title: Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting

city: Norwich

first: Daniel

last: Zilberman

address: Norwich Research Park

institute: John Innes Centre

type: Methylation profiling by high throughput sequencing

summary: To understand the evolution of imprinting mechanisms in the rice species Oryza sativa, we analyzed DNA methylation, transcription and small RNA expression in embryo and endosperm. Cultivars chosen to represent the genetic diversity of cultivated Oryza sativa comprised Nipponbare and Kitaake of the japonica subspecies, and IR64 and 93-11 cultivars of the indica subspecies. While imprinted expression is generally conserved among rice cultivars, approximately 10% of imprinted genes show imprinting divergence across the four cultivars.   Analyses of DNA methylation and small RNAs revealed that small RNA producing loci are closely associated with genic regions and four times more likely to be imprinted than genes. However, imprinting divergence most often correlated with DNA methylation epimutations. Correlative epialleles were largely stable within subspecies. Small indels and transposable element insertions were found at half of the epimutated loci and associated with imprinting divergence at half of the remaining loci. Correlating epigenetic and genetic variation occurred at key regulatory regions – the promoter and transcription start site of maternally-biased genes, and the promoter and gene body of paternally-biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprint formation at both maternally and paternally biased genes, and highlight the role of transposition events and epimutation in rice imprinting evolution.

overall_design: Examination of DNA methylation, total RNA and small RNA populations in dissected 7 to 8 DAF endosperm and embryo of seeds obtained from four cultivars of Oryza sativa L. and select reciprocal crosses

first: Jessica

middle: A

last: Rodrigues

first: Ping-Hung

last: Hsieh

first: Robert

last: Fischer


title: Mechanical competition promotes intestinal  tumorigenesis by inducing innate immune signaling and PGRP-LA dependent cell death

status: Public on Jun 30 2021

city: Heidelberg

first: Erica

last: Valentini

address: Im Neuenheimer Feld 580

country: Germany

institute: DKFZ

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Direct regulons of the master virulence regulator AtxA of Bacillus anthracis

status: Public on Jun 28 2021

city: Sapporo

first: Yoshikazu

last: Furuta

state: Hokkaido

address: North 20 West 10, Kita-ku

department: International Institute for Zoonosis Control

country: Japan

institute: Hokkaido University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins that are required for the pathogenicity of Bacillus anthracis. Recent transcriptome analyses also showed that AtxA affects a large number of genes on both chromosome and plasmid, suggesting its role as a global regulator. Its mechanism of gene regulation nor binding target in vivo was, however, not well understood. In this work, we conducted ChIP-seq for cataloging binding sites of AtxA in vivo and Cappable-seq for catalogging the transcription start sites on the B. anthracis genome. For detected regulons, single knockout strains were constructed and RNA-seq was conducted for each strain.

overall_design: ChIP-seq was conducted for genomic DNA of B. anthracis 34F2 WT and the strain that produce AtxA with 1xFLAG tag at its C-terminus. Cappable-seq was conducted for B. anthracis 34F2 WT and ΔatxA. RNA-seq was conducted for B. anthracis 34F2 WT, ΔatxA, ΔxrrA, ΔxrrB, and ΔxrrC. All strains were grown in NBY medium supplemented with 8% NaHCO3 under 15% CO2 at 37°C.

first: Cheng

last: Cheng

first: Tuvshinzaya

last: Zorigt

first: Atmika

last: Paudel

first: Shun

last: Izumi

first: Mai

last: Tsujinouchi

first: Tomoko

last: Shimizu

first: Wim

last: Meijer

first: Hideaki

last: Higashi


title: Chromatin-associated RNAchIP and transcriptome analyses of the relationship between HP1g/CBX3 and RNA [RIP-seq]

status: Public on Jun 29 2021

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: RNA-seq and RNAchIP-seq experiments were performed on MEF-derived cell lines knock-out for the expression of HP1g/CBX3 (R cell line) or recomplemented for the expression of HP1g (HPg cell line). Cells were tested under normal growth or conditions of stress (p samples) by treatment with the phorbol ester PMA. Each experiment was performed in biological triplicates.

first: C

last: Rachez

first: R

first: H

last: Varet

last: Proux

last: Muchardt


title: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and 16p11.2+/- striatum Transcriptomes

city: Shenzhen

first: Jun

last: Ju

state: China

address: No. 628, Zhenyuan Road, Guangming District,  Shenzhen518107, China

country: China

institute: Tomas Lindahl Nobel Laureate Laboratory

summary: Purpose: The goals of this study are to find myelination related pathway alteration in 16p11.2+/- mice.

overall_design: Female B6/C57 WT and 16p11.2+/- mice (4 each) were used at postnatal day 60 (P60). Striatum tissues were dissected out from these mice under deep terminal anesthesia and immediately frozen in liquid nitrogen.

first: Xiuyan

last: Yang

first: Jian

last: Jiang

first: Dilong

last: Wang

first: Yumeng

last: Zhang

first: Xiaofeng

last: Zhao

first: Xiaoyi

last: Fang

first: Huanquan

last: Liao

first: Lei

last: Zheng

first: Shupeng

last: Li

first: Sheng-Tao

last: Hou

first: Liyang

last: Liang

first: Yihang

last: Pan

first: Huilliang

first: Ningning


title: A multi-omics approach using a mouse model of cardiac malformations for prioritization of human congenital heart disease contributing genes [RNA-seq]

city: Columbus

first: Vidu

last: Garg

state: OH

address: 700 Children's Drive WB4239

department: Cardiovascular Research

country: USA

institute: Research Institute at Nationwide Children's Hospital

summary: Congenital heart disease (CHD) is the most common type of birth defect, affecting ~1% of all live births. Malformations of the cardiac outflow tract (OFT) account for ~30% of all CHD and include a range of CHDs from bicuspid aortic valve (BAV) to tetralogy of Fallot (TOF). We hypothesized that transcriptomic profiling of a mouse model of CHD would highlight disease-contributing genes implicated in congenital cardiac malformations in humans. To test this hypothesis, we utilized global transcriptional profiling differences from a mouse model of OFT malformations to prioritize damaging, de novo variants identified from exome sequencing datasets from published cohorts of CHD patients. Notch1+/-;Nos3-/- mice display a spectrum of cardiac OFT malformations ranging from BAV, semilunar valve (SLV) stenosis to TOF. Global transcriptional profiling of the E13.5 Notch1+/-;Nos3-/- mutant mouse OFTs and wildtype controls was performed by RNA sequencing (RNA-Seq). Analysis of the RNA-Seq dataset demonstrated genes belonging to the Hif1α, Tgf-β, Hippo, and Wnt signaling pathways were differentially expressed in the mutant OFT. Mouse to human comparative analysis was then performed to determine if patients with TOF and SLV stenosis display an increased burden of damaging, genetic variants in gene homologs that were dysregulated in Notch1+/-; Nos3-/- OFT. We found an enrichment of de novo variants in the TOF population among the 1,352 significantly differentially expressed genes in Notch1+/-;Nos3-/- mouse OFT but not the SLV population. This association was not significant when compared to only highly expressed genes in the murine OFT and of de novo variants in the TOF population. These results suggest that transcriptomic datasets generated from the appropriate temporal, anatomic and cellular tissues from murine models of CHD may provide a novel approach for the prioritization of disease-contributing genes in patients with CHD.

first: Sathiyanarayanan

last: Manivannan

first: Uddalak

last: Majumdar

first: Adrianna

last: Matos-Nieves


title: RNA-seq of ΔDS deletion vs +WT Complemented seeds

city: Stanford

first: Yanniv

last: Dorone

address: 371 Jane Stanford Way

institute: Stanford University

summary: We identified a regulator of Arabidopsis thaliana seed germination: FLOE1 (AT4G28300). We used RNA-seq to uncover genes that are differentially regulated in dry seeds, imbibed seeds and seeds imbibed in 220mM NaCl in mutant lines complemented with a ΔDS deletion version of FLOE1 (ΔDS) compared to mutants complemented with a WT version of FLOE1 (+WT).

overall_design: Imbibition and salt: after 5 days of stratification at 4C in the dark on MS media containing either 0 or 220mM NaCl, seeds were transferred to a growth chamber at 22C with normal light conditions for 4hours. RNA was then extracted from these seeds as well as from dry seeds. RNA was then sent to Novogene Corporation Inc. for library preparation (250-300 bp insert cDNA library) and sequencing (2x150 bp paired-end reads on an Illumina Platform). Three replicates were conducted for each genotype (+ΔDS or +WT) and condition (dry, imbibed, salt).


title: Small and large intestine differ in basal ERK pathway activity

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

summary: In this experiment, we determined the differences in the transcriptomes of freshly isolated murine small intestine and colon derived crypts. The data shows that the mRNA profiles of the two tissues significantly differ in their ground state. Interestingly, we found that the expression levels of ERK pathway components as well as their positive and negative regulators significantly differ between small intestinal and colonic crypts. This observation indicates that the ERK pathway displays higher basal activity in the small intestine compared to the colon.

overall_design: RNA was extracted from freshly isolated crypts of the small and large intestine of four (two female and male, respectively) mice and sequenced on an Illumina HiSeq4000.

first: Nadine

last: Reischmann

first: Tilman

last: Brummer

first: Melanie

last: Börries


title: The effects of corticosterone and background colour on tadpole physiological plasticity

city: Chengdu

first: Liming

last: Chang

state: Sichuan

address: No.9 Section 4,Renmin Nan Road,Chengdu, Sichuan, P.R. China

institute: Chengdu Institute of Biology

summary: Corticosterone (CORT)-mediated adaptive plasticity improves animal fitness in stressful environments. Although it brings ecological benefits, the cost potentially constrains its expression and evolution. Revealing the factors affecting plasticity costs is of great ecological and evolutionary significance. Evidence indicates that both CORT and background colour can induce metabolic changes in animals, which in turn determine phenotypic plasticity. However, whether and/or how CORT and background colour jointly act on plastic responses has not been studied. Here, this question has been investigated in amphibian tadpoles (Microhyla fissipes) exposed to CORT at different background colours (white or black) using integrated morphological, histological, and transcriptomic analyses. The results showed that CORT exposure increased relative tail length, immune function, and metabolic maintenance (i.e., transcription of substrate catabolism and oxidative phosphorylation) at the expense of reduction in growth rate and skin melanin level. The black background also increased relative tail length and metabolic maintenance (i.e., transcription of oxidative phosphorylation) at the cost of reduction in growth rate, but increased skin melanin level. The expression of critical pigmentation genes indicated that black background activated a distinct and opposite pigmentation regulating route to CORT. Although there was no interactive effect of background colour and CORT on phenotypic and metabolic variations, their additive effects further impact the trade-off between somatic growth, metabolic maintenance, and pigmentation in terms of resource allocation. In conclusion, the individual and additive effects of background colour and CORT exposure on tadpole plasticity were revealed. These results likely provide new insights into the environmental adaptation of animals.

overall_design: Two background colours (white, W and black, B), and two corticosterone (Shanghai Aladdin Biochemical Technology, Co., Ltd.) exposure concentrations (0 μmol/L, CK, and 1μmol/L, CORT) were set to conduct experiment. Embryos of M. fissipes were divided into four groups (CK-W, CK-B, CORT-W and CORT-B for each group n=15) were reared in containers with different corticosterone exposure for 10 days. Compare the transcriptomics of tadpoles at different treatment.

first: Wei

last: Zhu

first: Bin

last: Wang

first: Jianping

last: Jiang

first: Tian

last: Zhao

first: Jiongyu

last: Liu

first: Meihua

last: Zhang


title: RNA sequencing of T cells from individuals with variants in CD101

city: Seattle

first: Jennifer

middle: M

last: Lund

state: WA

address: 1100 Fairview Ave N., E5-110

department: Vaccine and Infectious Disease Division

institute: Fred Hutchinson Cancer Research Center

summary: In this study, we sought to determine if there are transcriptional differences in CD4 and CD8 T cells in individuals with different types of variants in the gene CD101.

overall_design: We FACS-sorted CD4+ or CD8+ T cells from 3 individuals with no variants in CD101, from 3 individuals with a variant in the Ig-like domain of CD101, and from 3 individuals with a variant in the cytoplasmic region of CD101.

first: Jairam

last: Lingappa


title: Prognostic Liver Signature profiles of Jc1-infected Huh7.5.1dif cells treated with various drugs

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Hepatocellular carcinoma (HCC) is the second leading cause of cancer death worldwide, indicating urgent need for preventive strategies. Cancer chemoprevention discovery is challenged by the absence of tractable and clinically relevant human model systems and the complex cell circuits supporting carcinogenesis. Here, we developed a simple and robust human liver cell-based system in which persistent hepatitis B/C virus infection or ethanol induce an HCC risk signature robustly predicting long-term HCC risk in cirrhotic patients. Using a computationally enriched small molecule cell-based screen followed by ex/in vivo validation in human liver tissues and animal models, we identified captopril as an HCC chemopreventive agent that antagonizes the EGF/EGFR pathway, a key driver of liver disease and hepatocarcinogenesis. Our system, modeling the cell circuits encoded in the clinical HCC risk signature, enables fast-track cancer chemoprevention discovery and provides an urgently needed approach for improving the dismal prognosis of patients at risk of HCC.

overall_design: DMSO-differentiated Huh7.5.1 cells (Huh7.5.1dif) were exposed to mock or HCV Jc1 clone, then treated with various drugs to measure modulation of Prognostic Liver Signature genes.

first: Simonetta

last: Bandiera

first: Anu

last: Venkatesh

first: Catherine

last: Fauvelle

first: Christine

last: Thumann

first: Sarah

middle: C

last: Durand

first: Hussein

last: El Saghire

first: Anna

last: Koh

first: Mirjam

middle: B

last: Zeisel

first: Thomas

middle: F

last: Baumert


title: Chromatin-associated RNAchIP and transcriptome analyses of the relationship between HP1g/CBX3 and RNA

first: Rachel

last: Legendre


title: The naturally occurring ∆40p53 isoform inhibits eRNA transcription and enables context-specific regulatory inputs during p53 activation [5FU_RNA]

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: Campus Box 596

department: Biochemistry

institute: University of Colorado Boulder

summary: The naturally occurring p53 isoform ∆40p53 lacks the first N-terminal transactivation domain of WTp53 and is implicated in mammalian aging. ∆40p53 is preferentially translated during cell stress. The ∆40p53 isoform oligomerizes with WTp53 to form hetero-tetramers with altered function compared to WTp53 tetramers. Co-expression of ∆40p53 and WTp53 results in the formation of a mixed population ∆40p53:WTp53 tetramers, including “contaminating” WTp53 tetramers. Here we implemented a strategy—based upon the native p53 tetramer structure—in which ∆40p53 was tethered to WTp53 (∆40p53:WTp53) as a single transcript, resulting in tetramers with a defined 2:2 ratio of Δ40p53 to WTp53. Using CRISPR/Cas9, human cell lines were generated in which ∆40p53:WTp53 (and controls) was inserted at the native TP53 locus. This enabled ∆40p53:WTp53 expression and induction in a physiologically relevant manner. As with WTp53, activation of ∆40p53:WTp53 with Nutlin-3a causes increased genome occupancy. However, unlike WTp53, precision run-on nuclear sequencing (PRO-seq) showed that increased ∆40p53:WTp53 occupancy does not correlate with robust transcriptional activation. Activated ∆40p53:WTp53 only induces transcription of a small subset of WTp53 enhancer RNAs (eRNAs) and other annotated regions. Defective eRNA production correlates with loss of downstream mature mRNA and p53-dependent cell-cycle arrest. Pathway analysis of ∆40p53:WTp53 induced transcriptional changes identified increased activation of stress and aging related pathways in ∆40p53:WTp53 compared to WTp53. However, these pathways never mature to full activation under Nutlin-3a treatment. Therefore, we propose a model where activation of ∆40p53 results in the transcription of a subset of WTp53 targets, setting the stage for synergistic pathway activation with other stress specific transcription factors driving cellular response in ways that differ from WTp53. Implications of these results provide an additional mechanistic layer of p53 regulation, in which expression of ∆40p53 isoform allows for modulation of WTp53 activities in a context dependent manner, tipping the scales towards activation of aging-associated pathways.

overall_design: CRISPR/Cas9 edited MCF10A cells were treated with 375uM 5-Fluorouracil (5FU) and 0.375% DMSO (control) for 20 hours with a total of 2 biological replicates. Total RNA was isolated and enriched for mRNA and directional RNA-seq libraries were constructed and sequenced.

first: Cecilia

last: Levandowski

first: Margaret

last: Gruca

first: Taylor

last: Jones


title: Transcriptome profiles of liver from cirrhotic rat treated with nizatidine

summary: Male rats received repeated low-dose diethylnitrosamine (DEN) to induce liver cirrhosis, and were treated with nizatidine to examine change of liver transcriptome and its association with liver cancer chemopreventive effect of nizatidine.

first: Hadassa

last: Hirschfield

first: Won-Min

last: Song

first: Bryan

last: Fuchs


title: Gene expression profiles of Huh7.5.1 and HepG2 cells infected with HCV, HBV, HDV, and alcohol, and clinical liver tissues treated with various compounds of co-culture with LX2 cells

first: Yujin

last: Hoshida

summary: Hepatocellular carcinoma (HCC) is the second leading cause of cancer death. Curative approaches are limited and chemoprevention is not available. A 186-gene signature in liver tissue predicts HCC risk in cirrhotic patients of various etiologies. However, the drivers of the HCC risk gene signature remain to be fully elucidated. Here, we develop a simple and robust liver cell-based system in which persistent hepatitis B and C virus infection or ethanol exposure induce this signature. We identified candidate drivers of the HCC high-risk signature and hepatocarcinogenesis and uncovered reversal of the signature by an EGFR inhibitor and pioglitazone, a computationally predicted inhibitory compound. This cell-based model unravels the cell circuits of liver disease progression and identifies HCC chemoprevention targets for clinical evaluation.

overall_design: DMSO-differentiated Huh7.5.1 cells, HepG2-NTCP cells, Huh7.5.1-NTCP cells, or clinical liver tissue slices were exposed to mock, HCV, HBV, or EtOH, and treated with variety of compounds or co-culture with hepatic stellate cell line, LX2. After 2 to 10 days of culture, cells/tissues were harvested for RNA isolation and gene expression profiling by NanoString assay.

first: Simonetta

last: Bandiera

first: Nicolaas

last: Van Renne

first: Xiaochen

last: Sun


title: A multi-omics approach using a mouse model of cardiac malformations for prioritization of human congenital heart disease contributing genes

first: Vidu

last: Garg


title: Systems Biology of Influenza A (H5N1) Virus Monovalent Vaccine with and without AS03 adjuvant

city: Palo Alto

first: Dmitri

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

summary: H5N1 influenza vaccine is known to induce diminished antibody responses in vaccine recipients without the use of adjuvant. We hypothesize that this is due to intrinsic defects in innate responses that could explain the poor immunogenicity of the vaccine. These innate responses may be improved with use of an adjuvant, e.g., AS03.

overall_design: Single site, Phase II randomized (2:1) double blinded study in which adult healthy subjects will receive 2 intramuscular doses of Influenza A (H5N1) Virus Monovalent Vaccine with AS03 adjuvant or Influenza A (H5N1) Virus Monovalent Vaccine without AS03 adjuvant given 21 days (+/- 3 days) apart.

last: Hagan

first: Mario

last: Cortese

first: Helder

last: Nakaya

first: Bali

last: Pulendran


title: RNA-seq of floe1-1 vs Col-0 seeds

first: Yanniv

last: Dorone

summary: We identified a regulator of Arabidopsis thaliana seed germination: FLOE1 (AT4G28300). We used RNA-seq to uncover genes that are diffenrentially regulated in dry seeds, imbibed seeds and seeds imbibed in 220mM NaCl.

overall_design: Imbibition and salt: after 5 days of stratification at 4C in the dark on MS media containing either 0 or 220mM NaCl, seeds were transferred to a growth chamber at 22C with normal light conditions for 4hours. RNA was then extracted from these seeds as well as from dry seeds. RNA was then sent to Novogene Corporation Inc. for library preparation (250-300 bp insert cDNA library) and sequencing (2x150 bp paired-end reads on an Illumina Platform). Three replicates were conducted for each genotype (floe1-1 or Col-0) and condition (dry, imbibed, salt).

first: Steven

last: Boeynaems

first: Aaron

middle: D

last: Gitler

first: Seung

middle: Y

last: Rhee


title: Adipose stromal cell niche reprograms the colorectal cancer stem cell metastatic machinery

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

summary: Study the effect of paracrine action of adipose stromal cells on colorectal cancer cells

overall_design: CMS2 primary colorectal cancer cells (#8 and #9) were treated for 48 hours with conditioned medium from subcutaneous (S-ASCs) or visceral (V-ASCs) adipose stromal cells to investigate the possible reprogramming toward aggressive (CMS4) phenotype

first: Simone

last: Di Franco

first: Jan

middle: P

last: Medema

first: Giorgio

last: Stassi


title: Dusp1 deletion unveils its central role in the regulation of redox homeostasis and inflammation in the mouse cochlea

city: Madrid

first: Jose M

middle: Bermúdez

last: Muñoz

state: Madrid

address: ARTURO DUPERIER 4

country: Spain

institute: INSTITUTO DE INVESTIGACIONES BIOMÉDICAS "ALBERTO SOLS"

summary: Stress-activated protein kinases (SAPK) have been associated with sensorineural hearing loss (SNHL) of multiple etiologies.  The activity of these kinases is tightly regulated by the dual-specificity phosphatase 1 (DUSP1), thus, DUSP1 loss of function leads to the sustained activation of SAPK. In the hearing organ, DUSP1 is an indispensable component of the stress response machinery, and its deficit accelerates SNHL progression, triggers the inflammatory response and promotes hair cell (HC) and spiral neurons (SGN) death. Here, we have studied the link between inflammation and redox imbalance in the cochlea by further characterizing the transcriptome of the Dusp1-/- mouse.  RNAseq and subsequent GSEA indicated that Dusp1-/- mice present a distinct gene expression pattern of key cellular programs, including altered expression of genes of the inflammatory response and glutathione metabolism.  To dissociate both components, Dusp1-/- mice were treated with the antioxidant N-acetylcysteine (NAC). Treatment with NAC delayed the onset of SNHL and reduced cochlear damage. Less HC were TUNEL+ and SGN showed less p-H2AX foci. NAC treatment not only improved redox balance but also reduced cytokine production and macrophage recruitment in Dusp1-/ -mice. In conclusion, our data point to DUSP1 as an essential node to control the cross-regulation of oxidative stress and inflammation.

overall_design: Cochlear mRNA profiles of 5 and 8-months-old wild type (WT) and Dusp1-/- mice

first: Jose

last: Bermúdez-Muñoz

first: Isabel

last: Varela-Nieto


title: Gene expression profiles of differentiated Huh7.5.1 cells infected with HCV Jc1 clone

first: Yujin

last: Hoshida

overall_design: DMSO-differentiated Huh7.5.1 cells were infected with HCV Jc1 clone, and harvested for RNA isolation and gene expression profiling by DNA microarrays.

first: Simonetta

last: Bandiera

first: Anu

last: Venkatesh

first: Nicolaas

last: Van Renne

first: Xiaochen

last: Sun

first: Mirjam

last: Zeisel

first: Thomas

last: Baumert


title: Chromatin accessibility and gene expression maps of Plasma Cells and Myeloma Plasma Cells

city: Sheffield

first: Ian

last: Sudbery

address: Firth Court, Western Bank

department: Molecular Biology and Biotechnology

country: United Kingdom

institute: University of Sheffield

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


title: Vibrio campbellii DS40M4 is a tractable model strain that diverges from the canonical quorum-sensing regulatory circuit in vibrios

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

institute: Indiana University

summary: Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi) is a fundamental model strain for studying population density-based cell-to-cell communication, known as quorum sensing, among gram-negative bacteria. In V. campbellii BB120, sensing of autoinducers at high cell densities activates the expression of the master transcriptional regulator, LuxR, which controls the expression of genes involved in group behaviors. Unlike BB120, the Vibrio campbellii environmental isolate DS40M4 was recently shown to be capable of natural transformation, a process by which bacteria take up exogenous DNA and incorporate it into their genome via homologous recombination. Here, we compare other phenotypes between DS40M4 and BB120. We find that DS40M4 has a faster growth rate and stronger type VI secretion-mediated cell killing, whereas BB120 forms more robust biofilms and is bioluminescent. We exploited the power of natural transformation to rapidly generate >30 mutant strains to explore the function of DS40M4-encoded homologs of the BB120 quorum-sensing system. Our results show that DS40M4 has a similar quorum-sensing circuit to BB120 but with three distinct differences: 1) DS40M4 lacks the canonical HAI-1 autoinducer LuxM synthase but has an active LuxN receptor, 2) the quorum regulatory small RNAs (Qrrs) are not solely regulated by autoinducer signaling through the response regulator LuxO, and 3) the DS40M4 LuxR regulon is <100 genes, which is relatively small compared to the >400 genes regulated in BB120. This work illustrates that DS40M4 is a tractable and relevant model strain for studying quorum-sensing phenotypes in Vibrio campbellii.

overall_design: RNA-Seq of WT and ∆luxR cultures grown to OD600=1.0

first: Chelsea

last: Simpson

first: Blake

last: Petersen

first: Logan

last: Geyman

first: Aimee

last: Lee

first: Michael

last: Manzella

first: Kai

last: Papenfort


title: TDRD3 promotes DHX9 chromatin recruitment and R-loop resolution

status: Public on Jun 26 2021

city: Monrovia

first: Xiwei

last: Wu

address: 655 HUNTINGTON DR.

institute: City of Hope

summary: R-loops, which consist of a DNA/RNA hybrid and a displaced single-stranded DNA (ssDNA), are increasingly recognized as critical regulators of chromatin biology. R-loops are particularly enriched at gene promoters, where they play important roles in regulating gene expression. However, the molecular mechanisms that control promoter-associated R-loops remain unclear. The epigenetic “reader” Tudor domain-containing protein 3 (TDRD3), which recognizes methylarginine marks on histones and on the C-terminal domain of RNA polymerase II, was previously shown to recruit DNA topoisomerase 3B (TOP3B) to relax negatively supercoiled DNA and prevent R-loop formation. Here, we further characterize the function of TDRD3 in R-loop metabolism and introduce the DExH-box helicase 9 (DHX9) as a novel interaction partner of the TDRD3/TOP3B complex. TDRD3 directly interacts with DHX9 via its Tudor domain. This interaction is important for recruiting DHX9 to target gene promoters, where it resolves R-loops in a helicase activity-dependent manner to facilitate gene expression. Additionally, TDRD3 also stimulates the helicase activity of DHX9. This stimulation relies on the OB-fold of TDRD3, which likely binds the ssDNA in the R-loop structure. Thus, DHX9 functions together with TOP3B to suppress promoter-associated R-loops. Collectively, these findings reveal new functions of TDRD3 and provide important mechanistic insights into the regulation of R-loop metabolism.

overall_design: Examination of expression profiles of WT, and two TDRD3 knockout (by different guide RNAs) MCF7 cells

first: Wei

last: Yuan

first: Qais

last: Al-Hadid

first: Hyejin

last: Cho

first: Yanzhong

last: Yang


title: Human neuroblastoma cell lines: control vs treated with verlindamycin and ATRA

city: London

first: Zuzanna

last: Urban-Wojciuk

address: 15 Cotswold Rd

institute: Institute of Cancer Research

summary: Analysis of differential gene expression in response to treatment of neuroblastoma cell lines (MYCN-amplified SK-N-BE(2)-C and non-amplified SKNAS) with retinoic acid and verlindamycin (a novel polyamine analogue and LSD1 inhibitor). This compound combination was found efficient in inducing differentiation in neuroblastoma cell lines and the goal of this microarray experiment was to analyse which genes and pathways were altered upon this treatment.

overall_design: Two-condition experiment for two cell lines: for both SK-N-BE(2)-C and SKNAS treated (verlindamycin+ATRA) vs control

first: James

last: Campbell


title: Multifactorial role of mitochondria in echinocandin tolerance revealed by transcriptome analysis of drug-tolerant cells

status: Public on Jun 25 2021

city: Nutley

first: Rocio

last: Garcia-Rubio

state: New Jersey

address: 111 Ideation way

institute: Center for Discovery and Innovation, Hackensack Meridian Health

summary: This study compared the transcriptional response of Candida glabrata echinocandin tolerant cells relative to no treated controls.

overall_design: We cultured C. glabrata in YPD containing 0.06 µg/ml micafungin or 0.25 µg/ml caspofungin for 24 hours, harvested the cells, used fluorescence-activated cell sorting to enrich for echinocandin-tolerant cells, followed by modified single cell RNA sequencing at the Columbia University Genome Center. Untreated stationary or logarithmic phase cells were used as controls.

first: Erika

last: Shor

first: David

middle: S

last: Perlin


title: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans [ATAC-seq]

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Dr

institute: University of California, San Diego

summary: Human subjects were vaccinated with seasonal influenza vaccine at day 0 (TIV, 2014-2015). A  subgroup of subjects (abx) received an additional oral antibiotic regimen, consisting of neomycin, vancomycin, and metronidazole, between days -3 and 1. CD14+ monocytes, mDCs, and pDCs were isolated from PBMCs of vaccinated subjects (3 antibiotic treated, 5 controls) at day -21 (BL), 0 and 30 using FACS. ATAC-seq was used to analyze the chromatin accessibility landscape in these cells.

overall_design: A total of 51 samples from 8 healthy donors (5x control, 3x antibiotics-treated) was analyzed. For each subject, three cell types were analyzed: CD14+ monocytes, mDCs, and pDCs. All subjects: d0 before vaccination and d30 after vaccination. PBMCs from antibiotics-treated subjects were additionally analyzed at d-21 before antibiotics treatment.

first: Pulendran

last: Bali

first: Wimmers

last: Florian

first: Gupta

last: Shakti


title: RNA-seq of human myoblasts where AR isoform 2 was either knocked-down or upregulated.

city: Oxford

first: Carlo

last: Rinaldi

address: South Parks Road

department: Department of Paediatrics

institute: University of Oxford

summary: The goal of this study is to unravel the function of this AR isoform in the cell. In particular we are interested in understanding the function of AR isoform 2 on the biology of AR.

overall_design: RNA-seq analysis was performed comparing the data set from human myoblasts transfected with plasmid expressing AR-2 (AR45) or mock sequence. Additionally RNA-seq analysis was also performed comparing data from human myoblasts treated with siRNA targeting AR-2 expression specifically or mock sequence. Conclusion: our study shows that AR-2 mainly alter genes containing an androgen responsive element in their promoter region.

first: Jesse

last: Dabney


title: A multi-omics approach using a mouse model of cardiac malformations for prioritization of human congenital heart disease contributing genes [scRNA-seq]

city: Columbus

first: Vidu

last: Garg

address: 700 Children's Drive WB4239

summary: Congenital heart disease (CHD) is the most common type of birth defect, affecting ~1% of all live births. Malformations of the cardiac outflow tract (OFT) account for ~30% of all CHD and include a range of CHDs from bicuspid aortic valve (BAV) to tetralogy of Fallot (TOF). We hypothesized that transcriptomic profiling of a mouse model of CHD would highlight disease-contributing genes implicated in congenital cardiac malformations in humans. To test this hypothesis, we utilized global transcriptional profiling differences from a mouse model of OFT malformations to prioritize damaging, de novo variants identified from exome sequencing datasets from published cohorts of CHD patients. Notch1+/-;Nos3-/- mice display a spectrum of cardiac OFT malformations ranging from BAV, semilunar valve (SLV) stenosis to TOF. Global transcriptional profiling of the E13.5 Notch1+/-;Nos3-/- mutant mouse OFTs and wildtype controls was performed by RNA sequencing (RNA-Seq). Analysis of the RNA-Seq dataset demonstrated genes belonging to the Hif1α, Tgf-β, Hippo, and Wnt signaling pathways were differentially expressed in the mutant OFT. Mouse to human comparative analysis was then performed to determine if patients with TOF and SLV stenosis display an increased burden of damaging, genetic variants in gene homologs that were dysregulated in Notch1+/-; Nos3-/- OFT. We found an enrichment of de novo variants in the TOF population among the 1,352 significantly differentially expressed genes in Notch1+/-;Nos3-/- mouse OFT but not the SLV population. This association was not significant when compared to only highly expressed genes in the murine OFT and of de novo variants in the TOF population. These results suggest that transcriptomic datasets generated from the appropriate temporal, anatomic and cellular tissues from murine models of CHD may provide a novel approach for the prioritization of disease-contributing genes in patients with CHD.

overall_design: E12.5 cardiac OFTs (both Notch1+/- and wildtype) were microdissected from five mouse embryos and pooled for single-cell RNA sequencing

first: Sathiyanarayanan

last: Manivannan

first: Uddalak

last: Majumdar

first: Adrianna

last: Matos-Nieves


title: Chromatin accessibility and gene expression maps of Plasma Cells and Myeloma Plasma Cells [ATAC-seq]

first: Ian

last: Sudbery

summary: We report the application of paired Assay for Transposase-Accessible Chromatin (ATAC-seq) and RNA-seq data to profile the regulatory landscape and expression of 5 primary Plasma Cell (PC), 28 Multiple Myeloma (MM) PC as well as 5 cell lines samples. Findings discriminated MM and MM subgroup-specific changes such as the exclusive overexpression of CCND1 and CCND2 oncogenes. DNA accessibility changes were correlated to gene expression in a topologically constrained manner to elucidate novel enhancer - promoter interactions, genes and pathways critical for myeloma biology and developmentally activated or de novo formed enhancers. Additionally, the MM subgroup-specific TF network dependencies were studied to help identify prognostic markers. Finally, we discover and functionally validate the critical enhancer that regulates ectopic expression of CCND2 in MM.

overall_design: Examination of paired ATAC-seq and RNA-seq data of 5 primary Plasma Cell (PC), 28 Multiple Myeloma (MM) PC as well as 5 cell lines samples.

first: Jaime

last: Alvarez-Benayas

first: Alexia

last: Katsarou

first: Nikolaos

last: Trasanidis

first: Aristeidis

last: Chaidos

first: Kanagaraju

last: Ponnusamy

first: Xiaolin

last: Xiao

first: Marco

last: Bua

first: Maria

last: Atta

first: Irene

last: Roberts

first: Holger

middle: W

last: Auner

first: Evdoxia

last: Hatjiharissi

last: Papaioannou

first: Valentina

last: Caputo

first: Anastasios

last: Karadimitris

first: Philippa

last: May


title: Doxorubicin treatment effects on the young mouse brain transcriptome

city: Fort Collins

first: Alyssa

middle: N

last: Cavalier

address: 1582 Campus Delivery, Moby Reception

department: Health and Exercise Science

institute: Colorado State University

summary: Doxorubicin (Doxo) is a common chemotherapeutic reagent associated with mitochondrial dysfunction, DNA damage, and cognitive impairment in human cancer patients. The purpose of this study was to determine the transcriptional effects of Doxo on the brains of young mice. 4 month old C57B6/J male mice were injected with saline sham or 10mg/kg Doxo +/- MitoQ (a mitochondria-specific antioxidant). Hippocampi were harvested from these mice and RNA was isolated to perform polyA RNA-seq to profile gene expression.

overall_design: PolyA RNA-seq on hippocampi isolated from mice treated with saline sham, Doxo injection, and Doxo injection + MitoQ supplementation.

first: Thomas

last: LaRocca


title: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans (TIV_scATAC-seq)

first: Florian

last: Wimmers

address: 1651 Page Mill Road

department: School of Medicine

summary: Human subjects were vaccinated with seasonal influenza vaccine (TIV, 2014-2015). We then used scATAC-seq to construct the single-cell landscape of the innate immune response to TIV at the epigenomic level. PBMCs from vaccinated individuals were isolated at day 0, 1, and 30, then enriched for DC subsets using flow cytometry and analyzed using droplet-based single-cell chromatin accessibility profiling.

overall_design: A total of 9 samples from 3 healthy individuals at 3 time points was analyzed: day 0 before vaccination, and day 1 and day 30 after vaccination.

first: Tal

last: Ashuach

first: Sanne

middle: E

last: deJong


title: BAP1 activity regulates Polycomb occupancy and global chromatin condensation counteracting diffuse PCGF3/5-dependent H2AK119ub1 deposition

status: Public on Jun 27 2021

city: Milan

first: Federico

last: Rossi

address: Via Adamello 16

country: Italy

institute: Istituto Europeo Oncologia

summary: BAP1 is recurrently mutated or deleted in a large number of diverse cancer types, including mesothelioma, uveal melanoma and hepatocellular cholangiocarcinoma. BAP1 is the catalytic subunit of the Polycomb Repressive De-Ubiquitination complex (PR-DUB) which removes PRC1 mediated H2AK119ub1. We and others have shown that H2AK119ub1 is essential for maintaining transcriptional repression and contributes to PRC2 chromatin recruitment. However, the precise relationship between BAP1 and PRC1 remains mechanistically elusive. Using embryonic stem cells, we show that a major function of BAP1 is to restrict H2AK119ub1 deposition to target sites. This increases the stability of PcG complexes with their targets and prevents diffuse accumulation of H2AK119ub1 and H3K27me3 modifications. Loss of BAP1 results in a broad increase in H2AK119ub1 levels that are primarily dependent on PCGF3/5-PRC1 complexes with a mechanism that is reminiscent of X-chromosome inactivation. Increased genome-wide H2AK119ub1 levels titrates away PRC2 from its targets and stimulates diffuse H3K27me3 accumulation across the genome. This decreases the activity of PcG repressive machineries at physiological targets and induces a general compaction of the entire chromatin. Our findings provide evidences for a unifying model that resolves the apparent contradiction between BAP1 catalytic activity and its role in vivo, uncovering molecular vulnerabilities that could be useful for BAP1-related pathologies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Profiling of histone modification and gene expression in mouse embryonic stem cells in wild-type and BAP1-KO. Characterisation of chromatin conformation structure by HiC.

first: Eric

last: Conway

first: Simone

last: Tamburri

first: Eleonora

last: Ponzo

first: Karin

last: Ferrari

first: Marika

last: Zanotti

first: Daniel

last: Fernandez-Perez

first: Daria

last: Manganaro

first: Simona

last: Rodighiero

first: Diego

last: Pasini


title: RNA-seq profiles of rat cardiomyocytes overexpressing hsa-miR-106b-5p, hsa-miR-93-5p, hsa-miR-25-3p or cel-miR-67

city: Klosterneuburg

first: Ryan John

last: Cubero

state: Lower Austria

address: Am Campus 1

country: Austria

institute: IST Austria

summary: Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. We report that the miR-106b~25cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. To identify the relevant targets of individual miRNAs in the miR-106b~15 cluster and elucidate the molecular mechanisms underlying the proliferative effects of this microRNA cluster, we assessed the global transcriptomic changes by deep-sequencing total neonatal mouse cardiomyocyte RNA after exogeneous transfection with hsa-miR-106b-5p, hsa-miR-93-5p, hsa-miR-25-3p and compared the transcriptomic profiles to cardiomyocytes transfected with cel-miR-67, a control miRNA.

overall_design: Cardiomyocyte RNA profiles of 1-day old wild type (WT) rats overexpressing individual members of the miR-106b~25 microRNA cluster were generated by deep sequencing using Illumina Hiseq 2000; Four condition experiment; one replicate per condition

first: Leon

last: de Windt

first: Ellen

last: Dirkx


title: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans (H5N1_scATAC-seq)

institute: Stanford University

summary: Human subjects were vaccinated with adjuvanted (AS03) or unadjuvanted pre-pandemic influenza vaccines H5N1 at day 0 and d21. We then used scATAC-seq to construct the single-cell landscape of the innate immune response to those vaccines at the epigenomic level. PBMCs from vaccinated individuals were isolated at day 0, 21, and 42, then enriched for DC subsets using flow cytometry and analyzed using droplet-based single-cell chromatin accessibility profiling.

overall_design: A total of 12 samples from 4 healthy individuals at 3 time points was analyzed: day 0 before vaccination,  and day 21 and 42 after first vaccination.


title: A chemical screen identifies compounds limiting the toxicity of C9ORF72 dipeptide repeats [drug treatment]

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

institute: CNIO

summary:
Purpose: Compare the effect of PR20 alone or together with PFI or NaPhen

Methods: NSC-34 cells are wildtype in the non-coding hexanucleotide repeat status of C9orf72. NSC-34 cell cultures were treated with PR20, PFI or NaPhen alone for 48 hours, or in combination (48 hours with PR20 and the last 24 hours with PFI or NaPhen). mRNA profiles of the different conditions were generated by RNAseq. Sequencing reads were aligned and analyzed for differential gene expression.

Results: The analysis reveals that the transcriptional changes induced by PR20 are alleviated by the treatment with PFI or NaPhen.

overall_design: mRNA profiles of NSC34-treated cells and untreated cells were generated by deep sequencing. Differential gene expression (DGE) analyses were performed.

first: Alba

last: Corman

first: Jordi

last: Carreras

first: Vanesa

last: Lafarga

first: Óscar


title: A Critical Role of Nuclear m6A Reader YTHDC1 in Leukemogenesis by Regulating MCM Complex-Mediated DNA Replication

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: PLKO.1 lentiviral vectors contained scramble shRNA, YTHDC1 shRNA 1# and YTHDC1 shRNA 2# were transfected into 293T cells together with package plasmids pMDG.2 and Δ8.91.  The supernatant medium contained virus was collected and subjected to infect MOLM-13 cells by spinoculation, MOLM-13 cell is an AML cell line. The positive cells were collected 3 days after viral infection and subjected to RNA-seq.

overall_design: YTHDC1 knockdown

first: Yue

last: Sheng

first: Jiangbo

last: Wei

first: Chuan

last: He

first: Zhijian

last: Qian


title: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans

first: Shankar

last: Subramaniam

summary: Human subjects were vaccinated with seasonal influenza vaccine at day 0 (TIV, 2014-2015). A  subgroup of subjects (abx) received an additional oral antibiotic regimen, consisting of neomycin, vancomycin, and metronidazole, between days -3 and 1. CD14+ monocytes were isolated from PBMCs of vaccinated subjects (2 antibiotic treated, 3 controls) at day 0 and 30 using FACS. RNA-seq was used to analyze the transcriptional landscape in these cells.

overall_design: A total of 10 samples from 5 healthy donors (3x control, 2x antibiotics-treated) was analyzed. Time points: d0 before vaccination and d30 after vaccination. Cell types: purified CD14+ monocytes.

first: Bali

last: Pulendran

first: Florian

last: Wimmers

first: Shakti

last: Gupta


title: Substrate Stiffness Modulates the Growth, Phenotype, and Chemoresistance of Ovarian Cancer Cells

city: Beijing

first: Quanmei

last: Sun

address: No.11 ZhongGuanCun BeiYiTiao

institute: National Centre for Nanoscience and Technology

summary:
Purpose: Identify the effect of substrate stiffness on gene expression
Methods:Evaluating for differentially expressed mRNAs in the SKOV-3 cells grown on the different substrates via High-throughput sequence
Results: We found that the general direction of changes in gene expression of cells grown on the different substrates and the most significant signalling pathways and the expression of gene orthologs broadly involved in platinum drug resistance, apoptosis, cell cycle.
Conclusions: Our study represents the first detailed analysis of the effects of substrate stiffness on gene expression of ovarian cancer cells.

overall_design: SKOV-3 cells were seeded in the petri dishes, coated with hydrogel substrates of different stiffness (0.5kPa, 4kPa, 25kPa).

first: Yali

last: Fan

first: Xia

last: Li

first: Jiantao

last: Feng

first: Zhuo

last: Ao

first: Xiang

first: Jiandong

last: Wang


title: Identification of potential genomic alterations in primary and recurrent synovial sarcoma

city: Shihezi

first: Yan

last: Qi

state: Xinjiang province

address: North 2 road

department: Department of Pathology

institute: Shihezi University School of Medicine & the First Affiliated Hospital to Shihezi University School of Medicine

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

summary:
This study aimed to analyze the mutated genes of primary and recurrent SSs (PRSSs), to discover whether these sarcomas exhibit some potential mutated genes between primary and recurrent cases
Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples.

overall_design: Ten samples were analyzed by Illumina HumanExome-12 v1.1 BeadChip

first: Feng


title: Mammary-specific expression of Trim24 establishes a mouse model of human metaplastic breast cancer and nominates c-Met and TRIM24 as therapeutic targets

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

summary: Conditional overexpression of histone reader Tripartite motif containing protein 24 (TRIM24) in mouse mammary epithelia (Trim24COE) drives spontaneous development of carcinosarcoma tumors, lacking ER, PR and HER2. Human carcinosarcomas or metaplastic breast cancers (MpBC) are a rare, chemorefractory subclass of triple-negative breast cancers (TNBC). Comparison of Trim24COE carcinosarcoma morphology, TRIM24 protein levels and a derived Trim24COE gene signature revealed strong correlation with human MpBC tumors and MpBC xenograft (PDX) models. Global and single-cell tumor profiling revealed Met as a direct oncogenic target of TRIM24, leading to aberrant PI3K/mTOR activation. Pharmacological inhibition of these pathways in primary Trim24COE tumor cells and TRIM24-PROTAC treatment of MpBC PDX tumorspheres revealed the therapeutic potential of targeting TRIM24. Altogether, global expression, single-cell immunophenotyping and mechanistic studies of tumors and MpBC PDX nominated TRIM24-activated c-MET/PI3K/mTOR pathways and TRIM24, which were validated as potential MpBC therapeutic targets.

overall_design:
We have obtained gene expression profiles of 8 treatment-naïve metaplastic tumors and 20 treatment-naïve non-metaplastic tumors from triple-negative breast cancer patients.
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***Submitter states the following:
Due to IRB restrictions, we are required to use a controlled-access database for the raw data.  Thus, we cannot upload the raw data to SRA.  We are currently in the process of uploading it to EGA.
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first: Vrutant

middle: V

last: Shah

first: Aundrietta

last: Duncan

first: Shiming

last: Jiang

first: Sabrina

last: Stratton

first: Kendra

middle: L

last: Allton

first: Clinton

last: Yam

first: Abhinav

last: Jain

first: Yue

last: Lu

first: Shirong

last: Cai

first: Yizheng

last: Tu

first: Xinhui

last: Zhou

first: Xiaomei

last: Zhang

first: Christopher

last: Carroll

first: Zhijun

last: Kang

first: Jianjun

last: Shen

first: Reid

middle: T

last: Powell

first: Lei

last: Guo

first: Clifford

last: Stephan

first: Jan

last: Parker-Thornburg

first: Guillermina

last: Lozano

first: Richard

middle: R

last: Behringer

first: Michael

last: Gilcrease

first: Peter

last: Davies

first: Helen

last: Piwnica-Worms

first: Stacy

last: Moulder

first: Michelle

last: Barton


title: Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

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

overall_design: Refer to individual Series


title: MethylC-capture sequencing and RNA sequencing of control (CTL), chronic nonbacterial prostatitis (CNP) and polysaccharide (PPs)-treated SD rats [Bisulfite-Seq]

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

summary: SD rats were intramuscular injected with dexamethasone to induce osteCPorosis, and treated with APS. Then, colonic epithelia of control, osteCPorotic and APS-treated osteCPorotic rats were collected for MethylC-capture sequencing .

overall_design: examination of DNA methylation in colonic epithelia of  three groups of rats

first: Junsheng

last: Liu

first: Xichun

last: Peng


title: Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis (RNA-Seq 2)

summary: One of the cellular processes influenced by microRNAs is senescence, a state of indefinite growth arrest triggered by sublethal cell damage. Here, through bioinformatic analysis and experimental validation, we identified miR-340-5p as a novel miRNA that foments cellular senescence. miR340-5p was highly abundant in diverse senescence models, and miR-340-5p overexpression in proliferating cells rendered them senescent. Among the target mRNAs, miR-340-5p prominently reduced the levels of LBR mRNA, encoding Lamin B Receptor (LBR). Loss of LBR by ectopic overexpression of miR-340-5p derepressed heterochromatin in lamina-associated domains (LADs), promoting the expression of DNA repetitive elements characteristic of senescence. Importantly, overexpressing miR-340-5p enhanced cellular sensitivity to senolytic compounds, while antagonization of miR-340-5p reduced senescent-cell markers and engendered resistance to senolytic-induced cell death. We propose that miR-340-5p can be exploited for clearing senescent cells to restore tissue homeostasis and mitigate damage by senescent cells in aging human pathologies.

overall_design: WI-38 fibroblasts (PDL 20) were transfected either with control miRNA or a precursor miRNA mimic of miR-340-5p, and  cultured for four days before RNA extraction and sequencing.

first: Allison

last: Herman

first: Carlos

last: Anerillas

first: Sophia

middle: C

last: Harris

first: Rachel

last: Munk

first: Jennifer

last: Martindale

first: Xiaoling

last: Yang

first: Krystyna

last: Mazan-Mamczarz

first: Indra

last: Heckenbach

first: Morten

last: Scheibye-Knudsen

first: Yongqing

last: Zhang

first: Payel

last: Sen

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


city: Palo Alto

first: Florian

last: Wimmers


title: Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis (ATAC-Seq)

first: Supriyo

last: De

summary: The goal of this study was to identify accessible chromatin peaks in lamina-associated domains of senescent cells. To establish senescence we used ionizing radiation (IR), overexpression of miR-340-5p, and knockdown of Lamin B Receptor (LBR).One of the cellular processes influenced by microRNAs is senescence, a state of indefinite growth arrest triggered by sublethal cell damage. Here, through bioinformatic analysis and experimental validation, we identified miR-340-5p as a novel miRNA that foments cellular senescence. miR340-5p was highly abundant in diverse senescence models, and miR-340-5p overexpression in proliferating cells rendered them senescent. Among the target mRNAs, miR-340-5p prominently reduced the levels of LBR mRNA, encoding Lamin B Receptor (LBR). Loss of LBR by ectopic overexpression of miR-340-5p derepressed heterochromatin in lamina-associated domains (LADs), promoting the expression of DNA repetitive elements characteristic of senescence. Importantly, overexpressing miR-340-5p enhanced cellular sensitivity to senolytic compounds, while antagonization of miR-340-5p reduced senescent-cell markers and engendered resistance to senolytic-induced cell death. We propose that miR-340-5p can be exploited for clearing senescent cells to restore tissue homeostasis and mitigate damage by senescent cells in aging human pathologies.

overall_design: ATAC-sequencing of WI-38 fbroblasts to identify accessible chromatin in various cellular senescence models: PDL20 WI-38 fibroblasts were transfected with a control miRNA (N=2), precursor miRNA mimic of miR-340-5p (N=2), a siRNA to Lamin B Receptor (LBR, N=2), or exposure to ionizing radiation (10 Gy, siLBr, N=2), and cultured for 4 days before harvest for RNA extraction and RNA sequencing. Cells exposed to IR were cultured for an additional 10 days after expsoure.

middle: B


title: Single-cell transcriptomic analysis of mouse lung CD11b+ dendritic cells post allergic sensitization

city: Research Triangle Park

first: Hideki

last: Nakano

state: NC

address: 111 TW Alexander Drive

department: Immunity, Inflammation and Disease Laboratory

institute: NIEHS

summary: Conventional dendritic cells (cDCs) in the lung that drive effector T cell differentiation, and initiate allergic responses upon inhalation of allergens. However, since CD11b+ cDCs are heterogeneous, the specific function of each subpopulation has been elusive. To identify subpopulations of CD11b+ cDCs, we performed single cell RNA-sequencing (scRNAS-Seq) of total lung CD11b+ cDCs following inhalation of house dust extracts, and detected multiple clusters based on their differential transcriptomes. The data will be applicable for studies of cDC function in induction of T cell differentiation as well as the maturation pathway of cDCs.

overall_design: CD11b+ cDCs (CD45+ CD11c+ I-A+ Siglec-F– CD88– F4/80– CD103– Live/Dead–) from C57BL/6 mice inhaled house dust extract together with ovalbumin were loaded into the Single Cell Chip followed by forming single cell. The Gene Expression library and the ADT Library were prepared using the Chromium single cell 3′ v2 library and gel bead kit (10x Genomics) and additional reagents recommended in the protocol of Total A-seq (Biolegend). The two libraries were mixed at 10:1 molar ratio (Gene Expression library to ADT library) and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Laboratory on NextSeq 500 (Illumina) with paired-end sequencing (Read 1: 31; Read 2: 101).

first: Gentaro

last: Izumi

first: Peer

last: Karmaus

first: Donald

last: Cook


title: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans (H5N1_scRNA-seq)

summary: Human subjects were vaccinated with adjuvanted (AS03) or unadjuvanted pre-pandemic influenza vaccines H5N1 at day 0 and d21. We then used scRNA-seq to construct the single-cell landscape of the innate immune response to those vaccines at the transcriptional level. PBMCs from vaccinated individuals were isolated at day 0, 21, and 42, then enriched for DC subsets using flow cytometry and analyzed using droplet-based single-cell gene expression profiling.

overall_design: A total of 11 samples from 4 healthy individuals at 3 time points was analyzed: day 0 before vaccination, and day 21 and 42 after first vaccination. The day 42 time point is missing for one of the individuals.

first: Tal

last: Ashuach

first: Sanne

last: deJong


title: High-resolution, genome-wide mapping of positive supercoiling in chromosomes [yChIP]

city: Seattle

first: Monica

last: Guo

address: 750 Republican St

department: Microbiology

institute: University of Washington

summary: Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and enriched between convergently-oriented genes, consistent with the ?twin-domain? model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, replication-transcription encounters, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach that can be applied in any organism to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

overall_design: Sequencing data from E. coli MG1655 and S. cerevisiae. (i) E. coli GapR and GapR1-76 ChIP-seq, (ii) E. coli RNA-seq +/- GapR-3xFLAG expression, (iii) S. cerevisiae GapR ChIP-seq in raffinose +/- alpha-factor and in glycerol, (iv) S. cerevisiae RNA-seq +/- GapR, and (v) S. cerevisiae RNA-seq in raffinose +/- alpha-factor and in glycerol after GapR induction

first: Ryo

last: Kawamura

first: Megan

last: Littlehale

first: John

middle: F

last: Marko

first: Michael

last: Laub


title: Multiplexed profiling facilitates robust m6A   quantification at site, gene and sample resolution

city: Rehovot

first: David

last: Dierks

state: Central District

address: Herzl St 234, Weizmann Institute of Science to the Department of Biomolecular Sciences, Laboratory of Dr. Scherz-Shouval

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

summary: N6-methyladenosine (m6A) is the most prevalent modification of mRNA in mammals  and plays a major role in the post-transcriptional regulation of gene expression. To interrogate its functions and dynamics, there is a critical need to quantify m6A at three levels of granularity: The modified site, the overall m6A levels per gene, and the global levels per sample. Current approaches address these needs in a highly limited manner. Here we develop m6A-seq2, relying on multiplexed m6A immunoprecipitation of pre-barcoded and pooled samples. m6A-seq2 allows a major increase in throughput, while dramatically reducing technical variability, requirements of input material, cost, and labor. m6A-seq2 is furthermore uniquely capable of providing sample-level relative quantitations of m6A, serving as an important, orthogonal alternative to mass spectrometry based approaches. Finally, we develop a computational approach for gene-level quantitation of m6A. We demonstrate that using this metric, roughly 30% of the variability in RNA half-life in mouse embryonic stem cells can be explained in terms of m6A levels. This is ~10 fold higher than could be observed using previous approaches and establishes m6A as a major driver of RNA stability. m6A-seq2 thus provides an experimental and analytic framework for dissecting m6A-based regulation at three critical resolutions.

sample_organism:
Saccharomyces cerevisiae
Mus musculus

platform_organism:
Saccharomyces cerevisiae
Mus musculus

overall_design: polyA-selected SK1 RNA. 12 technical replicates for m6A-seq2 analysis, 3 technical replicates for m6A-seq. 4 batches of m6A-seq2 analysis of various genetic perturbations in SK1 Ndt-/- background. Yeast meiosis timecourse 12 samples (5 timepoints, duplicates) and a positive and negative control prepared with m6A-seq2 protocol. 5 clones with m6A-'writer' genetic perturbation (partial knock-out), 2 Wtap and 2 Mettl3 perturbations in mouse embryonic stem cells prepared with m6A-seq2 protocol. 24 samples poly-A selected samples (serial dilution of WT and Mettl3 KO mESC RNA in technical triplicates) conducted to m6A-seq2. 10 technical replicates of MEF poly-selected RNA

first: Schraga

last: Schwartz


title: High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-Seq 2]

summary: Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and enriched between convergently-oriented genes, consistent with the “twin-domain” model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, replication-transcription encounters, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach that can be applied in any organism to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.


title: High-resolution, genome-wide mapping of positive supercoiling in chromosomes [ecChIP]

summary: Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three- dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently-oriented genes, consistent with the “twin-domain” model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

sample_organism: Escherichia coli str. K-12 substr. MG1655


title: MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion [RNA-seq]

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

summary: The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with significantly modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg133, a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.

overall_design: In this work we have carried out an in-depth study on the role of MeCP2 in mouse embryonic fibroblasts. The use of cell lines WT and KO for MeCP2 combined with biochemical, genomic and structural approaches, has allowed to demonstrate that MeCP2 is a (CA)n microsatellite DNA binding protein. We show that within the MBD family, MeCP2 is the only protein that specifically recognizes and binds to CA repeats, with much stronger affinity as compared to mCG and mCA. While MeCP2 can bind in vitro to modified and non-modified CA repeats, it exhibits impressive selectivity towards hydromethylated CA repeats, which are modified by the enzyme DNMT3A. The modified cytosine, only when located within a CA repeat, serves as a nucleation point for both MeCP2 accumulation and spreading around the repeat, which correlates in turn with nucleosome exclusion. In addition, loss of MeCP2 results in widespread increase in nucleosome density within lamina-associated domains (LADs) and transcriptional dysregulation of CA repeat–enriched genes located outside LADs.

first: Abdulkhaleg

last: Ibrahim

first: Kareem

last: Mohideen-Abdul

first: Stéphanie

last: Le Gras

first: Isabelle

last: Stoll

first: Christian

last: Bronner

first: Stefan

last: Dimitrov

first: Bruno

last: Klaholz

first: Ali

last: Hamiche


title: Transcriptome sequencing of epididymal adipose tissue harvested from 2-month-old Tfrcfl/fl and TfrcAKO mice on high fat diet for 10 more weeks

city: Wuhan

first: Zhuzhen

last: Zhang

state: Hubei

address: 6015Shengke Building, College of life sciences, 299 Bayi Road, Wuchang

institute: Wuhan University

summary:
Purpose: The goals of this study are to compare the transcription difference of epididymal fat between Tfrcfl/fl and TfrcAKO mice after high fat diet treatment
Methods: Transcriptome of epididymal adipose tissue was generated by deep sequencing, using Illumina Novaseq 6000 sequencing system.

overall_design: 2-month-old male Tfrcfl/fl and TfrcAKO mice were challenged with high fat diet for 10 weeks, RNA are extracted from the epididymal adipose tissues for whole transcriptome RNA-seq

first: Philipp

last: Scherer


title: High-resolution, genome-wide mapping of positive supercoiling in chromosomes [RNA-seq]

first: Monica

last: Guo

platform_organism: Escherichia coli str. K-12 substr. MG1655

first: Ryo

last: Kawamura


title: Suppression of LBR by miR-340 disrupts chromatin, promotes cell senescence, and enhances senolysis (RNA-Seq 1)

first: Supriyo

last: De

overall_design: WI-38 fibroblasts (PDL 20) were transfected either with control miRNA (N=2) or an antagomiR of miR-340-5p (anti_miR-340-5p, N=2), and  cultured for four days before RNA extraction and sequencing.

first: Allison

last: Herman

first: Carlos

last: Anerillas

first: Sophia

last: Harris

first: Rachel

last: Munk

first: Jennifer

last: Martindale

first: Xiaoling

last: Yang

first: Krystyna

last: Mazan-Mamczarz

first: Indra

middle: J

last: Heckenbach

first: Morten

last: Scheibye-Knudsen

first: Yongqing

first: Payel

last: Sen

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Conservation genomics reveals pesticide and pathogen exposure in the declining bumblebee Bombus terricola

city: Toronto

first: Amro

last: Zayed

state: Ontario

address: 4700 Keele Street

country: Canada

institute: York University

summary: We use high-thoughput RNA sequencing to investigate the stressors experienced by the vulnerable Bombus terricola near agricultural areas.

overall_design: We used RNAseq to sequence the abdomens of thirty Bombus terricola workers collected in agricultural and non-agricultural landscapes

first: Nadejda

last: Tsvetkov

first: Victoria

last: MacPhail

first: Sheila

last: Colla


title: MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion

first: Christophe

last: Papin

first: Abdulkhaleg

last: Ibrahim

first: Kareem

last: Mohideen-Abdul

first: Stéphanie

last: Le Gras

first: Isabelle

last: Stoll

first: Christian

last: Bronner

first: Stefan

last: Dimitrov

first: Bruno

last: Klaholz

first: Ali

last: Hamiche


title: Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors

status: Public on Jun 24 2021

city: Amsterdam

first: Sander

last: van Hooff

address: Meibergdreef 9

institute: AUMC

summary: Malignant rhabdoid tumors (MRT) represent one of the most aggressive childhood malignancies. No effective treatment options are available, and prognosis is therefore dismal. Previous studies have demonstrated that tumor organoids capture the heterogeneity of patient tumors and can be used to predict patient therapy response. Here, we perform drug screening on patient-derived normal and tumor organoids to identify MRT-specific therapeutic vulnerabilities. We identify neddylation inhibitor MLN4924 as a potential therapeutic agent. Mechanistically, we find increased neddylation in MRT organoids and tissues and show that MLN4924 induces a cytotoxic response via upregulation of the unfolded protein response. Lastly, we demonstrate in vivo efficacy in an MRT PDX mouse model, in which single agent MLN4924 treatment significantly extends survival. Our study demonstrates that organoids can be used to find drugs selectively targeting tumor cells while leaving healthy cells unharmed and proposes neddylation inhibition as therapeutic strategy in MRT.

overall_design: Methylation profiling was performedon on a malignant rhabdoid tumor (MRT) with a IlluminaHumanMethylation850k array

first: Camilla

last: Calandrini

first: Irene

last: Paassen

first: Jarno

last: Drost


title: Gene expression in anergic and naïve CD4 T cells deficient for Nr4a1 and Nr4a3

city: San Francisco

first: Julie

last: Zikherman

address: Koret Way

department: Medicine - Rheumatology

institute: University of California, San Francisco

summary: The NR4A family of nuclear receptors are upregulated by acute and chronic antigen stimulation, and play redundant, tolerogenic roles in T and B cells. To bypass their obligate function in the Treg lineage, we generated competitive chimeras with Nr4a1-/-Nr4a3-/- (double knockout or DKO) bone marrow mixed with congenically marked WT bone marrow at a 1:5 ratio. As a result of a defect in Treg production by DKO cells, Treg in mixed chimeras are almost exclusively of WT origin. By contrast, we generate an approximately 1:1 DKO:WT ratio in the peripheral T cell compartment because DKO cells escape negative selection. After reconstitution, we observed pronounced accumulation of anergic DKO CD4 T cells, but a defect in functional tolerance resulting in autoantibody production. Based on these studies and published literature, we hypothesize that the NR4A family regulate TCR-induced transcripts in both naive and anergic CD4 T cells. To identify such targets, we sorted naive and anergic CD4 T cells of either WT or DKO genotype (CD45.1+ or CD45.1-) on the basis of CD73/FR4/CD44 expression from these chimeras directly into RLT buffer.  In parallel, we stimulated sorted naive CD4 T cells of each genotype in vitro with plate-bound anti-CD3 and anti-CD28 stimulation for 3 hrs and then generated RLT lysates. We made biological triplicate samples of each condition (naive WT and DKO, naive stimulated WT and DKO, anergic WT and DKO) resulting in 6 different populations x 3 replicates  = 18 samples. Samples were subjected to library prep and bulk RNA sequencing to identify DEG.

overall_design: As described above, DKO and WT CD25-CD4+ T cells were sorted from competitive chimeras on the basis of CD62L/CD44/FR4/CD73 surface expression to identify either naïve (CD62LhiCD44loFR4loCD73lo) or anergic (CD62LloCD44hiFR4hiCD73hi) populations. Naïve and anergic cell populations were sorted directly into RLT buffer. In parallel, sorted naive CD4 samples were stimulated ex vivo withplate-bound anti-CD3 and anti-CD28 for 3 hrs. Libraries were constructed by the Emory EIGC core. Libraries were sequenced in an individual lane of an S1 flowcell on the NovaSeq6000 with a PE100 configuration using a NovaSeq 6000 SP Reagent Kit. Fastq files were trimmed for adapters and low quality base pairs using Fastp (https://academic.oup.com/bioinformatics/article/34/17/i884/5093234) then aligned to mouse genome assembly mm10 using STAR (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/). FeatureCounts (https://pubmed.ncbi.nlm.nih.gov/24227677/) was used to obtain read count data and a paired differential expression analysis comparing samples from the same chimeras was performed with edgeR (https://pubmed.ncbi.nlm.nih.gov/19910308/).

first: Ryosuke

last: Hiwa

first: James

last: L. Mueller

first: Ravi

last: Mandla


first: Christophe

last: Papin

last: Mohideen


title: Requirement of mitochondrial transcription factor A in interleukin-17-producing gdT cells to regulate the small intestine homeostasis and metabolism

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

summary: Interleukin 17 (IL-17)-producing gamma delta T (gdT17) cells are one of the major cellular sources of IL-17 under the steady state and in disease. However, gdT17 cell metabolism and its role in tissue homeostasis remain poorly understood. Here, we show that the tissue milieu shapes splenic and intestinal gdT17 cell gene signatures. Conditional deletion of mitochondrial transcription factor A (Tfam) in gdT17 cells significantly affected gdT17 cell maintenance systemically. In vivo deletion of Tfam in gdT17 cells resulted in small intestinal tissue remodeling and increased small intestine length that was caused by the enhanced tuft cell–group 2 innate lymphoid cell (ILC2) circuit in mice. In vitro, IL-22, a cytokine highly produced by gdT17 cells, inhibited IL-13-induced tuft cell differentiation. Mice with Tfam deletion in gdT17 cells also showed dysregulation of the small intestine transcriptome and metabolism with less body weight but enhanced anti-helminth immunity. Thus, our work revealed a critical role of mitochondrial metabolism in gdT17 cell maintenance and in regulating small intestine homeostasis and metabolism.

overall_design: RNA-seq (3 replicates) analysis of spleeen, small intestine, and large intestine gdT17 cells from Tfam cKO and control mice as well as (3 replicates) analysis of small intestine tissue from Tfam cKO and control mice

first: Zheng

last: Fu

first: Joseph

last: Dean


title: Tumor cells generate astrocytes that contribute to SHH-driven medulloblastoma relapse

city: Philadelphia

first: Duancheng

last: Guo

state: PA

address: 333 Cottman AVE

institute: Fox Chase Cancer Center

summary: Astrocytes, a major glial cell type in the brain, play a critical role in supporting the progression of medulloblastoma (MB), the most common malignant pediatric brain tumor. By lineage tracing analyses and single cell RNA sequencing, we demonstrate that astrocytes are predominately derived from the transdifferentiation of tumor cells in relapsed MB (but not in primary MB), although MB cells are generally believed to be neuronal-lineage committed. Such transdifferentiation of MB cells relies on Sox9, a transcription factor critical for gliogenesis. Our studies further reveal that bone morphogenetic proteins (BMPs) stimulate the transdifferentiation of MB cells by inducing the phosphorylation of Sox9. Pharmaceutical inhibition of BMP signaling represses MB cell transdifferentiation into astrocytes, and suppresses tumor relapse. Our studies establish the distinct cellular sources of astrocytes in primary and relapsed MB, and provide an avenue to prevent and treat MB relapse by targeting tumor cell transdifferentiation.

overall_design: In this study, we used single-cell sequencing to analyze the composition of primary and relapsed medulloblastoma;  RNA sequencing to analyze the gene expression of astrocytes in primary and ralapsed medulloblastoma.

first: Zeng-jie

last: Yang

first: Shengyou

last: Liao

first: Yan

last: Cheng


title: Characterization of a novel mouse model of undifferentiated pleomorphic sarcoma that  is lymphocyte poor, macrophage rich, and resistant to immune checkpoint blockade

city: Calgary

first: Reid

last: Mcneil

state: Alberta

address: 18 Simcrest Manor Sw

department: Biochemistry and Molecular Biology

institute: University of Calgary

summary: Sarcomas are rare, difficult to treat, mesenchymal lineage tumours that  disproportionately affect children and young adults. Immunologically-based therapies  have improved outcomes for numerous adult cancers, however, such approaches have  proven ineffective for the majority of individuals with advanced sarcomas. Clinically  relevant, immunologically-competent, and transplantable pre-clinical sarcoma models  are needed in order to test and develop novel immunologically-based therapies for  sarcoma. Herein we show that Cre- lox P-mediated simultaneous activation of  Kras  G12D , and deletion  Trp53,  in the hindlimb muscles of C57Bl/6 mice results in the  development of highly penetrant, rapid onset undifferentiated pleomorphic sarcomas  (UPS). The latter represents a model one of the most common human sarcoma  subtypes both histologically and genetically. Furthermore, cell lines derived from the  UPS tumors induced in C57Bl/6 mice can be transplanted into the hindlimbs or lungs of  naïve, immune competent syngeneic mice. Immunological characterization of both the  spontaneous and transplanted UPS tumours demonstrates an immunologically-  ‘quiescent’ microenvironment, characterized by a paucity of lymphocytes and  spontaneous adaptive immune pathways in addition to dense macrophage infiltrates.  UPS cell line induced tumours demonstrate mildly increased lymphocytic infiltrates as  compared with the spontaneous UPS tumours, furthermore, growth of transplanted  UPS was unaltered in lymphocyte deficient hosts. Despite expression of PD-1 on the  tumour infiltrating lymphocytes, UPS tumours were resistant to immunological  checkpoint blockade. This syngeneic transplantable UPS model that recapitulates  many of the immunological features of human UPS will prove invaluable for the preclinical development and evaluation of novel immunotherapeutic approaches for  targeting sarcomas.

overall_design: Examination of spontaneous tumor and control muscle

first: Karys

middle: M

last: Hildebrand

first: Kayla

last: Marritt

first: Kurt

first: Arvind

middle: K

last: Singla

last: McNeil

first: Franz

last: Zemp

first: Jahanara

last: Rajwani

first: Doha

last: Itani

first: Pinaki

last: Bose

first: Douglas

last: Mahoney

first: Frank

last: Jirik

first: Michael

last: Monument


title: Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma [ChIP-seq]

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

institute: Princess Margaret Cancer Centre

summary: To explore the therapeutic opportunities to enhance the clinical efficacy of EZH2 inhibitors in treating diffuse large B-cell lymphoma (DLBCL), a genome-wide drug sensitizing CRISPR/Cas9 screen was conducted in the presence of tazemetostat. We found that the loss of IKZF1 or IKZF3 augmented the potency of tazemetostat on DLBCL. Treating cells with lenalidomide, an immunomodulatory drug that degrades IKZF1 and IKZF3, in combination with tazemetostat, recapitulated the effects observed in the drug sensitizing screen. The combined drug treatment showed even higher synergistic effects, by triggering either cell cycle arrest or apoptosis, on a broader range of DLBCL cell lines, regardless of EZH2 mutation status. RNAseq analysis revealed strong upregulation of the interferon signaling and antiviral immune response signatures. Gene expression of key factors such as IRF7 and DDX58 were highly induced in cells treated with lenalidomide and tazemetostat, with a concomitant enrichment of H3K27 acetylation at their promoters as delineated in ChIPseq and ChIP qPCR analyses. Furthermore, transcriptome analysis and immunofluorescence staining demonstrated pronounced expression of a wide range of endogenous retroviruses (ERVs), with significant overlaps between the upregulated ERV loci and well-defined H3K27me3 enriched regions in EZH2-mutant lymphoma cell lines. Our data underscore the synergistic interplay between lenalidomide and tazemetostat on modulating epigenetic changes, resulting in upregulation of the interferon response and de-repression of ERVs, and ultimately to reduced growth of GCB-type DLBCL.

overall_design: 1 cell lines, 4 conditions, 2 technical replicates per sample

first: Kit

last: Tong

first: Sharon

last: Yoon

first: Keren

last: Isaev


title: MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion [Flag-HA ChIP-seq]

first: Christophe

last: Papin

first: Abdulkhaleg

last: Ibrahim

first: Kareem

last: Mohideen-Abdul

first: Stéphanie

last: Le Gras

first: Isabelle

last: Stoll

first: Christian

last: Bronner

first: Stefan

last: Dimitrov

first: Bruno

last: Klaholz

first: Ali

last: Hamiche


title: Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor

city: Stanford

first: Yung-Hsin

last: Huang

address: CCSR 2155, 269 Campus drive

institute: Stanford University

summary: Clonal hematopoiesis is a prevalent age-related condition associated with greatly increased risk of hematologic malignancies. Mutations in DNA methyltransferase 3A (DNMT3A) are the most common drivers of this state and contribute to multiple types of hematologic malignancy. DNMT3A variants occur across the gene and some are associated with particular disease states, but the functional relevance and mechanisms of pathogenesis of the majority of the mutations is unknown. Here, we systematically investigated the methyltransferase activity and protein stability of 253 disease-associated DNMT3A mutations, finding that 74% were loss-of-function mutations. Nearly half of these variants exhibited reduced protein stability and, as a class, correlated with greater clonal expansion and AML development. To identify the mechanisms underlying the instability, we conducted a CRISPR screen and uncovered regulated destruction of DNMT3A mediated by the DCAF8 E3 ubiquitin ligase adaptor. We establish a new paradigm to classify novel variants that has prognostic and therapeutic significance for patients with hematologic disease.

overall_design: Examination of WGBS and RNAseq under proteasome inhibitor treatment in patient-derived LCLs.

first: Dapeng

last: Hao


title: Mouse intestinal epithelial cells in the deficiency of Foxo1

status: Public on Jun 23 2021

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

summary: Mucus produced by goblet cells in the gastrointestinal (GI) tract forms a biological barrier that protects the intestine from invasion by commensals and pathogens. However, the host-derived regulatory network that controls mucus secretion and thereby changing gut microbiota has not been well studied. We found Forkhead box protein O1 (Foxo1) regulates mucus secretion by goblet cells and determines intestinal homeostasis. Loss of Foxo1 in intestinal epithelial cells (IECs) results in a defect in goblet cell autophagy and mucus secretion, leading to impaired gut microenvironment and dysbiosis.

overall_design: RNA sequence of mouse intestinal epithelial cells from Foxo1flox and VilCre Foxo1flox mice


title: MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion [ChIP-seq]


title: Yeast AlaRS mutants

city: College Park

first: Jiqiang

last: Ling

address: 2202 Microbiology Bldg., 4062 Campus Dr.

department: Cell Biology and Molecular Genetics

institute: The University of Maryland, College Park

summary: RNA sequencing of Saccharomyces cerevisiae wild type and alanyl-tRNA synthetase mutants grown at 30 degrees and challenged at 37 degrees

overall_design: WT, AlaRS C719A and G906D mutant yeast strains were pregrown at 30 degrees, and shifted to 37 degrees for 1 or 2 hours. Cells before and after shifting to 37 degrees were collected and total RNA was prepared for Illumina sequencing

first: Hong

last: Zhang


title: Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma [RNA-seq]

first: Robert

last: Kridel

overall_design: 4 cell lines, 4 conditions, 2 technical replicates per sample

first: Kit

last: Tong


title: Identification of the potential gene regulatory networks and therapeutics in aged mice with postoperative neurocognitive disorder (mRNA)

city: Guangzhou

first: Wensi

address: No. 135, West Xingang Street

institute: SUN YAT-SEN UNIVERSITY

summary: Postoperative neurocognitive disorder (PND) is one of the most common postoperative neurological complications in aged patients.  In order to detect the differential expression profiles of genes caused by PND, a total of 26 18-month-old male C57BL/6 mice were randomly assigned to control group and PND group.  Behavioral tests showed that mice in the PND group had impaired cognitive function compared with the control group.  Three mice in each group were randomly selected to harvest the brain for analysis the expressions of circRNAs, miRNAs and mRNAs in the prefrontal cortex by next-generation sequencing (NGS) technology.  Differentially expressed genes, including 1192 circRNAs, 27 miRNAs and 266 mRNAs were identified, and its accuracy was further confirmed by qRT-PCR.

overall_design: mRNA expression profiles in the prefrontal cortex of 18-months-old control and PND mice

first: Yongpai

last: Peng

first: Jiaxin

last: Zhou

first: Xiaojun

first: Lin

last: Cao

first: Wei-jye

last: Lin

first: Yanan

last: Lu

first: Jing

last: Wen

first: Zhi

last: Wang


title: Multifactorial role of mitochondria in echinocandin tolerance revealed by transcriptome analysis of drug-tolerant cells

city: Nutley

first: Erika

last: Shor

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack Meridian Health

summary: This study compared the transcriptional response of Candida glabrata micafungin exposed cells.

overall_design: We cultured C. glabrata in YPD containing 0.06 µg/ml micafungin for 24 hours, harvested the cells, isolated total RNA using the Qiagen Rneasy kit, and sent the RNA to Genewiz for RNAseq. Untreated cells were used as controls. 3 biological replicates for micafungin treated samples and 2 biological replicates for untreated samples were collected.

first: Rocio

last: Garcia-Rubio

first: David

last: Perlin


title: Identification of the potential gene regulatory networks and therapeutics in aged mice with postoperative neurocognitive disorder (miRNA)

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA expression profiles in the prefrontal cortex of 18-months-old control and PND mice


title: ActD timecourse in mESCs

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

summary: mRNAs are generally assumed to be loaded instantly with ribosomes upon entry into the cytoplasm. To measure ribosome density on nascent mRNA, we developed nascent Ribo-Seq (nRibo-Seq) by combining Ribo-Seq with progressive 4-thiouridine labelling. In mouse macrophages, we experimentally determined, for the first time, the lag between the appearance of nascent RNA and its association with ribosomes, which was calculated to be 20 - 22 min for bulk mRNA, and approximated the time it takes for mRNAs to be fully loaded with ribosomes to be 41 - 44 min. Notably, ribosomal loading time is adapted to gene function as rapid loading was observed with highly regulated genes. The lag and ribosomal loading time correlate positively with ORF size and half-life, and negatively with tRNA adaptation indices. Similar results were obtained in mESCs, where the lag between IN and FP was even more pronounced with 35 - 38 min. We validated our measurements after stimulation of macrophages with lipopolysaccharide, where the lag between cytoplasmic and translated mRNA leads to a corresponding uncoupling between input and ribosome-protected fragments. Uncoupling is stronger for mRNAs with long ORFs or half-lives, a finding we also confirmed at the level of protein production by nascent chain proteomics. As a consequence of the lag in ribosome loading, ribosome density measurements are distorted when performed under conditions where mRNA levels are far from steady state expression, and transcriptional changes affect ribosome density in a passive way. This study uncovers an unexpected and considerable lag in ribosome loading, and provides guidelines for the interpretation of Ribo-Seq data taking passive effects on ribosome density into account.

overall_design: Transcriptional shut-off with ActD followed by RNA-Seq to determine mRNA half-lives on a transcriptome-wide scale in mouse embryonic stem cells (mESCs).

first: Sonja

last: Reitter

first: Doris

last: Lindner

first: Jan

last: Grosser

first: Marius

last: Bruer

first: Anjana

last: Shenoy

first: Tamar

last: Geiger

first: Arthur

last: Mathes

first: Gergana

last: Dobreva

first: Georg

last: Stoecklin


title: nRibo-Seq timecourse in mESCs

overall_design: Limited RNaseI digest or alkaline fragmentation of cytoplasmic input mRNA after metabolic labelling with 4-thiouridine (4sU) to asses ribosome density on nascent mRNAs in mouse embryonic stem cells (mESCs).


title: ActD, Ribo-Seq and nRibo-Seq timecourses in RAW264.7 cells and mESCs

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

overall_design: Refer to individual Series


title: Targeted protein degradation reveals direct roles of SPT6 in POL2 elongation and termination

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

summary: SPT6 is both, an important histone chaperone and POL2 elongation factor but its primary role on transcription in mammalian cells remains open, as no acute depletion system is available. We used targeted protein degradation to rapidly deplete SPT6 and analyzed defects in POL2 behavior by a multi-omics approach and estimated POL2 processivity, elongation rates and termination and compared it to gene transcription. Our data indicate that SPT6 is a crucial factor for POL2 elongation. Unexpectedly, SPT6 has also a vital role in POL2 termination, as acute depletion induces POL2 read through at most protein coding genes. In contrast, acute depletion did not induce spurious intragenic initiation, while this behavior can be induced by long-term depletion of SPT6 and can therefore be attributed to its function as a histone chaperone. In conclusion, targeted protein degradation of SPT6 allows the kinetic discrimination of its function as a histone chaperone and POL2 elongation factor.

overall_design:
4sU-seq, ChIP-seq (SPT6, Ser2 Pol2 and Total Pol2), DRB-4sU-seq and SLAM-seq in presence or absence of SPT6
ChIP-seq (CSTF2,H3,TFIIF,TBP,pH2AX) in presence or absence of SPT6

first: Ashwin

last: Narain

first: Pranjali

last: Bhandare

first: Florian

last: Erhard

first: Apoorva

last: Baluapuri


title: nRibo-Seq timecourse in RAW264.7 cells

overall_design: Limited RNaseI digest or alkaline fragmentation of cytoplasmic input mRNA after metabolic labelling with 4-thiouridine (4sU) to asses ribosome density on nascent mRNAs in RAW264.7 cells


title: Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma

first: Robert

last: Kridel


title: Ribo-Seq timecourse in RAW264.7 cells upon LPS treatment

overall_design: Limited RNaseI digest or alkaline fragmentation of cytoplasmic input mRNA to asses ribosome density in RAW264.7 cells upon LPS treatment