3k9ac (datasets for pol II, TFIIB and H3kac submitted before) from control and hypertrophied hearts reveal that NelfA associates with all active gene promoters. High NelfA occupancy is seen at promoters of essential and cardiac-enriched genes, expressed under both quiescent and hypertrophic conditions. Conversely, de novo NelfA recruitment is observed at inducible gene promoters with pressure overload, accompanied by significant increase in expression of latter genes with hypertrophy.

overall_design: Hearts were extracted from C57/Blk mice subjected to sham ot TAC operations. Hearts were sent to Active Motif, Inc for NelfA_ChIP-Seq


title: Transcriptional profiling of YF-naïve participants after vaccination against yellow fever.

first: Slim

last: Fourati

summary: Mechanisms of poor responses to vaccines remain unknown. Yellow fever-naïve adults were vaccinated with a yellow fever vaccine (YF-17D, Stamaril). Transcriptomic profilling of blood collected pre-vaccination and post-vaccination (day 3, 7, 14 and 84) was performed in order to identify candidate biomarkers of antibody response to the vaccine.

overall_design: Post-vaccination transcriptomic profiling at days 3, 7, 14 and 84 and other immune parameters have been investigated in association with the immune response, at day 80 post-vaccination, to Yellow Fever vaccine (YF-17D) in a cohort of 36 participants recruited in Entebee (Uganda).

first: Rafick-Pierre

last: Sékaly


title: CDYL2 epigenetically regulates MIR124 to control NF-kB/STAT3-dependent breast cancer cell plasticity [ChIP-seq]

status: Public on May 17 2020

city: Lyon

first: Peter

last: Mulligan

state: If applicable (USA / Canada)

address: 28 rue Laennec

country: France

institute: Inserm Research Unit 1052, Cancer Research Center of Lyon (CRCL)

summary: Epigenetic deregulation of gene transcription is central to cancer cell plasticity and malignant progression, but remains poorly understood. We found that the uncharacterized epigenetic factor Chromodomain on Y-like 2 (CDYL2) is commonly over-expressed in breast cancer, and that high CDYL2 levels correlate with poor prognosis. Supporting a functional role for CDYL2 in malignancy, it positively regulated breast cancer cell migration, invasion, stem-like phenotypes, and epithelial-to-mesenchymal transition (EMT). CDYL2 regulation of these plasticity-associated processes depended on signaling via p65/NF-kB and STAT3. This, in turn, was downstream of CDYL2 regulation of MIR124 gene transcription. CDYL2 co-immunoprecipitated with G9a/EHMT2 and GLP/EHMT1, and regulated the chromatin enrichment of G9a and EZH2 at MIR124 genes. We propose that CDYL2 contributes to poor prognosis in breast cancer by recruiting G9a and EZH2 to epigenetically repress MIR124 genes, thereby promoting NF-kB and STAT3 signaling, as well as downstream cancer cell plasticity and malignant progression.

overall_design: Anti-CDYL2 ChIP-seq was performed on MCF7 cells stably transduced with an MSCV-CDYL2 expression construct (MCF7-CDYL2) or the empty vector (MCF7-Vector). A sample of input chromatin was also sequenced as a control.


title: CDYL2 epigenetically regulates MIR124 to control NF-kB/STAT3-dependent breast cancer cell plasticity [RNA-seq]

overall_design: RNA was extracted from MCF7 cells stably transduced with a CDYL2 expression plasmid (MCF7-CDYL2), or the empty vector (MCF7-Vector), and differentially expressed genes identified.


title: Next generation sequencing identifies differentially expressed genes between breast cancer with diabetes and breast cancer without diabetes

status: Public on May 16 2020

first: Rihong

last: Zhai

summary: We report the application of RNA-sequencing for high-throughput profiling of transcriptomes in tumor tissues from patients with breast cancer and diabetes, and in tumor tissues from breast cancer patients without diabetes.

overall_design: Comparison of mRNA expression profiles between breast cancer with diabetes and breast cancer without diabetes

first: Qihan

last: He


title: Integrative analysis of genomic amplification-dependent expression and loss-of-function screen identifies ASAP1 as a driver gene in triple negative breast cancer progression

city: Leiden

first: Jichao

address: Einsteinweg 55

department: Drug Discovery and Safety

country: Netherlands

institute: Leiden University

summary:
Purpose: To investigate the impact of ASAP1 depletion on the transcriptomic profile of TNBC cells using TempO-Seq-based high-throughput RNA sequencing.

Methods: Three TNBC cell lines (BT549, SUM149PT and Hs578T) were treated with siRNA control or siRNA targeting ASAP1 for 72 hours. RNA was isolated with RNeasy Plus Mini Kit as described by manufacturer (QIAGEN, Cat. 74136). Transcriptome RNA-Sequencing (TempO-Seq) was performed using Illumina high-throughput RNA sequencing.

Results: We mapped about 7 million sequence reads per sample to the human genome. Normalization and differential expression analysis were performed using DESeq2 package. Genes with significant down- or up-regulation (Log2 FC ≥ |1|) under indicated conditions were analysed by web-based functional analysis tool Metascape to visualise and annotate their biological functions and pathways.

Conclusions: Genes with 2-fold changes (absolute Log2 FC ≥ 1) in down- or up-regulation were selected in BT549 (311 down / 495 up), Hs578T (133 down / 117 up) and SUM149PT (500 down / 401 up) cells, respectively. Consequently, 95 DEGs were downregulated, and 79 DEGs upregulated in ≥ 2/3 of the TNBC cell lines, in total 174 DEGs, which were considered as common DEGs that were susceptible to the depletion of the amplification-dependent ASAP1. 53 of  these commonly differentially expressed transcripts were linked to relapse-free survival in TNBC patients.

overall_design: ASAP1 depletion-mediated transcriptional reprogramming of triple-negative breast cancer cells harboring ASAP1 amplification and high expression depletion was generated in triplicate using Illumina RNA sequencing.

first: Bob

last: van de Water


title: Global analysis of circRNA-associated ceRNA network for investigating underlying pathogenesis of constrictive pericarditis

city: SHENYANG

first: Yixin

last: Chen

address: No.36 Sanhao Street, Heping District

institute: SHENGJING HOSPITAL OF CHINA MEDICAL UNIVERSITY


title: Single cell RNA sequencing analysis of in vitro DENV1 infected cells

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

summary: CEM.NKR.DC-SIGN cells were infected in vitro with DENV1 (strain WestPac74) for 18 hours, after which either total viable cells or viable cells expressing surface DENV1 NS1 were isolated by flow cytometric sorting. Sorted cells were processed for scRNAseq analysis using either a standard Oligo(dT) primer, or an Oligo(dT) primer supplemented with a DENV-specific RT primer

sample_organism:
Homo sapiens
Dengue virus 1 Nauru/West Pac/1974

overall_design: Single cell RNA sequencing analysis of CEM.NKR.DC-SIGN cells infected with DENV1 (strain WestPac74)

first: Jeffrey

last: Currier


title: Global analysis of circRNA-associated ceRNA network for investigating underlying pathogenesis of constrictive pericarditis (miRNA-Seq)

summary:
Purpose:The purpose of this study is to investigate the potential mechanisms that triggering the onset of constrictive pericarditis and to screen hub genes that exert impact on pathogenesis of patients with constrictive pericarditis.
Methods: We screened differentially expressed genes with the data obtained from RNA-seq on CP samples and matched normal samples. Functional annotation analysis and protein-protein interaction (PPI) network were performed to investigate the potential key pathways and genes that play significant roles in CP. Furthermore, the ceRNA network was established and the Gene Set Enrichment Analysis (GSEA) was executed to dig key circRNAs.
Results: Following the identification of differentially expressed genes, functional annotation analysis was conducted, suggesting that differentially expressed mRNAs (DEMs) were mainly involved in inflammatory response related pathways. The top 11 genes with the highest degree were extracted from PPI network. A total of 377 predicted regulatory relationships among the differentially expressed genes were found and the ceRNA network was established. Finally, GSEA was conducted on the circRNAs and the key biological pathways were identified.
Conclusion: Our study is the pioneering research to analyze the pathogenesis of CP with integrated informatics and we have identified several hub genes, which reveals that the generation of CP is closely related to inflammation and fibrosis.

overall_design: Pericardial miRNA profiles of three test and three control samples were generated by deep sequencing, using Illumina NextSeq 500.

first: Feifei

last: Sun

first: Yong

last: Zhang

first: Guang

last: Song

first: Wei

last: Qiao

first: Ke

last: Zhou

first: Sihua

last: Ren

first: Qian

last: Zhao

first: Weidong


title: Global analysis of circRNA-associated ceRNA network for investigating underlying pathogenesis of constrictive pericarditis (RNA-Seq)

overall_design: Pericardial RNA profiles of three test and three control samples were generated by deep sequencing, using Illumina HiSeq 4000.


title: Analysis of cell-associated DENV RNA by oligo(dT) primed 5' capture scRNAseq

sample_organism:
Homo sapiens
Dengue virus 1 Nauru/West Pac/1974
Dengue virus


title: FAM111B contributes to the growth of lung adenocarcinoma with KRAS mutation by degrading p16 and promoting cell cycle.

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

summary: Lung cancer is one of the most common cancers and remains a major worldwide health problem. Lung adenocarcinoma (LUAD) is the major subtype of lung cancer. Although several treatments for LUAD have been developed, still many patients lead to cancer-associated death because of uncontrollable LUAD progression. Further biological and clinical studies to elucidate molecular mechanisms associated with LUAD progression are required to resolve such problems. In this study, we screened family with sequence similarity 111 member B (FAM111B), of which precise functional role in cancers is not clear, as the molecule highly expressed in papillary predominant lung adenocarcinoma.

overall_design: We performed RNA sequencing analysis using human FFPE tissue specimens to compare gene expression of lepidic predominant adenocarcinoma with that of papillary predominant adenocarcinoma.

first: Satoshi

last: Nojima

first: Eiichi

last: Morii


title: TEX15 silences transposable elements in male germ cells

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

type: Methylation profiling by high throughput sequencing

summary:
This SuperSeries is composed of the SubSeries listed below.
DNA methylation is a major silencing mechanism of transposable elements (TEs). Here we report that TEX15, a testis-specific protein, is required for TE silencing. TEX15 is both cytoplasmic and nuclear in embryonic germ cells and functions during genome-wide epigenetic reprogramming. Tex15 mutant exhibits DNA hypomethylation in TEs at a level similar to Mili but not Miwi2 mutant. As loss of Tex15 causes TE de-silencing without abolishing piRNA production, our results identify TEX15 as a new essential epigenetic regulator that appears to function independently or downstream of the piRNA biogenesis machineries to silence TEs by DNA methylation in male germ cells.


title: Sequence analysis of CD4 Treg, CD8 Treg and CD8 effector

city: San Antonio

first: Nu

address: 7703 Floyd Curl

institute: UT Health San Antonio

summary: We show that Ly49+CD122+ CD8+ Treg have a distinct expression profie compared to conventional Foxp3+ CD4+ Treg and CD49 lo CD122+ CD8 effector like cells. RNA was extracted from sorted cells and sent for sequencing

overall_design: Comparison of RNA profiles of sorted CD4+ Tregs, CD8+ Tregs and CD8+ effector like cells

first: Shruti

last: Mishra


title: Expression profiling of Tex15 wt, Tex15 ht and Tex15 ko germ cells

summary: We repport the effect of Tex15 inactivation on the transcriptome of male germ cells at embryonic day 16.5 (e16.5), 18.5 (e18.5), and postnatal day 2 (d2). We find upregulation of a large number of transposable elements in Tex15-/- germ cells.

overall_design: RNA-seq of Tex15 wt (d2 only), Tex15+/- and Tex15-/- male germ cells at three timepoints (e16.5, e18.5 and d2) in biological triplicates (Illumina HiSeq 4000); Germ cells were FACS-sorted (Oct4-GFP) from testes of embryos or pups from Tex15+/- x Tex15+/- matings.

first: Fang

last: Yang

first: Marisa

last: Bartolomei

first: Jeremy

last: Wang


title: SE-driven metabolic reprogramming in ADPKD (RNA-Seq)

city: Tianjin

first: Zeyun

last: Mi

address: Qi Xiang Tai Road

institute: Tianjin Medical University

summary: Metabolic reprogramming is emerging as a key pathological contributor to the progression of autosomal dominant polycystic kidney disease (ADPKD), but the molecular mechanisms underlying dysregulated cellular metabolism in cystic cells remain elusive. Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive robust expression of cell identity and disease genes. Here, we establish a prominent role for SEs in regulating metabolic gene expression and ADPKD progression. Characterization of cis-acting SE landscapes in cystic renal epithelial cells reveals extensive remodeling of SEs during cystogenesis. Gene ontology analysis indicates that SE-associated transcripts in the metabolic pathway category are most significantly enriched in cystic cells. Cystic cells are highly sensitive to the inhibition of cyclin-dependent kinase 7 (CDK7), a critical component of the trans-acting SE complex. THZ1, a specific CDK7 inhibitor, exerts a potent anti-cystogenesis effect in ADPKD cells and mouse models. Integrative analyses of transcriptomics and SE profiling identify AMP deaminase 3 (AMPD3) as a SE-driven metabolic gene. Up-regulation of AMPD3 in cystic cells results in reduced AMP level and decreased AMPK activity, while inhibition of AMPD3 suppresses cyst development in a zebrafish ADPKD model. In a cohort of ADPKD patients, CDK7 expression is frequently elevated, and its expression is significantly correlated with AMPD3 expression and disease severity. Taken together, our findings elucidate a mechanism by which SE controls metabolic gene transcription during cystogenesis, and identifies SE-driven metabolic reprogramming as a promising therapeutic target for ADPKD treatment.

overall_design: RNA-sequencing of different conditions: pkd1, null cell lines before and after treatment with THZ1.

first: Yupeng

last: Chen


title: SE-driven metabolic reprogramming in ADPKD (ChIP-Seq)

overall_design: ChIPmentation sequencing with H3K27ac antibody in pkd1 and null cell lines.


title: SE-driven metabolic reprogramming in ADPKD (kidney RNA-seq)

overall_design: RNA-sequencing of WT and ADPKD kidney tissues from mice


city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

summary: To explore the downstream genes of TRIM11,we performed RNA-seq to screen after knocking out TRIM11 in CNE2-DDP cells.

overall_design: We used Cas9 to knock out TRIM11 in CNE2-DDP cells.

first: Runan


title: Patient iPSCs identify vascular smooth muscle AADAC as protective against atherosclerosis

city: Basel

first: Filip

last: Roudnicky

state: Basel

address: Grenzacherstrasse 124

department: Chemical Biology

country: Switzerland

institute: F.Hoffmann-La Roche Ltd

summary: Cardiovascular disease (CVD) is the most common cause of death in patients with type II diabetes mellitus (T2DM). Although susceptibility to CVD is different for every patient, why some patients with T2DM develop CVD while others are protected has not yet been clarified. Patient-derived induced pluripotent stem cells (iPSCs) have been utilized to reveal the influence of genotype on phenotype and have the potential to connect a clinical phenotype to a causal gene. Using T2DM patient-derived iPSCs, we found that in patients protected from CVD there was significantly elevated expression of an esterase, arylacetamide deacetylase (AADAC) in vascular smooth muscle cells (VSMCs). To investigate the function of AADAC in CVD, we overexpressed this esterase in human primary coronary artery VSMCs and VSMCs differentiated from iPSCs and observed that the number of lipid droplets per cell was significantly diminished. Further metabolomic analyses revealed a marked reduction in storage lipids such as triacylglycerol and diacylglycerol and an increase in membrane phospholipids suggesting changes in the Kennedy pathway of lipid bioassembly. Cell migration, proliferation, and apoptosis were also significantly decreased in AADAC-overexpressing VSMCs. Moreover, apolipoprotein (Apo) E knockout mice overexpressing VSMC-specific Aadac showed significant amelioration of atherosclerotic lesions. Isolated VSMCs from these mice also displayed decreased lipid droplets, storage lipids, cell migration, proliferation, and apoptosis, all of which were consistent with human data. Our findings suggest that elevated AADAC expression in VSMCs protects T2DM patients from CVD. This study also highlights the potential of patient-derived iPSCs to investigate disease associated phenotypes as a means of elaborating the molecular mechanisms underlying disease pathology.

overall_design: Endothelial cells and vascular smooth muscle cells differentiated from 7 iPS lines (T2DM patients without CVD) and 7 iPS cell lines (T2DM patients with CVD)

first: Chad

last: Cowan

first: Takafumi

last: Toyohara


title: Whole genome bisulfite sequencing (WGBS) of Tex15 wt, Tex15 ht, and Tex15 ko male germ cells at postnatal day 2.5

summary: DNA methylation is a major silencing mechanism of transposable elements (TEs). Here we report that TEX15, a testis-specific protein, is required for TE silencing. Through WGBS, we find that Tex15 mutant germ cells exhibit DNA hypomethylation in TEs. Our results identify TEX15 as a new essential epigenetic regulator that appears to function independently or downstream of the piRNA biogenesis machineries to silence TEs by DNA methylation in male germ cells.

overall_design:
We report hypomethylation in retrotransposons in Tex15-/- male germ cells at day 2.5
WGBS-seq of Tex15+/+, Tex15+/-, and Tex15-/- male germ cells at postnatal day 2.5 in biological duplicates (75PE-HiSeq4000); Germ cells were FACS-sorted (Oct4-GFP) from testes of pups from Tex15+/- x Tex15+/- matings.


title: H3S10ph cistromes after eccentric contractions of mouse skeletal muscles

city: Munich

first: Nina

middle: Henriette

last: Uhlenhaut

state: Bavaria

address: Ingolstädter Landstraße 1,  Neuherberg

department: Molecular Endocrinology

institute: HelmholtzZentrum München - IDC

summary: Genome-wide H3S10ph marks from mouse gastrocnemius muscles after 50 eccentric contractions compared to contralateral unstimulated gastrocnemius muscles from the same mice.

overall_design: To map genome-wide H3S10ph marks, we performed ChIP-seq of H3S10ph in gastrocnemius muscles from mice after 50 unilateral eccentric contractions. 2 independent biological replicates (each a pool of gastrocnemius muscles from 6 different mice) were used for each condition (stimulated vs unstimulated contralateral), for a total of 4 ChIP-seq samples.

first: Ashfaq

middle: A

last: Mir

first: Kenneth

last: Dyar


title: CDYL2 epigenetically regulates MIR124 to control NF-kB/STAT3-dependent breast cancer cell plasticity [MDA-MB-231 RNA-seq]

first: Peter

last: Mulligan

overall_design: RNA was extracted from MDA-MB-231 cells transietly transfected with either CDYL2 siRNA or a control siLuciferase RNAi and  differentially expressed genes identified.


title: Detection of DENV infected cells following natural dengue infection

first: Adam

last: Waickman

summary: Viable T cells (CD3+ CD19-) and B cells (CD3- CD19+) were sorted from PBMC samples obtained from 1 individual experiencing a natural secondary DENV infection. Single cell RNA sequencing analysis was performed on 3 time points

sample_organism:
Homo sapiens
Dengue virus

platform_organism:
Homo sapiens
Dengue virus

overall_design: Single cell RNA sequencing analysis of 3 time points from 1 subject experiencing a natural DENV infection

first: Jeffrey

last: Currier


title: Exposure to mites sensitizes intestinal stem cell maintenance, splenic marginal zone B cell homeostasis, and heart development to Notch dosage and cooperativity

status: Public on May 15 2020

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

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

overall_design: Refer to individual Series


title: CDYL2 epigenetically regulates MIR124 to control NF-kB/STAT3-dependent breast cancer cell plasticity


title: Genomic basis of socially-cued sex change in the New Zealand spotty

city: Geelong

first: Erica

last: Todd

address: Pigdons Rd

country: Australia

institute: Deakin University

summary: Spotty wrasses (Notolabrus celidotus) undergo socially cued female-to-male sex change as adults. We combine captive social manipulations and time-series sampling with transcriptomic and methylome approaches to describe the molecular cascade that orchestrates gonadal metamorphosis. Our findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.

overall_design: Captive social groups of wild-caught spotty wrasses from the Tauranga region in New Zealand were established and females induced to change sex using chemical (aromatase inhibitor fadrozole) or social (removal of dominant male) manipulations in 2014-2018. Time-series sampling was used to obtain biological replicates of transitional animals at early, mid and late stages of sex change. Females from unmanipulated tanks, plus the original males served as controls. Gonadal tissue was collected from each animal for genomic and histological analyses. RNA sequencing libraries were prepared for 95 total samples using Illumina’s tru-seq stranded mRNA kit and sequenced using 2x125bp paired end Illumina HiSeq 2500. Cleaned reads were mapped to the N. celidotus genome using Rsubread and read counts were generated using FeatureCounts.

middle: V

first: Oscar

last: Ortega-Recalde

first: Alexander

last: Goikoetxea

first: Simon

last: Muncaster

first: Holly

last: Robertson

first: Dona

last: Bond

first: Timothy

last: Hore

first: Neil

middle: J

last: Gemmell


title: Exposure to mites sensitizes intestinal stem cell maintenance, splenic marginal zone B cell homeostasis, and heart development to Notch dosage and cooperativity [ATAC-seq]

summary: Cooperative DNA binding is a key feature of transcriptional regulation. Here we examined the role of cooperativity in Notch signaling by CRISPR-mediated engineering of mice in which neither Notch1 nor Notch2 can homo- or heterodimerize, essential for cooperative binding to sequence paired sites (SPS) located near many Notch-regulated genes. While most known Notch-dependent phenotypes were unaffected in Notch1/2 dimer-deficient mice, a subset of tissues proved highly sensitive to loss of cooperativity. These phenotypes include heart development, compromising viability in combination with low gene dose, and the gut, developing ulcerative colitis in response to 1% DSS. The most striking phenotypes – gender imbalance and splenic marginal zone B cell lymphoma – emerged in combination with gene dose reduction or when challenged by chronic fur mite infestation. This study highlights the role of the environment in malignancy and colitis, and is consistent with Notch-dependent anti-parasite immune responses being compromised in the dimer deficient animals.

overall_design: Determining the effect of Notch2 dimerization mutation in MZB cells at the chromatin accesibility level for WT and N2RA (arginine to alanine at position Arg1934).

first: Eric

middle: W

last: Brunskill


title: A single-cell survey of Drosophila blood

city: Quechee

first: Michael

last: Steinbaugh

state: VT

address: PO Box 1520

institute: Acid Genomics

summary: Drosophila blood cells, called the hemocytes, are composed of three distinct cell populations: plasmatocytes (PM), crystal cells (CC), and lamellocytes (LM). These cell types have been extensively characterized based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Further, intermediate states along the course of maturation of these cell types have been poorly characterized. Here, we used single-cell RNA sequencing (scRNA-seq) to map the Drosophila larval hemocytes across different inflammatory conditions. We identified all known cell types, resolved PMs into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the detection of CC and LM intermediates. Further, we discovered rare cells within CC and LM populations that express the fibroblast growth factor (FGF) ligand branchless (bnl) and receptor breathless (btl), respectively. We demonstrate that both bnl and btl are required for mediating effective immune responses against parasitoid wasp eggs in vivo, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocyte populations and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.

overall_design: inDrops, 10x Genomics Chromium, and Drop-seq based single-cell RNA-sequencing of ~20K hemocytes from the Drosophila larvae across different inflammatory conditions

first: Sudhir

middle: G

last: Tattikota

first: Bumsik

last: Cho

first: Yifang

last: Liu

first: Yanhui

last: Hu

first: Victor

last: Barrera

first: Sang-Ho

last: Yoon

first: Aram

last: Comjean

first: Fangge

last: Li

first: Franz

last: Dervis

first: Ruei-Jiun

last: Hung

first: Jin-Wu

last: Nam

first: Shannan

last: Sui

first: Jiwon

last: Shim

first: Norbert

last: Perrimon


title: The CCR4-NOT complex component NOT1 regulates RNA-directed DNA methylation and transcriptional silencing by facilitating Pol IV-dependent siRNA production [small RNA-seq]

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

summary: Small interfering RNAs (siRNAs) are required for establishment and maintenance of DNA methylation through RNA-directed DNA methylation (RdDM) pathway in plants. While the siRNA biogenesis is well known, relatively little is known about how the process is regulated. By a forward genetic screen in Arabidopsis thaliana, we identified a mutant defective in NOT1 and demonstrated that NOT1 is required for transcriptional silencing at RdDM target genomic loci. Furthermore, we revealed that NOT1 is required for Pol IV-dependent siRNA accumulation and DNA methylation at a subset of RdDM target loci. By immunoprecipitation combined with mass spectrometry, we showed that NOT1 is a constituent of a multi-subunit CCR4-NOT deadenylase complex. We demonstrated that the CCR4-NOT components can function as a whole to mediate chromatin silencing. Our work thus establishes that the CCR4-NOT complex regulates the production of Pol IV-dependent siRNAs and thereby facilitates DNA methylation and transcriptional silencing in Arabidopsis.

overall_design: Examination of the smallRNA expression in Arabidopsis

first: Xin-jian


title: Interferon lambda promotes immune dysregulation and tissue inflammation in TLR7-induced lupus [scRNA-seq]

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

summary: Interferon lambdas share important functional similarities with type I interferons, but their role in inflammation and autoimmune disease remains controversial and is not well studied. Here, we present the first evidence that interferon lambda is pathogenic and has nonredundant functions in TLR7-associated lupus inflammation. Most notably, we found that interferon lambda promotes systemic immune dysregulation through localized effects in the skin and kidneys. These data identify a novel role for interferon lambda in lupus immunobiology and tissue-specific pathology.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: This dataset includes 6 scRNA samples. Immune cells were isolated from mouse spleen and human peripheral blood. Cells were treated with recombinant interferon alpha or interferon lambda for 4 hours. Single cell RNA seq analysis was subsequently performed to analyze responsiveness to stimulation with interferon alpha and interferon lambda cytokine across different immune cell clusters.

first: R

middle: R

last: Goel

first: X

last: Wang

first: L

last: O'Neil

first: S

last: Nakabo

first: K

last: Hasneen

last: Gupta

first: G

last: Wigerblad

last: Blanco

first: J

middle: B

last: Kopp

first: M

last: Morasso

last: Kotenko

first: Z

last: Yu

first: C

last: Carmona-Rivera

last: Kaplan


title: SE-driven metabolic reprogramming in ADPKD

first: Zeyun

last: Mi


title: Lactate Efflux From Intervertebral Disc Cells Is Required for Maintenance of Spine Health

first: Makarand

last: Risbud

address: 1015 Walnut Street

institute: Thomas Jefferson University

summary: Monocarboxylate Transporter 4 (MCT4) is important for H+/lactate efflux from nucleus pulposus cells in the intervertebral disc of mice. We examined the transcriptomic profile of nucleus pulposus cells in wild-type and MCT4 global knock-out mice using microarrays.

overall_design: Nucleus pulposus tissue was harvested from the intervertebral discs of four wild-type (WT) (C57Bl/6) and three MCT4 global knock-out mice (MCT4 KO) (C57Bl/6N) between 13-14 months of age. Nucleus pulposus tissue was pooled from all discs in each animal for RNA extraction and hybridization on Affymetrix microarrays.

first: Elizabeth

middle: S

last: Silagi

first: Emanuel

last: Novais


title: Expression levels of genes of in vitro generated Th1 and Th17 cells from OT-II and OT-II x NKG2D-/- mice

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

summary: We performed RNA-Seq and compared expression levels of genes of NKG2D+ OT-II Th1 or Th17 cells to OT-II x NKG2D-/- Th1 and Th17 cells, respectively.

overall_design: Naive CD4+ T cells were isolated from lymph nodes and spleen of OT-II and OT-II x NKG2D-/- mice and were co-cultured and activated in vitro with OVA323-339 and a-CD28, in the presence of APCs, and differentiated with IL-2, IL-12 and a-IL-4 in the case of Th1 and IL-1b, IL-6, IL-23, a-IFNg and a-IL4 in the case of Th17. IL-12 was added to the Th17 culture after the second triggering event. Co-cultured cells were subjected to two rounds of polarization (day 0 and day 5), harvested on day 8 and sorted with the help of congenic markers as Thy1.2+ NKG2D+ OT-II and Thy1.1+ OT-II x NKG2D-/- before being subjected to RNA isolation.

first: Marina

last: Babic

first: Christoforos

last: Dimitropoulos

first: Quirin

last: Hammer

first: Christina

last: Stehle

first: Frederik

middle: F

last: Heinrich

first: Assel

last: Sarsenbayeva

first: Almut

last: Eisele

first: Mir-Farzin

last: Mashreghi

first: Berislav

last: Lisnic

first: Jacques

last: Van Snick

first: Max

last: Löhning

first: Simon

last: Fillatreau

first: David

last: Withers

first: Nicola

last: Gagliani

first: Samuel

last: Huber

first: Richard

last: Flavell

first: Bojan

last: Polic

first: Chiara

last: Romagnani


title: Amino acid supplementation for enhancing recombinant protein production in E. coli

city: NEW DELHI

first: Anurag

last: Rathore

address: Lab no. 356, Block III

institute: Indian Institute of Technology

summary: Amino acid starvation during recombinant protein production (RPP) induces metabolic stress to cellular host which results in reduced productivity of the recombinant bioprocess. In present study, supplementation of amino acids in a chemically defined medium showed several folds increase in recombinant product titers in E. coli BL21 DE3 strain. To understand, the effect of amino acid supplementation in alleviating cellular stress during RPP a deep insight of cellular physiology must be studied. Here, we performed transcriptomic analysis of E. coli expressing a recombinant protein in two different conditions: with (5 mM of all 20 amino acids) as test and without supplementation of amino acids as control. RNA-seq data revealed downregulation of several genes associated with stress in test culture confirming the critical role of amino acids supplementation in improving RPP.

overall_design: Examination of differential genes expression at two different phases (Growth and Protein production phase) of E. coli were studied.

first: Jashwant

last: Kumar

first: Ashish

last: Chauhan

first: Rohan

middle: L

last: Shah

first: Jaya

last: Gupta


title: Gene expression profiling for: activin-2 is required for regeneration of polarity on the planarian anterior-posterior axis

city: Cambridge

first: Peter

last: Reddien

state: MA

address: 9 Cambridge Center

department: MIT Biology

institute: Whitehead Institute for Biomedical Research

summary: The goal of this data set is to identify transcriptional changes in activin-2 RNAi animals vs control animals. We did bulk RNA sequencing of a wound induced time course to try to identify changes in the context of activin-2 RNAi, and targets of activin-2. These changes may help explain some of the phenotypic chnages seen in activin-2 RNAi animals.

overall_design: Polyadenylated RNA was isolated from post-pharyngeal fragments at 0, 6, 18, 24, and 48 hours post-amputation (hpa) from planarians following RNAi of a control gene (C.elegans unc-22; 3-4 replicates) and activin-2 (3-4 replicates). Either anterior- or posterior-facing wound fragments were taken. Worms were fed four times over 14 days and cut 7 days after 4th feeding.

first: Jennifer

middle: K

last: Cloutier


title: Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)

city: Campinas

first: Mariana

middle: Vargas

last: Cruz

state: Sao Paulo

address: 400 Avenida Candido Rondon

department: Department of Plant Biology

country: Brazil

institute: UNICAMP

summary: Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming and changing precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here, we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the black mangrove (Avicennia germinans). A total of 57 trees were sampled at seven sites differing markedly in precipitation regime and riverine freshwater inputs. Using 2,297 genome‐wide single nucleotide polymorphic markers, we found signatures of natural selection by the association between variations in allele frequencies and environmental variables, including the precipitation of the warmest quarter and the annual precipitation. Additionally, we found candidate loci for selection based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci within transcribed sequences were functionally associated with central aspects of drought tolerance or plant response to drought. Moreover, our results suggest the occurrence of the rapid evolution of a population, probably in response to sudden and persistent limitations in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included the reduction in tree size and changes in allele frequencies and in transcript expression associated with increased drought tolerance through the accumulation of osmoprotectants and antioxidants, biosynthesis of cuticles, protection against protein degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.

overall_design: mRNA profiles of leaves, stems and roots from three seedlings grown in each of two contrasting forest in terms of freshwater availability, salt, solar irradiance and temperature, were transferred to pots, filled with mangrove soil and acclimated for 72 hours under shadowed and well watered conditions. Paired-end RNA-Sequencing platform: Illumina GA IIx

first: Gustavo

middle: M

last: Mori

first: Maria

middle: I

last: Zucchi

first: Anete

last: Souza

first: Rafael

last: Oliveira

first: Maheshi

last: Dassanayake

first: Dong-Ha

last: Oh


title: Exposure to mites sensitizes intestinal stem cell maintenance, splenic marginal zone B cell homeostasis, and heart development to Notch dosage and cooperativity [RNA-seq]

first: Raphael

last: Kopan

overall_design: Determining the effect of Notch2 dimerization mutation in MZB cells at the transciptional level using RNA-SEQ for WT and N2RA (arginine to alanine at position Arg1934).

first: Eric

last: Brunskill