title: CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300 mutated lymphomas [ChIP-seq]

city: Houston

first: Margarida

last: Almeida Santos

state: Texas

address: 1515 Holcombe Blvd Mail code 1000

department: Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

summary: Somatic mutations affecting CREBBP and EP300 are a hallmark of Diffuse Large B Cell Lymphoma (DLBCL). These mutations are frequently monoallelic, within the histone acetyltransferase (HAT) domain and usually mutually exclusive, suggesting that they might affect a common pathway and their residual WT expression is required for cell survival. Using in vitro and in vivo models, we found that inhibition of CARM1 activity (CARM1i) slows DLBCL growth and that the levels of sensitivity are positively correlated with the CREBBP/EP300 mutation load. Conversely, treatment of DLBCLs that do not have CREBBP/EP300 mutations with CARM1i and a CBP/p300 inhibitor revealed a strong synergistic effect. Our mechanistic data show that CARM1i further reduces the HAT activity of CBP genome wide and downregulates CBP target genes in DLBCL cells, resulting in a synthetic lethality that leverages the mutational status of CREBBP/EP300 as a biomarker for the use of small molecule inhibitors of CARM1 in DLBCL and other cancers.

overall_design: 16 samples - 2 replicates CARM1 inhibitor-treated, 2 replicates DMSO-treated per 3 ChIP antibodies, plus input controls for each replicate

first: Kylee

middle: J

last: Veazey

first: Dongheng

last: Cheng

first: Kevin

last: Lin

first: Oscar

last: Villarreal

first: Guozhen

last: Gao

first: Mabel

last: Perez-Oquendo

first: Hieu

middle: T

last: Van

first: Sabrina

middle: A

last: Stratton

first: Michael

last: Green

first: Han

last: Xu

first: Yue

last: Lu

first: Mark

last: Bedford

last: Santos


title: CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300 mutated lymphomas [RNA-seq_Toledo]

status: Public on Jun 18 2020

country: USA

type: Expression profiling by high throughput sequencing

overall_design: 6 samples - 3 replicates DMSO-treated, 3 replicates CARM1i treated

middle: D


title: CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300 mutated lymphomas [RNA-seq_MEF]

overall_design: 9 samples - 3 replicates WT MEFs, 3 replicates KO MEFs tamoxifen-treated, 3 replicates CARM1i treated


title: Setd2 knockdown.

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

country: United Kingdom

institute: King's College London

summary: Setd2 knockdown leads to subtle but significant changes in gene expression and alternative splicing.

overall_design: Three independent transfections of NIH/3T3 cells were performed for two Setd2-specific siRNAs as well as a Scrambled (non-targeting) siRNA.

first: Samuele

middle: M

last: Amante

last: Cowley

first: Nikolaos

last: Barkas

first: Jessica

last: Setiadi


title: CARM1 inhibition reduces histone acetyltransferase activity causing synthetic lethality in CREBBP/EP300 mutated lymphomas

first: Margarida

last: Almeida Santos

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptome analysis of ACKR3+ and ACKR3- Marginal Zone B cells (MZBs) in mice

status: Public on Jun 19 2020

city: Bellinzona

first: Mathilde

last: Foglierini

address: Via Vincenzo Vela 6

country: Switzerland

institute: Institute for Research in Biomedicine

summary: The marginal zone (MZ) of the spleen contains a specialized set of innate-like B cells that are in direct contact with the blood. Here we show that expression of the atypical chemokine receptor 3 (ACKR3) defines two phenotypically, transcriptionally and functionally distinct, equal-sized populations of mouse MZ B cells (MZBs). The ACKR3-expressing population is required for optimal development and function of the MZ and for the differentiation and positioning of all MZBs. In the absence of ACKR3 expression on B cells the MZ is distorted and the MZBs fail to deliver blood-borne antigens to follicular dendritic cells (FDCs), leading to a reduced early humoral immune response. Effective reconstitution of MZ deficient CD19ko mice with either of the two MZB subsets shows that ACKR3- MZBs can differentiate into the more mature ACKR3+ MZBs, but not vice versa. The phenotype of CD19ko mice lacking a MZ is readily rescued by the adoptive transfer of ACKR3-sufficient, and to a much lower degree by ACKR3-deficient follicular B cells (FoBs), indicating that ACKR3 expression is crucial for the establishment of the MZ developmental niche. Similarly, the inability of CD19ko mice to respond to T-independent antigen is rescued when ACKR3-proficient, but not ACKR3-deficient FoBs are adoptively transferred. Accordingly, ACKR3-deficient FoBs are able to reconstitute the MZ if the niche is pre-established by ACKR3 proficient MZBs. Our data uncover a new unexpected role of ACKR3 on B cells for forming the splenic microarchitecture.

overall_design: RNA profile of ACKR3+ and ACKR3- mice MZBs were generated by deep sequencing with 4 mice/group

first: Egle

last: Radice

first: Rafet

last: Ameti

first: Serena

last: Melgrati

first: Paola

last: Antonello

first: Rolf

last: Stahl

first: Sylvia

last: Thelen

first: David

last: Jarrossay

first: Marcus


title: Fluid-electrolyte homeostasis requires histone deacetylase function

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

summary: We report the transcriptional changes with knock down of HDAC1 and HDAC2 from the epithelium of the adult mouse kidney

overall_design: Single nucleus sequencing of a male control mouse, female control mouse, male, inducible, nephron epithelium HDAC1 and HDAC2 knockout mouse, and a female, inducible, nephron epithelium HDAC1 and HDAC2 knockout mouse

first: Jennifer

middle: S

last: Pollock


title: RNA-Seq time-series of Adventitious root development in Populus ussuriensis

city: Harbin City

first: Chenghao

last: Li

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

country: China

institute: Northeast Forestry University

summary: For the RNA-seq experiments approximately 3 cm stem segments were excised from 2-week-old in vitro plants and subsequently transfer to 1/2 MS medium and harvested the basal ends of stem cuttings (0.5 cm) at different time points(0, 0.5, 1, 2, 6, 12, 24, 48 and 96 h). Samples were collected from two biological replicates (40 cuttings each).

overall_design: RNA-seq of the basal ends of stem cuttings (0.5 cm)

first: Hairong

last: Wei

first: Quangang

last: Liu

first: Wenlong

first: Ming


title: A genetic network mediating the control of adventitious root formation in Populus ussuriensis

summary: We identified coherent type 4 feed-forward loops (FFLs) from this ML-hGRN, where PuHox52 repressed the expression of PuHDA9, which in turn augmented the histone H3K9 acetylation around the proximal regions of three direct target genes of PuHox52, PuWRKY51, PuLBD21 and PuIAA7, resulting in further enhanced expression levels of these target genes. Our study manifests evidence that supports a ML-hGRN with at least three coherent type 4 FFLs governed AR formation process at basal ends of stem cuttings in poplar.

overall_design: Examination of histone modifications (H3K9ac) in Populus ussuriensis.


title: Transcriptional profiling of intramembranous and endochondral ossification after fracture in mice

city: St. Louis

middle: Ann

last: McKenzie

state: MO

address: 425 S. Euclid

department: Orthopedics

institute: Washington University in St. Louis

summary: Bone fracture repair represents an important clinical challenge with nearly 1 million non-union fractures occurring annually in the U.S. Gene expression differs between non-union and healthy repair, suggesting there is a pattern of gene expression that is indicative of optimal repair. Despite this, the gene expression profile of fracture repair remains incompletely understood. In this work, we used RNA-seq of two well-established murine fracture models to describe gene expression of intramembranous and endochondral bone formation. We used top differentially expressed genes, enriched gene ontology terms and pathways, callus cellular phenotyping, and histology to describe and contrast these bone formation processes across time. Intramembranous repair, as modeled by ulnar stress fracture, and endochondral repair, as modeled by femur full fracture, exhibited vastly different transcriptional profiles throughout repair. Stress fracture healing had enriched differentially expressed genes associated with bone repair and osteoblasts, highlighting the strong osteogenic repair process of this model. Interestingly, the PI3K-Akt signaling pathway was one of only a few pathways uniquely enriched in stress fracture repair. Full fracture repair involved a higher level of inflammatory and immune cell related genes than did stress fracture repair. Full fracture repair also differed from stress fracture in a robust downregulation of ion channel genes following injury, the role of which in fracture repair is unclear. This study offers a broad description of gene expression in intramembranous and endochondral ossification across several time points throughout repair and suggests several potentially intriguing genes, pathways, and cells whose role in fracture repair requires further study

overall_design: Following either a femur full fracture or ulnar stress fracture injury 70 female C57BL/6J mice were sacrificed at 4 h, 1, 3, 5, 7, or 14 days post-injury, and processed for RNA-seq. RNA-seq analysis began with RNA extraction from pulverized bone tissue. RNA was sequenced and reads were mapped to mm10 genome. Differential expression analysis was performed to create lists of differentially expressed genes (DEGs) for each time point. Comparison to previously generated qPCR data of stress and full fracture callus was used to validate RNA-seq data. Callus component analysis using transcriptional profiling of callus cells was performed at each time point. Pathway analysis and GO annotation were performed on the DEG lists of each time point.

first: Brandon

last: Coates

first: Evan

middle: G

last: Buettmann

first: Xiaochen

first: Paul

last: Gontarz

first: Bo

last: Zhang

first: Matthew

last: Silva


title: METTL6 is a tRNA m3C methyltransferase that regulates translation and cell proliferation

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Here, we identified  METTL6 as a bona fide tRNA methyltransferase, catalysing the formation of 3-methylcytidine (m3C) at C32 of specific serine tRNA isoacceptors. Accordingly, deletion of METTL6 in mouse stem cells results in changes in ribosome occupancy and RNA levels, as well as a spontaneous loss of pluripotency

overall_design: Two biological replicates of RNAseq + Ribosome profiling for METTL6 KO G6 and WT mESCs

first: Oliver

last: Rando

first: Xinyang

last: Bing


title: Expression profiling by RNA-Seq of 3T3 mouse pre-adipocyte cells after treatment with Indoxyl Sulphate or Oxidative LDL, with or without pNaKtide

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

summary: We performed expression profiling by RNA-Seq on 3T3 mouse pre-adipocyte cells. Cells were divided into six groups of five replicates each and were treated with either control (DMSO), Indoxyl Sulphate, or Oxidative LDL, either with or without pNaKtide (NaK).

overall_design: RNA was extracted from cells in each group, and sequenced in a 2x50 base-pair design on an Illumina 1500 sequencer.

first: Komal

last: Sodhi

first: Jun

last: Fan

first: Jiang

first: Sanabria

last: Juan

first: Chen

last: Yiliang

first: Silverstein

last: Roy

first: Zijian

last: Xie

first: Nader

last: Abraham

first: Joseph

middle: I

last: Shapiro


title: Transcriptome-wide sites of collided ribosomes reveal sequence determinants of translational pausing in vivo

city: Lasuanne

first: David

last: Gatfield

address: UNIL CIG

department: CIG

institute: University of Lausanne

summary: Translation initiation is considered overall rate-limiting for protein biosynthesis, whereas the impact of non-uniform ribosomal elongation rates is largely unknown. Using a modified ribosome profiling protocol based on footprints from two closely packed ribosomes (disomes), we have mapped ribosomal collisions transcriptome-wide in mouse liver. We uncover that the stacking of an elongating onto a paused ribosome occurs frequently and scales with translation rate, trapping ~10% of translating ribosomes in the disome state. A distinct class of pause sites, independent of translation rate, is indicative of deterministic pausing signals. We find pause sites associated with specific codons, amino acids, and peptide motifs, and with structural features of the nascent polypeptide, suggestive of programmed pausing as a widespread mechanism associated with protein folding. Evolutionary conservation at disome sites and experiments indicate functional relevance of translational pausing. Collectively, our disome profiling approach allows novel and unexpected insights into gene regulation occurring at the step of translation elongation.

overall_design: Six biological samples (3 timepoints x 2 replicates) from GSE67305 were used. Briefly, mice were entrained under 12hours light:dark conditions for 2 weeks and also collected under 12hours light:dark. Mice were sacrificed at 0, 2, and 12h during the 24 hours daily cycle. Two replicates per time point, each replicate is a pool of 2 livers (2 mice).

first: Alaaddin

middle: B

last: Arpat

first: Peggy

last: Janich


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [IGF2BP1 KD in MV3 (total RNA)]

status: Public on Jun 17 2020

city: Halle

first: Markus

last: Glaß

address: Kurt-Mothes-Str. 3a

department: Institute of Molecular Medicine

country: Germany

institute: Martin Luther University Halle-Wittenberg

summary: The IGF2 mRNA-binding protein 1 (IGF2BP1) is a post-transcriptional enhancer of tumor growth. However, conserved effector pathway(s) and the feasibility of targeting IGF2BP1 in cancer cells remained elusive.   We demonstrate that IGF2BP1 is a conserved regulator of E2F-driven gene expression and cancer cell cycle progression. IGF2BP1 promotes positive regulators of G1/S transition by stabilizing the respective mRNAs. This regulation is 3’UTR-, miRNA- and m6A-dependent, suggesting a conserved role of m6A-enhanced cell cycle progression across cancers. IGF2BP1 stabilizes E2F-encoding mRNAs and some of their target transcripts revealing a post-transcriptional super-enhancer role of the protein in E2F-driven gene expression. The small molecule BTYNB disrupts this super-enhancer function by impairing IGF2BP1-RNA association and consequently interferes with tumor cell proliferation and tumor growth.

overall_design: total RNA-Seq of MV3 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1. Four replicates per condition.

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Marcell

last: Lederer

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alice

last: Wedler

first: Jacob

last: Haase

first: Jean

last: Borges Bertoldo

first: Patrick

last: Michl

first: Stefan

last: Hüttelmaier


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [METTL KD in PANC-1 (polyA RNA)]

overall_design: polyA RNA-Seq of PANC-1 cells transfected with either control siRNAs (siC) or siRNAs directed against METTL3 and METTL14. Three replicates per condition.


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [IGF2BP1 KD in HepG2 (polyA RNA)]

overall_design: polyA RNA-Seq of HepG2 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1. Three replicates per condition.


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [E2F1-3 KD in PANC-1 (polyA RNA)]

overall_design: polyA RNA-Seq of PANC-1 cells transfected with either control siRNAs (siC) or siRNAs directed against E2F1, E2F2 and E2F3. Three replicates per condition.


title: RNA-seq analysis during adventitious root formation in cuttings of PuHox52 overexpression and wild type Populus ussuriensis.

first: Chenghao

last: Li

summary: RNA-seq was performed to examine the differential expressed transcriptomes with five-point experiment (6, 12, 24, 48 and 96 h) at the stem bases of cuttings in PuHox52 overexpression line compare to wild type Populus ussuriensis.

overall_design: For the RNA-seq experiments of PuHox52-mediated adventitious root formation, two week-old WT and 35S::PuHox52 in vitro plants were grown on the 1/2 MS medium at different rooting stages (6, 12, 24, 48 and 96 h) and harvested the basal ends of stem cuttings (0.5 cm). Samples were collected from two biological replicates (40 cuttings each). Total RNA isolation, library construction and sequencing were performed by Biomarker Technologies (Beijing, China). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (#E7530L, NEB, USA) following manufacturer’s recommendations. The library preparations were sequenced on an Illumina Hiseq 2500 platform and paired-end reads were generated. About 4 Gb of high-quality 125-bp paired-end reads were generated from each library.

first: Hairong

last: Wei

first: Quangang

last: Liu

first: Ming


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [IGF2BP1 KD in A549 (polyA RNA)]

overall_design: polyA RNA-Seq of A549 cells transfected with either control siRNAs (siC) or siRNAs directed against IGF2BP1. Three replicates per condition.

last: Bertoldo


title: MicroRNA alterations in a mouse model of prion disease

city: Zaragoza

first: Janne

last: Toivonen

address: Miguel servet 177

department: Departamento de Anatomía, Embriología y Genética Animal

country: Spain

institute: Universidad de Zaragoza

summary: MicroRNA alterations were investigated in a Tg501 mouse model of prion disases that express the goat prion protein (PRNP). Age-matched Tg501 mice without inoculation (controls) and intracranially inoculated with caprine scrapie strain were compared in presymptomatic and symptomatic stages.

overall_design: Small RNA profiles from cervical spinal cord of prion-inoculated (n=11) and non-inoculated (n=13), age-matched Tg501 mice were generated at symptomatic (n=12) and presymptomatic (n=12) stage using HiSeq v4 chemistry on Illumina HiSeq 2500.

first: Inmaculada

last: Martin Burriel


title: Spinal cord gene expression profiling of the effect of EHP-101 in EAE model

status: Public on Jun 21 2020

city: Córdoba

first: Eduardo

last: Muñoz

address: Avda Menéndez Pidal s/n

institute: Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), University of Córdoba

overall_design: To evaluate the global expression changes produced by the EHP-101 treatment, we performed an RNA-Seq analysis of the spinal cord from mice in the following conditions: Control, EAE and EAE with EHP-101 oral treatment (20 mg/kg) (three biological replicates, N=3).

first: Carmen

last: Navarrete

first: Adela

last: García-Martín

first: Martín

last: Garrido-Rodríguez

first: Leyre

last: Mestre

first: Miriam

last: Mecha

first: Ana

last: Feliú

last: Guaza

first: Alain

last: Rolland


title: Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

overall_design: Refer to individual Series


title: Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection [RNA-seq]

summary: scRNA-seq of CD45+ leukocytes isolated from WT and triple mutant-infected mice identified several genes with concordant changes in H3Ac status and transcriptional expression.

overall_design: Live, CD45+ leukocytes were isolated by FACs from implant-associated tissue at day 14-post infection for scRNA-seq.  While these samples were prepared  and sequenced for single-cell RNA-seq, they were analyzed as bulk RNA for this study.  All raw data for a single-cell analysis have been included.

first: Cortney

middle: E

last: Hem

first: David

last: Klinkebiel

first: Tammy

last: Kielian


title: IGF2BP1 is a druggable, post-transcriptional super-enhancer of E2F-driven gene expression hallmark in cancer [IGF2BP1 KO in A-549 (polyA RNA)]

first: Markus

last: Glaß

overall_design: polyA RNA-Seq of parental or IGF2BP1-deleted A549 cells. Deletion of IGF2BP1 was generated by using Crispr/Cas9.

first: Simon

last: Müller

first: Nadine

last: Bley

first: Bianca

last: Busch

first: Marcell

last: Lederer

first: Claudia

last: Misiak

first: Tommy

last: Fuchs

first: Alice

last: Wedler

first: Jacob

last: Haase

first: Jean

first: Patrick

last: Michl

first: Stefan

last: Hüttelmaier


title: SPOCD1 is a novel executor of piRNA-directed DNA methylation that links MIWI2 to the de novo DNA methylation machinery

city: Edinburgh

first: Ansgar

last: Zoch

address: 5 Little France Drive

department: MRC Centre for Regenerative Medicine

institute: University of Edinburgh

type: Non-coding RNA profiling by high throughput sequencing

summary: In mammals, the acquisition of the germline from the soma provides the germline with an essential challenge, the necessity to erase and reset genomic methylation. De novo genome methylation re-encodes the epigenome including transposable element (TE) silencing. In the male germline RNA-directed DNA methylation silences young active TEs. The PIWI protein MIWI2 (PIWIL4) and its associated PIWI-interacting RNA (piRNAs) act to tether MIWI2 to nascent TE transcripts and instruct DNA methylation of the active TE. The mechanism by which MIWI2 directs de novo TE methylation is poorly understood but central to the immortality of the germline. Here, we define the interactome of MIWI2 in fetal gonocytes that are undergoing de novo genome methylation and identify a novel MIWI2-associated factor SPOCD1 that is essential for TE silencing. The loss of Spocd1 in mice phenocopies that of Miwi2-deficient mice and does not impact on piRNA biogenesis nor localization of MIWI2 to the nucleus. SPOCD1 is a nuclear protein and its expression is restricted to the period of de novo genome methylation. We found SPOCD1 co-purified in vivo with constituents of several repressive chromatin remodelling complexes (NURD and BAF) as well as DNMT3L and DNMT3A, components of the de novo methylation machinery. We propose a model whereby tethering of MIWI2 to a nascent TE transcript recruits repressive chromatin remodelling activities and the de novo methylation apparatus through its association with SPOCD1. In summary, we have identified a novel and essential executor of mammalian piRNA-directed DNA methylation.

overall_design:
Examination of piRNA expression profiles in control (Spocd1+/-) and Spocd1-/- E16.5 foetal testis.
Examination of RNA expression profiles in control (Spocd1+/-) and Spocd1-/- gonocytes from E16.5 foetal testis.
Examination of RNA expression profiles in control (wildtype), Miwi2-/- and Spocd1-/- P20 testis.

first: Yuka

last: Kabayama

first: Theresa

last: Schöpp


title: Heat-shock molecular chaperone Hsp90 is involved in heterochromatin assembly in Schizosaccharomyces pombe.

city: Wuxi

first: Li

last: Sun

state: Jiangsu

address: No. 1800, Lihu Avenue

institute: Jiangnan University

summary: Here, we report the high-throughput profiling of histone modification (H3K9me2) in fission yeast Schizosaccharomyces pombe. We generated genome-wide H3K9me2 maps of fission yeast mutants in swo1-26 (temperature sensitive, ts) cells at 25℃ and 37℃.  We find that H3K9me2 enrichment at heterochromatin regions, especially at the mating-type locus and subtelomeres, is compromised, suggesting heterochromatin assembly defects.

overall_design: Examination of H3K9me2 in wt, ago1D and tas3D growing at 25℃. Particularly, swo1-26 mutant cells are cultured under permissive condition (25℃) and non-permissive condition (25℃ shifted to 37℃ for 4 h).

first: Wen-zhu

last: Li

first: Quanwen

last: Jin


title: Co-repressors Mtg8 and Mtg16 regulate niche exit and early fate decision of crypt stem cells (RNA-seq)

first: Vivian

address: 1 Midland Road

institute: The Francis Crick Institute

summary: In this experiment, the differential gene expression was examined in intestinal epithelial cells of Mtg16 null mice compared to wild type.

overall_design: Intestinal epithelial crypts were isolated from full length gut of WT or Mtg16 -/- mice after 30' incubation in 2mM EDTA (Sato et al., 2009). Experiments were performed in biological triplicates for each group. Mice of both groups were 12 weeks old males.

first: Anna

last: Baulies

first: Nikolaos

last: Angelis

first: Valentina

last: Foglizzo

first: Thomas

last: Danielson

first: Harshil

last: Patel

first: Laura

last: Novellasdemunt

last: Kucharska

first: Paolo

last: De Coppi


title: Evolution of vertebrate gill covers through shifts in an ancient gnathostome Pou3f3 enhancer

city: Cincinnati

first: Lindsey

last: Barske

state: OH

address: 3333 Burnet Ave MLC 7016

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: Whereas the gill chambers of extant jawless vertebrates (lampreys and hagfish) open directly into the environment, jawed vertebrates have evolved skeletal appendages that promote the unidirectional flow of oxygenated water over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single operculum covering a large common gill cavity in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here we find that these divergent gill cover patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs, and we identify a deeply conserved Pou3f3 arch enhancer that is present in nearly all jawed vertebrates but undetectable in lampreys. Despite only minor sequence differences, bony fish and cartilaginous fish versions of this enhancer are sufficient to drive the respective single versus multiple gill arch expression. In zebrafish, loss of Pou3f3 gene function or its conserved enhancer disrupts gill cover formation. Conversely, forced expression of Pou3f3b in the gill arches generates ectopic skeletal elements reminiscent of the multiple gill covers of cartilaginous fish. Emergence and modification of this ancient Pou3f3 enhancer may thus have contributed to the acquisition and diversification of gill covers during early gnathostome evolution.

overall_design: fli1a:GFP; sox10:DsRed double-positive embryos were selected under a fluorescent dissecting microscope at 36 hpf, dechorionated, and dissociated in batches of 25. Cells were sorted based on GFP and DsRed expression on a MoFlo Astrios instrument. Approximately 15,000 double -positive cells and 20,000 double-negative cells were collected into PBS with 5% FBS and used to construct ATAC-seq libraries using a low-input μATACseq protocol.

first: Peter

last: Fabian

first: Christine

last: Hirschberger

first: David

last: Jandzik

first: Tyler

last: Square

first: Pengfei

last: Xu

first: Nellie

last: Nelson

first: Haoze

middle: V

last: Yu

first: Daniel

last: Medeiros

first: J

last: Gillis

last: Crump


title: RNA-seq analysis in syp-2::AID and N2 controls with and without auxin treatment (4 hours at 4 mM concentration)

first: Enrique

last: Martinez-Perez

address: L Block - Level 2, Du Cane Road

institute: MRC London Institute of Medical Sciences (LMS)

summary: Chromosome movements and programmed DNA double-strand breaks (DSBs) promote homologue pairing and initiate recombination at meiosis onset. Checkpoints implement termination of these events when all chromosomes achieve synapsis and form crossover precursors, ensuring meiotic progression. We show that termination of chromosome movement and DSB formation is reversible and is continuously implemented by the synaptonemal complex (SC), which silences chromosome signals that promote CHK-2 activity. Forced removal of the SC or different meiosis-specific cohesin complexes, which are individually required for SC stability, causes rapid CHK-2-dependent reinstallation of the DSB-formation and chromosome-movement machinery. This nuclear reorganization occurs without transcriptional changes, but requires signalling from HORMA protein HTP-1. Conversely, CHK-2 inactivation causes rapid disassembly of the DSB-formation and chromosome-movement machinery. Thus, nuclear organization is constantly controlled by the level of CHK-2 activity. Our results uncover an unexpected plasticity of the meiotic program and show how chromosome signalling integrates nuclear organization with meiotic progression.

overall_design: 4 samples in quadruplicate: N2-wo (WT control); N2-IAA (N2 with auxin treatment); S-wo (syp-2::AID worms without auxin treatment); S-IAA (syp-2::AID worms with auxin treatment)

first: Sarai

last: Pacheco

first: Maikel

last: Castellano-Pozo

first: Marian

middle: H

last: Dore

first: Mohammad

last: Karimi


title: KP lung tumours

status: Public on Jun 16 2020

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: Glucose transporters are the first and rate-limiting step for cellular glucose usage, which is often exacerbated in tumour cells enabling their growth and proliferation. Although inhibiting glucose metabolism in lung tumours could become an efficient treatment strategy, whether and which glucose transporter(s) should be targeted remains unclear because of their possible functional redundancy, and because other nutrients or transporter-independent metabolic processes including autophagy and macropinocytosis can fuel tumour cell growth in certain contexts. Here we show that glucose transporter Glut1 gene deletion in tumour cells does not impact tumour initiation and only slightly delays progression in a genetically-engineered mouse model of lung adenocarcinoma. Using 13C-glucose tracing with correlated nanoscale secondary ion mass spectrometry (NanoSIMS) and electron microscopy, we report the presence of multiple lamellar body-like organelles produced by tumour cells. Glucose-derived biomass accumulates in these organelles, and this accumulation is decreased in Glut1-deficient tumour cells. Ex vivo, tumour cell glycolysis is impaired in absence of Glut1 except in case of strong expression of another glucose transporter, Glut3. We show that Glut3 is dispensable for Glut1 wild-type tumour development. In contrast, their combined deletion diminishes tumour growth and prevents the appearance of big lesions. Our results demonstrate the requirement for two glucose transporters in lung adenocarcinoma; dual blockade could reach therapeutic responses not achieved by individual targeting.

overall_design: Expression profile of KP lung tumours at 22 weeks and 5 days post-tumor initiation

first: Caroline

last: Contat

last: Zangger

first: Etienne

last: Meylan


title: Lactate production by Staphylococcus aureus biofilm inhibits HDAC11 to reprogramme the host immune response during persistent infection [ChIP-seq]

first: Adam

last: Karpf

summary: Using ChIP-seq we show that total H3Ac within ± 10,000 bp of all genomic transcription start sites was decreased by approximately two-fold in MDSCs recovered from mice infected with a triple mutant, unable to make lactate, compared to WT S. aureus.

overall_design: MDSCs for ChIP-seq were isolated from S. aureus-infected orthopedic implant-associated tissue at day 14 post-infection by FACS.

first: Cortney

last: Hem

last: Klinkebiel

first: Tammy

last: Kielian


title: Expansion of human iPSC-derived ureteric bud organoids with repeated branching potential

city: Kyoto

first: Makoto

last: Ryosaka

address: 53 Kawahara-cho, Shogoin,

country: Japan

institute: Center for iPS Cell Research and Application (CiRA), Kyoto University

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


title: CC10+ KP vs CC10+ KPG1 tumours

overall_design: Expression profile comparison between Glut1-WT and Glut1-KO KP lung tumours arising from CC10 positive cells, at 20 weeks and 1 day post-tumour initiation. Magnetic CD45 negative tumour cell fractions analysed.


title: Interferon Alpha Induces Multiple Cellular Proteins That Coordinately Suppress Hepadnaviral Covalently Closed Circular DNA Transcription

city: Shanghai

first: Junjun

last: CHENG

address: 371 Li Shizhen Road, Bldg 5  Pudong

department: Immunology, Infectious Diseases and Ophthalmology (I2O)

institute: Roche Innovation Center (Shanghai)

summary: To identify the cellular genes that mediate IFN-α suppression of cccDNA transcription, the total intracellular RNA were extracted from untreated or recombinant chicken IFN-α (rChIFN-α)-treated cells, and mRNA sequencing (mRNA-Seq) assays were performed in triplicate. And we found that treatment of dstet5 cells with 10 ng/ml of rChIFN-α for 6 h altered the expression of more than 100 cellular genes by more than 2 folds.

overall_design: mRNA sequencing (mRNA-Seq) assays were performed in triplicate for untreated or rChIFN-α-treated dstet5 cells

first: Yan

last: Zhou

first: Muhammad

last: Sheraz

first: Jinhong

last: Chang

first: Ju-Tao

last: Guo


title: RNA-seq of mRNA from whole mouse liver

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

summary: In this study we want to map the gene expression profile of liver infected with Adenovirus, either transgene-encoding Ad-CMV-GL or a non-coding control virus Ad-ctrl, to uninfected (healthy) livers. This comparison will reveal transcriptional signature of Ad-CMV-GL infected liver responsible for virus-mediated sensitization of hepatocytes towards TNF-induced apoptosis.

overall_design: three to four biological replicates of infected livers using different infections (Ad-CMV-GL, uninfected)

first: Sandra

last: Kurz

first: Sainitin

last: Donakonda

first: Rupert

last: Oellinger

first: Thomas

last: Engleitner

first: Percy

last: Knolle


title: Transcriptomic analysis of brian tissues identifies a role for CCAAT enhancer binding protein β in HIV- associated neurocognitive disorder

city: La jolla

first: Jerel

middle: Adam

last: Fields

address: 9500 Gilman Dr., BSB 3009

institute: UCSD

summary: In this study, using 33 postmortem frontal cortex (FC) tissues, neuropathological, molecular, and biochemical analyses were used to determine cellular localization and validate expression levels of the prolific transcription factor (TF), CCAAT enhancer binding protein (C/EBP) β, in brain tissues from HIV+ cognitively normal and HAND cases. RNA sequencing (seq) and transcriptomic analyses were performed on FC tissues including 24 specimens from well-characterized people with HIV that had undergone neurocognitive assessments. In vitro models for brain cells were used to investigate the role of C/EBPβ in mediating gene expression.

overall_design: Molecular changes in fontal cortex measured via mRNA between minor neurocognitive disorder compared to cognitive normals with HIV

first: Saranya

last: Canchi

last: Adam Fields


title: Detecting chromatin interactions along and between sister chromatids with SisterC

first: Marlies

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

summary: Novel chromosome conformation technique captures inter- and intra-sister interactions in mitotic yeast chromosomes

first: Adam

middle: K

last: Hedger

first: Jonanthan

last: Watts

first: Job

last: Dekker


title: gene expression in low and high mPTP opening cells

city: guangzhou

first: zhongfu

last: ying

state: guangdong

address: kaiyuan

department: stem cell research

institute: chinese academy of sciences

summary: We found high mPTP opening cells were more effcient to reprogramming compare to the low mPTP opening cells

overall_design: We use calcein release assay to analysis mPTP opening. Cells were treated with calcein and CoCl2 and then sorted by FACS. Cells were sorted into two pools corresponding to the cells with the low or high calcein fluorescence. High calcein fluorescence means low mPTP opening cells.

first: Ying

last: Zhongfu

first: Zheng

last: Lingjun


title: RNA sequence of PBMCs of macaques infected with SARS-CoV-2

status: Public on Jun 15 2020

city: Cheongju-si

first: Hanseul

last: Oh

state: Chungcheongbuk-do

address: 30 Yeongudanji-ro, Ochang-eup, Cheongwon-gu,

country: South Korea

institute: Korea Research Institute of Bioscience & Biotechnology

summary: The goals of this study are to analyze immune response of host against SARS-CoV-2 using PBMCs trascriptome

sample_organism:
Macaca fascicularis
Macaca mulatta

platform_organism:
Macaca fascicularis
Macaca mulatta

overall_design: Comparison of PBMC RNA sequence profiles between on 3 days after SARS-CoV-2 infection and 2 weeks before infection were generated by NGS using Illumina Casava

first: Jung

middle: J

last: Hong

first: Bon-Sang

last: Koo

first: Green

last: Kim

first: Eun-Ha

last: Hwang

first: Hoyin

last: Jung

first: Youngjeon

last: Lee

first: Philyong

last: Kang

first: Jae-Hak

last: Park

first: Choong-Min

last: Ryu


title: Viral transcriptomic analysis of single cell-sorted of DF1 or MDCK cell lines infected with influenza A virus

city: La Joll

first: Gene

last: Tan

address: 4120 Capricorn Lane

institute: J. Craig Venter Institute

summary: Infection with a single influenza A virus (IAV) is only rarely sufficient to initiate productive infection. Here, we exploit both single cell approaches and whole-animal systems to show that the extent of IAV reliance on multiple infection varies with virus strain and host species. Influenza A/guinea fowl/HK/WF10/99 (H9N2) [GFHK99] virus exhibits strong dependence on collective interactions in mammalian systems. This reliance focuses viral progeny production within coinfected cells and therefore results in frequent genetic exchange through reassortment. In contrast, GFHK99 virus has greatly reduced dependence on multiple infection in avian systems, indicating a role for host factors in viral collective interactions. Genetic mapping implicated the viral polymerase as a major driver of multiple infection dependence. Mechanistically, quantification of incomplete viral genomes showed that their complementation only partly accounts for the observed reliance on coinfection. Indeed, even when all polymerase components are detected in single cell mRNA sequencing, robust polymerase activity of GFHK99 virus in mammalian cells is reliant on multiple infection. In sum, IAV collective interactions not only augment reassortment, but can also overcome species-specific barriers to infection. These findings underscore the importance of virus-virus interactions in IAV infection, evolution and emergence. We used a single-cell sequencing platform (10x Genomics) to elucidate the differential infection rate of an avian influenza A virus on an avian cell line (DF1) and a mammalian (MDCK) cell line. Our work on IAV reassortment has raised new questions about the fundamental strategies that drive influenza virus evolution. Our data indicate that a large majority of influenza virus genomesare incomplete within cells, comprising less than the eight complete segments normally found in a replication competent infectious viral particle. This led us to ask: what underlying mechanisms give rise to incomplete genomes? What constitute an infectious unit? What are the implications for viral diversification, evolution and spread. By addressing these questions, we will advance he field by deepening our understanding how viral infections are initiated and propagated.

sample_organism:
Gallus gallus
Canis lupus familiaris

platform_organism:
Gallus gallus
Canis lupus familiaris

overall_design: Avian DF-1 cells or mammalian MDCK cells were infected with different multiplicity of infection using wildtype A/Guinea Fowl/Hong Kong/WF10/99 and barcoded A/Guinea Fowl/Hong Kong/WF10/99. At 8 hours post infection, cells were harvested for both experiments and processed for single-cell sorting and 3' transcript sequencing using the 10x Genomics platform.

first: Kara

last: Phipps

first: Ketaki

last: Ganti

first: Silvia

last: Carnaccini

first: Miglena

last: Manandhar

first: Nathan

middle: T

last: Jacobs

first: Brett

last: Pickett

first: Lucas

last: Ferreri

first: Daniel

middle: R

last: Perez

first: Anice

middle: C

last: Lowen


title: PPARaDN KP vs PPARaDN KPG1 tumours

first: Nadine

last: Fournier

overall_design: Expression profile comparisons between Glut1-WT, Glut1-KO, PPARalpha dominant negative (DN) Glut1-WT, and PPARalpha dominant negative (DN) Glut1-KO KP mice lung tumors at 26 weeks post-tumour initiation. Magnetic CD45 negative tumour cell fractions analysed.

first: Caroline

last: Contat

last: Zangger

first: Etienne

last: Meylan


title: Single-cell RNA sequencing of olfactory bulb dopaminergic neurons

city: London

first: Marcela

last: Lipovsek

address: 18-20 Newcomen Street - New Hunt's House

department: Centre for Developmental Neurobiology

institute: King's College London

summary: Here we performed single cell RNA sequencing of manually sorted olfactory bulb dopaminergic neurons with the goal of studying the transcriptomic basis of neuronal plasticity. Acute olfactory bulb 300 µm slices were obtained from Dat-Cre/Flox-tdTomato (B6.SJL-Slc6a3tm1.1(cre) Bkmn/J, Jax stock 006660 / B6.Cg– Gt(ROSA)26Sortm9(CAG-tdTomato)Hze, Jax stock 007909) juvenile mice. Single cell suspensions were generated using the Neural Tissue Dissociation Kit – Postnatal Neurons (Miltenyi Biotec. Cat no. 130-094-802). Dopaminergic neurons were identified by red fluorescence and manually sorted into individual wells. Analysis of the effects of the transcriptomic changes relating to neuronal plasticity triggered by sensory deprivation is ongoing.

overall_design: 284 single-cell samples, 11 positive controls, 7 no-cell negative controls and 5 negative controls.

first: Matthew

last: Grubb


title: Single cell sequencing of dissected mouse foreguts at embryonic day 8.5 to 9.5

first: Aaron

last: Zorn

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

overall_design: Mouse foreguts were dissected at embryonic day 8.5, 9.0 and 9.5. Tissue were dissociated into single cell suspension and used for single cell RNA library preparation and sequencing using 10X Genomics platform.


title: RNAseq comparison of Whole crypt mRNA levels between Control, conditional Notchless KO, Apc KO and Notchless-Apc KO mice 24h or 48h after induction

city: Paris

first: Michel

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

summary: Control (Villin-CreERT2tg/0; Apcflox/+; Nleflox/+), ApccKO (Villin-CreERT2tg/0; Apcflox/flox; Nleflox/+) and ApccKO; NlecKO (Villin-CreERT2tg/0; Apcflox/flox; Nleflox/null) mice were subjected to three daily intraperitoneal tamoxifen injections and their intestinal crypts were harvested at 24h (d1) or 48h (d2) post last tamoxifen injection. Total RNA was extracted according to the Trizol-chloroform extraction protocol provided by Invitrogen. RNAseq was performed on these extracted RNA to unravel the molecular mechanisms underlying the ApccKO;NlecKO phenotype.

overall_design: n=3 mice of each genotype at each time point were processed (total=24 mice)

first: Nick

last: Owens

last: Cohen-Tannoudji


title: The environmental stress response causes ribosome loss in aneuploid yeast cells.

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, whether and how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene expression patterns have been reported: an environmental stress response (ESR) and a “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. Here, we investigate and bring clarity to this controversy. We show that the CAGE signature is not an aneuploidy-specific gene expression signature but is the result of euploid control cells, but not aneuploid cells, having grown into stationary phase. Because growth into stationary phase is amongst the strongest inducers of the ESR, the ESR in aneuploid cells was masked when stationary phase euploid cells were used for normalization in transcriptomic studies. When exponentially growing euploid cells are used in gene expression comparisons with aneuploid cells, the CAGE signature is no longer evident in aneuploid cells. Instead, aneuploid cells are found to exhibit the ESR. We further show that the ESR causes a selective loss of ribosomes in aneuploid cells, providing an explanation for the decreased cellular density in aneuploid cells. We conclude that aneuploid budding yeast cells mount the ESR, rather than a CAGE signature, in response to aneuploidy-induced cellular stresses that results in selective ribosome loss.

overall_design: Examination of gene expression signatures in euploid and aneuploid yeast strains under different growth conditions.

first: Allegra

last: Terhorst

first: Arzu

last: Sandikci

first: Abigail

last: Keller

middle: A

first: Maitreya

last: Dunham

first: Angelika

last: Amon


title: Combined deletion of Glut1 and Glut3 impairs lung adenocarcinoma growth.

overall_design: Refer to individual Series


title: Differentiation of the human PAX7-positive myogenic precursors/satellite cell lineage in vitro

city: Boston

first: Jyoti

last: Rao

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

summary: Satellite cells (SC) are muscle stem cells which can regenerate adult muscles upon injury. Most SC originate from PAX7+ myogenic precursors set aside during development. Although myogenesis has been studied in mouse and chicken embryos, little is known about human muscle development. Here, we report the generation of human induced pluripotent stem cell (iPSC) reporter lines in which fluorescent proteins have been introduced into the PAX7 and MYOG loci. We use single cell RNA sequencing to analyze the developmental trajectory of the iPSC-derived PAX7+ myogenic precursors. We show that the PAX7+ cells generated in culture can produce myofibers and self-renew in vitro and in vivo. Together, we demonstrate that cells exhibiting characteristics of human fetal satellite cells can be produced in vitro from iPSC, opening interesting avenues for muscular dystrophy cell therapy. This work provides significant insights into the development of the human myogenic lineage.

overall_design: Single-cell mRNA sequencing of human induced pluripotent stem cell derived PAX7 cells.

first: Olivier

last: Pourquié


title: CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [ChIP-seq]

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl, Memphis, TN

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

summary: We recently developed CHANGE-seq (Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing), a fast, streamlined, Tn5 tagmentation-based assay for measuring the genome-wide activity of Cas9 in vitro that is easily scalable to many targets and samples. In this study, we directly compare CIRCLE-seq to CHANGE-seq and systematically evaluate Cas9 genome-wide activity on 110 targets across 13 therapeutically-relevant loci leveraging CHANGE-seq. We validate the sensitivity of CHANGE-seq for identifying sites of bona fide cellular off-target mutations using GUIDE-seq and sensitive targeted tag sequencing. Additionally, we sought to evaluate the impact of chromatin accessibility on cellular off-target activity by comparing CHANGE-seq with matched GUIDE-seq cellular off-target, chromatin, and transcriptional profiles generated from the same human primary T-cells.

overall_design:
Chromatin immunoprecipitation on 5-10 million cross-linked CD4+/CD8+ T-cells using antibody to H3K4me1 (Abcam, ab8895), H3K4me3 (Cell signaling, 9751), H3K9ac (Abcam, ab10812), H3K27me3(Abcam, ab6002), H3K27ac (Abcam, ab4729), H3K36me3 (Abcam, ab9050) or H3K9me3 (Abcam, ab8898)
Please note that each processed data file was generated from both replicates and is linked to the corresponding *rep1 sample records.

first: Cicera

last: Lazzarotto


title: Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

summary: We used SLAM-seq approach to define a contribution of RNA synthesis into RNA abundance changes after Tpr loss.  Basket nucleoporin Tpr was AID-tagged and depleted through Auxin Induced Degradation system. Loss of Tpr led to rapid changes in rates of RNA synthesis. The majority of transcripts were downregulated. Analysis of RNA-seq and SLAM-seq indicated that the changes in RNA abundance of most of Tpr-dependent up- and downregulated genes resulted from increased or decreased rates of RNA synthesis, respectively.

overall_design: Thiol (SH)-Linked Alkylation for the Metabolic (SLAM) sequencing of nascent RNAs was performed with 4-Thiouridine (S4U) incorporation using Anabolic (061.24) Kinetics Module kit purchased from Lexogen company. Briefly, before labelling of nascent RNA, each well of DLD-1 AID-Tpr cells from the 6-well plate was replaced with fresh media or media containing 1 mM auxin for 2 hours. For chasing, cells were treated with media containing 300 µM S4U or 300 µM S4U supplemented with 1 mM auxin for 0 min, 30 min, 60 min, or 2 hours.   Total RNAs were processed to allow conversion of S4U to cytosine, sequenced, and the T>C reads were used to identify genes that were up- and down-regulated in response to Tpr loss.

first: V

last: Aksenova

first: C

last: Esnault

first: A

first: M

last: Dasso


title: Gene expression profiling of human DLD-1 cells after block of CRM1 receptor with Leptomycin B inhibitor.

summary: We used RNA-seq approach to define a contribution of mammalian export receptor CRM1 (Chromosomal Maintenance 1 or Exportin 1) into Tpr-dependent export of RNA molecules from the nucleus to the cytoplasm.  Basket nucleoporin Tpr was AID-tagged and depleted through Auxin Induced Degradation system. Loss of Tpr led to rapid changes in gene expression profile, and gene expression changes were compared to GANP, NXF1, RanGAP1 (GSE132363) and CRM1 loss and inhibition, respectively. Altogether, we found a minimal subset of RNAs that are controlled both by Tpr nucleoporin and CRM1 receptor.

overall_design: We performed RNA-Seq analyses on human DLD-1 cells that were treated with 200 nM of Leptomycin B (LCLabs, #L-6100) for 3 hours or 1 hour with the following 2 hours of Leptomycin B and 1 mM of auxin treatment for Tpr depletion.

first: H

last: Lee

first: T

last: Li

first: J

last: Iben

last: Smith

last: Echeverria

first: S

last: Chen


title: SPC+ KP vs SPC+ KPG1 tumours

first: Nadine

last: Fournier

summary: Glucose transporters are the first and rate-limiting step for cellular glucose usage, which is often exacerbated in tumour cells enabling their growth and proliferation. Although inhibiting glucose metabolism in lung tumours could become an efficient treatment strategy, whether and which glucose transporter(s) should be targeted remains unclear because of their possible functional redundancy, and because other nutrients or transporter-independent metabolic processes including autophagy and macropinocytosis can fuel tumour cell growth in certain contexts. Here we show that glucose transporter Glut1 gene deletion in tumour cells does not impact tumour initiation and only slightly delays progression in a genetically-engineered mouse model of lung adenocarcinoma. Using 13C-glucose tracing with correlated nanoscale secondary ion mass spectrometry (NanoSIMS) and electron microscopy, we report the presence of multiple lamellar body-like organelles produced by tumour cells. Glucose-derived biomass accumulates in these organelles, and this accumulation is decreased in Glut1-deficient tumour cells. Ex vivo, tumour cell glycolysis is impaired in absence of Glut1 except in case of strong expression of another glucose transporter, Glut3. We show that Glut3 is dispensable for Glut1 wild-type tumour development. In contrast, their combined deletion diminishes tumour growth and prevents the appearance of big lesions. Our results demonstrate the requirement for two glucose transporters in lung adenocarcinoma; dual blockade could reach therapeutic responses not achieved by individual targeting.

overall_design: Expression profile comparison between Glut1-WT and Glut1-KO KP lung tumours arising from SPC positive cells, at 18 weeks and 6 days post-tumour initiation. Magnetic CD45 negative tumour cell fractions analysed.

first: Caroline

last: Contat

last: Zangger

first: Etienne

last: Meylan


title: Targeted RNASeq using a custom panel of metabolic genes

first: Ying-Lin Stefanie

last: Tan

address: 1 Portland St

institute: Pfizer

summary:
Purpose: The purpose of this experiment was to determine the time point following activation at which greatest transcriptional differences in metabolic genes were observed between primary human CD4+ T cells treated with metformin + 2-deoxyglucose combination regimen and cells treated with vehicle.
Methods: Targeted RNA-Seq data was generated from primary human CD4+ T cell mRNA  using a Qiagen custom designed panel of metabolic genes and the Illumina TruSeq stranded mRNA prep.
Results: We obtained differential gene expression between metformin + 2-deoxyglucose and vehicle-treated cells using the DESeq2 app in Illumina Basespace for a set of metabolic genes during different time points following activation, and found the greatest changes at 24hr.

overall_design: Targeted RNASeq transcriptomic profiling of primary human CD4+ T cells activated for 0, 3, 6, 9, and 24 hr with soluble anti-CD3 and anti-CD28 tetrameric complexes (Immunocult) in the presence  of metformin and 2-deoxyglucose, of 2 individual donors.

first: Stefanie

middle: Y


title: Gene expression profiling of paraganglioma (PGL)

city: Brussels

first: Laura

last: Saucedo

address: Laarbeeklaan 103

country: Belgium

institute: Follicle Biology Lab - VUB

summary: Transcriptional analysis of one primary paraganglioma.

overall_design: One primary Abdominal paraganglioma was hybridized onto a cDNA microarray.

last: Remacha

first: Mercedes

last: Robledo

first: Alberto

last: Cascon


title: Transcriptome profile of Primary Human Lung Fibroblasts (Cystic Fibrosis vs. Non-Cystic Fibrosis) arranged in a 3D model of the connective airways tissue

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: The 3D model of the connective airways tissue was obtained by using a specific bottom up approach of tissue engineering allowing to develop 3D tissues featured by the presence of fibroblasts embedded into an endogenous matrix produced by fibroblasts themselves.

overall_design: Total RNA was extracted from Cystic Fibrosis and Non-Cystic Fibrosis fibroblasts after 4 weeks of culture of the connective airways tissue in vitro.

first: R

first: G

last: Imparato


title: Epigenome analysis of pheochromocytoma/paraganglioma samples (II)

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of pheochromocytoma/paraganglioma samples carrying different mutations. The Illumina Infinium EPIC Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 850,000 CpGs. The main goal of this project was to find specific methylation profiles associated to the presence of mutations in the different genetic sub-classes of pheochromocytomas/paragangliomas.

overall_design: Bisulphite converted DNA from the 6 samples were hybridized to the Illumina Infinium EPIC Human Methylation Beadchip


title: Transcriptomic changes in the mouse foregut comparing Gli2,3 double mutant to heterozygous controls

city: Cincinnati

first: Aaron

last: Zorn

summary: We dissected foreguts from Gli2-/-,Gli3-/- and Gli2+/-,Gli3+/- mouse embryos at embryonic day 9.5. Three foreguts were obtained for each group and each foregut was individually processed for bulk RNA extraction and library preparation. Sequencing results identified Gli positively and negatively regulated genes in the foreguts.

overall_design: Examination of transcriptomic changes in the mouse foregut comparing Gli2,3 double mutant to heterozygous controls


title: Transcriptome profile of Primary Human Lung Fibroblasts (Cystic Fibrosis vs. Non-Cystic Fibrosis)

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


title: eIF3 associates with 80S ribosomes to promote translation elongation, mitochondrial homeostasis, and muscle health

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

institute: Universitaet Hamburg

summary: eIF3 is a multi-subunit complex thought to execute numerous functions in canonical translation initiation, including mRNA recruitment to the 40S ribosome, scanning for the start codon, and inhibition of 60S subunit joining 1–3. eIF3 was also found to interact with 40S and 60S ribosomal proteins and translation elongation factors 4, but a direct involvement in translation elongation has never been demonstrated. Using selective ribosome profiling, we made the unexpected observation that eIF3 remains bound to post-initiation 80S ribosomes, followed by release after translation of ~50 codons. Furthermore, eIF3 deficiency reduces early ribosomal elongation speed, particularly on mRNAs encoding proteins associated with membrane-associated functions, resulting in defective synthesis of their encoded proteins and abnormal mitochondrial and lysosomal physiology.  Accordingly, heterozygous eIF3e+/- knockout mice accumulate giant mitochondria in skeletal muscle and show a progressive decline in muscle strength with age. Hence, in addition to its canonical role in translation initiation, eIF3 interacts with 80S ribosomes to enhance, at the level of early elongation, the synthesis of proteins with membrane-associated functions, an activity that is critical for normal muscle health.

overall_design: Control  and eIF3e depleted cells used for tRNA abundance - 5 biological replicates in total; 3- wildtype and 2-eIF3e depleted

first: Yingying

last: Lin

first: Christine

last: Polte


title: SIZ1-mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis

status: Public on Jun 14 2020

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

type: Methylation profiling by high throughput sequencing

summary: The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hypermethylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately one thousand genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared to that in wild type plants, the protein level of ROS1 is significantly decreased, even though there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1 positively regulates active DNA demethylation by promoting the stability of ROS1 protein through SUMOylation.

overall_design: MethylC-Seq: siz1-2 mutant plant examined

first: Xiangfeng

last: Kong

first: Yechun

last: Hong

first: Yi-Feng

last: Hsu

first: Huan

last: Huang

first: Xue

last: Liu

first: Zhe

last: Song


title: CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9

first: Shengdar

last: Tsai

relation:
SuperSeries of: GSE149295
SuperSeries of: GSE149361
SuperSeries of: GSE149362


title: RNA-seq analysis of hepatocellular carcinoma plasma

city: Beijing

first: Jingyi

last: Cao

address: Haidian District

department: School of Life Science

institute: Tsinghua University

summary: Hepatocellular carcinoma (HCC) is currently the third leading cause of death worldwide and the most common type of primary liver cancer, finding noninvasive biomarkers for HCC diagnostic and prognostic are very urging. Previous genomic studies mainly focus on finding miRNA biomarkers for HCC. In this study, we focus on finding long noncoding RNA fragments suitable for serving as hcc biomarkers with plasma and exosomal RNA-seq

overall_design: RNA-seq of plasma and exosomal RNA collected from HCC patients, healthy donors and chronic hepatitis B patients

first: Chang

last: Tan

first: Lu

last: Chen


title: Genes induced by PDGF-BB in cells lacking Signal Transducer and Activator of Transcription-1 (Stat1)

status: Public on Jun 13 2020

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Comparison of gene expression between Stat1+/- and Stat1-/- dermal fibroblasts or vascular smooth muscle cells after treatment with PDGF-BB for one hour.

overall_design: Dermal fibroblasts (DF) and aortic vascular smooth muscle cells (VSMC) were isolated from two Stat1+/- mice (wt) and two Stat1-/- mice (mut). Cells were serum starved in DMEM + 0.1% serum for 24 hours, then treated with 30ng/mL PDGF-BB for 1 hour or left untreated, then harvested for RNA.

first: Shayna

last: Medley

first: Constantin

last: Georgescu

middle: D

first: Lorin

last: Olson


title: Effect of the USP7 inhibitor HBX41,108 on lipopolysaccharide induced gene expression in mouse bone marrow derived macrophages.

city: Glasgow

first: Ruaidhri

last: Carmody

address: Sir Graeme Davies Building, 120 University Place

department: Institute of Infection, Immunity and Inflammation

institute: University of Glasgow

summary: USP7 is a deubiquitinase enzyme that removes polyubiquitin chains form a number of substrates including MDM2, p53 and NF-κB. In this study we assessed the impact of the USP7 inhibitor HBX41,108 on lipopolysaccharide (LPS) induded transcriptional responses in murine bone marrow derived macrophages.

overall_design: Three experimental groups were analysed. Untreated cells, cells stimulated with 100ng/ml LPS for 4 hours and cells pre-treated with 10µM HBX41,108 for 30 mins prior to LPS treatment. Two samples from independent experiments were analysed per group.

last: O'Carroll


title: IRF5 promotes intestinal inflammation by guiding monocyte differentiation towards pathogenic CD11c+ macrophage phenotype [scrnaseq_steady_state]

status: Public on Jun 11 2020

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

institute: Kennedy Institute of Rheumatology

summary: Mononuclear phagocytes (MNPs) play a key role in maintaining intestinal homeostasis but also in triggering immunopathology in response to acute microbial stimulation, which induces the recruitment of masses of Ly6Chi monocytes to the gut. The regulators that control monocyte tissue adaptation in the gut remain poorly understood. Interferon Regulatory Factor 5 (IRF5) is a transcription factor previously shown to play a key role in maintaining the inflammatory phenotype of macrophages Here we investigate the impact of IRF5 on the MNP system and physiology of the gut at homeostasis and during inflammation. We demonstrate that IRF5 deficiency has a limited impact on colon physiology at steady state, but ameliorates immunopathology during Helicobacter hepaticus induced colitis. Inhibition of IRF5 activity in MNPs phenocopies global IRF5 deficiency. Using a combination of bone marrow chimera and single cell RNA-sequencing approaches we compare the differentiation trajectories of wild type and IRF5 deficient monocytes in a shared inflammatory environment and demonstrate that IRF5 stipulates a choice in monocyte differentiation towards macrophages. Specifically, IRF5 promotes the generation of pathogenic CD11c+ macrophages and controls the production of inflammatory mediators by these cells. Thus, we identify IRF5 as a key transcriptional controller of pathogenic monocyte differentiation in the gut.

overall_design: Mixed bone marrow chimeras (mice) were constructed using wildtype (CD45.1+ve) and Irf5 knockout (CD45.2+ve) cells that were also heterozygous for knock-in of GFP to the CX3CR1 locus. The steady state blood and cLP scRNA-seq datasets were generated in the same experiment from a set of MBMCs (n=5, cells pooled from all animals for both analyses).

first: Alastair

middle: L

last: Corbin

first: Maria

last: Gomez-Vazquez

first: Moustafa

last: Attar

first: Irina

last: Udalova

middle: N


title: RNA-Seq analysis of human CD56bright NK cells cultured with ascorbic acid

city: Minneapolis

first: Frank

middle: Martin

last: Cichocki

state: Minnesota

address: 420 Delaware Street SE

department: Department of Medicine

institute: University of Minnesota

summary: We report our results of RNA-seq analysis on freshly isolated, sorted subsets of natural killer cells cultured with ascorbic acid

overall_design: RNA was isolated from sorted cells. Libraries were created using standard Illumina reagents and analyzed using a NextSeq 550.

first: Cheng-Ying

last: Wu

first: Bin

last: Zhang

first: Hansol

last: Kim

last: Anderson

first: Jeffrey

middle: S

last: Miller

middle: M


title: Metformin and 2-Deoxyglucose Collaboratively Suppress Human CD4+ T Cell Inflammatory Functions and Activation-Induced Metabolic Reprogramming

first: Ying-Lin Stefanie

last: Tan

overall_design: Refer to individual Series


title: Untargeted transcriptomic profiling of activated primary human CD4+ T cells treated with metformin and 2-deoxyglucose

summary:
Purpose: To investigate the effects of metabolic inhibitors metformin and 2-deoxyglucose on the global transcriptome of primary human CD4+ T cells.
Methods: mRNA profiles of primary human CD4+ T cells were generated by RNA-Seq for 3 donors in triplicate using Illumina TruSeq library prep. Data was processed using Elucidata's workflow as described below.
Results: Our study presents the first transcriptomic analysis of how metformin + 2-deoxyglucose combination treatment affects activation-induced remodeling of metabolic gene expression in primary human CD4+ T cells.

overall_design: RNASeq transcriptomic profiling of primary human CD4+ T cells activated for 24 hr with soluble anti-CD3 and anti-CD28 tetrameric complexes (Immunocult) in the presence  of metformin and 2-deoxyglucose, of 3 individual donors.

first: Stefanie


title: Active turnover of genomic methylcytosine in pluripotent cells

city: Munich

first: Thomas

last: Carell

address: Butenandtstr. 5-13

department: Chemistry

institute: Ludwig Maximilian University Munich

summary: Epigenetic plasticity underpins cell potency, but the extent to which active turnover of DNA methylation contributes to such plasticity is not known and the underlying pathways are poorly understood. Here we use metabolic labelling with stable isotopes and mass spectrometry to quantitatively address the global turnover of genomic methylcytidine (mdC), hydroxymethylcytidine (hmdC) and formylcytidine (fdC) across mouse pluripotent cell states. High rates of mdC/hmdC oxidation and fdC turnover characterize a formative-like pluripotent state. In primed pluripotent cells the global mdC turnover rate is about 3-6% faster than can be explained by passive dilution through DNA synthesis. While this active component is largely dependent on Tet-mediated mdC oxidation, we unveil additional oxidation-independent mdC turnover, possibly through DNA repair. This process accelerates upon acquisition of primed pluripotency and returns to low levels in lineage committed cells. Thus, in pluripotent cells active mdC turnover involves both mdC oxidation-dependent and  independent processes.

overall_design: High throughput sequencing of a bisulfite amplicon library was used to measure CpG methylation levels at selected secondary imprints in mouse pluripotent stem cells, before and at three and five days during the transition from alternative naïve/formative-like state to primed state; mouse primary embryonic fibroblasts were used as somatic cell reference; no independent replicates were analyzed

first: Fabio

last: Spada

first: Sarah

last: Schiffers

first: Angie

last: Kirchner

first: Yingqian

first: Gautier

last: Arista

first: Olesea

last: Kosmatchev

first: Eva

last: Korytiakova

first: René

last: Rahimoff

first: Charlotte

last: Ebert


title: cDC1 prime and are licensed by CD4+ T cells to induce anti-tumour immunity

city: Saint Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Pathology & Immunology

institute: Washington University School of Medicine

summary: CD4 T cells are thought to help promote anti-tumour responses by ‘licensing’ antigen presenting cells (APCs) that activate CD8 T cells.  Conventional type 1 dendritic cells (cDC1s) are responsible for cross-presentation of tumour-derived antigens to CD8 T cells. Prevailing models presume that the cDC1 is licensed by CD4 T cells that are themselves activated by a distinct cDC subset, the cDC2.  The recent finding that neoantigens presented by major histocompatibility complex (MHC) class II molecules can promote rejection of tumours that lack MHC class II (MHC-II) surface expression is consistent with an indirect action of CD4 T cells, such as cDC1 licensing.  However, no study has directly identified the APC that primes the CD4 T cells responsible for licensing or clearly identified the target of CD4 licensing in vivo.  Here, we generated cDC1-specific Cre expressing mouse strain to inactivate or induce expression of MHC-I, MHC-II, or CD40 specifically within the cDC1 lineage.  Using a tumour model that relies on CD8 T cells and CD4 T cells for rejection, we discovered that early priming of CD4 T cells against tumour-derived antigens, in contrast to soluble antigens, relied overwhelmingly on the cDC1 and not the cDC2.  cDC1 do not simply transport antigen to lymph nodes for processing by cDC2, since lack of MHC-II expression on cDC1 prevented CD4 T cell priming.  We also found that CD40 signaling not only affects licensing of cDC1 for CD8 T cell priming, but is also critical for the activation of CD4 T cells.  Thus, in the setting of tumour-derived antigens, cDC1 can function as an autonomous platform, capable of priming both CD4 and CD8 T cells and orchestrating their cross-talk required for optimal anti-tumour immunity.

overall_design: We used microarrays to obtain and compare gene expression signatures for homeostatic cDC1 populations in the presence or absence of CD40 expression. cDC1 from spleen or skin draining lymph nodes of Xcr1+/+ or Xcr1Cre/+ CD40fl/fl mice were sort-purified for RNA extraction and hybridization on Affymetrix microarrays.

first: Renee


title: The Taiman transcriptional coactivator engages Toll signals to promote apoptosis and intertissue invasion in Drosophila

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

summary: The Drosophila Taiman (Tai) protein is homologous to the human steroid-receptor coactivators SRC1-3 and activates transcription in complex with the 20-hydroxyecdysone (20E) receptor (EcR). Tai has roles in intestinal homeostasis, germline maintenance, cell motility and proliferation through interactions with EcR and the coactivator Yorkie (Yki). Tai also promotes invasion of tumor cells in adjacent organs, but this pro-invasive mechanism is undefined. Here we show that Tai expression transforms sessile pupal wing cells into an invasive mass that penetrates the adjacent thorax during a period of high 20E. Candidate analysis confirms a reliance on elements of the 20E and Hippo pathways, such as Yki and the Yki-Tai target dilp8. Screening the Tai-induced wing transcriptome detects enrichment for innate immune factors, including the Spätzle (Spz) family of secreted Toll ligands that induce apoptosis during cell competition. Tai-expressing wing cells induce immune signaling and apoptosis among adjacent thoracic cells, and genetic reduction of spz, Toll or the rpr/hid/grim pro-apoptotic factors each suppresses invasion, suggesting an intercellular Spz-Toll circuit supports killing-mediated invasion. Modeling these interactions in larval epithelia confirms that Tai kills neighboring cells via a mechanism involving Toll, Spz factors, and the Spz-inhibitor Necrotic. Tai-expressing cells evade death signals by repressing the immune deficiency (IMD) pathway, which operates in parallel to Toll to control NFkB activity, and independently regulates JNK activity. In sum, these findings suggest that Tai promotes competitive cell killing via Spz-Toll, and that this killing mechanism supports pathologic intertissue invasion in Drosophila.

overall_design: Identify Tai-induced mRNAs in wing disc cells by comparing control GFP+ to Tai+/GFP+ samples in triplicate

first: Ken

last: Moberg


title: Stress induces the transcription of toxin-antitoxin systems but does not activate toxin

city: Cambridge

first: Michele

last: LeRoux

address: 31 Ames St

department: Biology

institute: MIT

summary: The purpose of this experiment was to determine whether there was evidence that the endoribonclease toxins of type II TA systems of E. coli were active following treatment of cells with chloramphenicol

overall_design: RNA-seq was performed on RNA extracted from E. coli MG1655 wildtype and a strain lacking ten toxin-antitoxin (TA)  systems (∆10TA) following 15, 30, and 60 min of chloramphenicol treatment. Evidence of endoribonuclease cleavage was assessed by examining the ratio of wildtype (+TA) to the deletion strain and comparing this to existing toxin overexpression datasets.

first: Peter

last: Culviner

first: Michael

last: Laub


title: Gene expression signatures in uteri from WT and Arg260-ERα mice in response to E2

city: Toulouse

first: Francoise

middle: B.

last: LENFANT

address: 1 avenue J. Poulhès

department: Team 9- I2MC

institute: INSERM U1048

summary: To further study gene expression regulated by 17b-estradiol in uteri, we have employed whole gene microarray profiling to identify genes specifically regulated by this site of methylation of ERa (Arg260). Control littermates were used named WT.

overall_design: 17b-estradiol induced gene expression in  uteri from ovariectomized mice was measured after 6 hours exposure to 0 (PLB) and 8µg/kg of 17b-estradiol (E2) injected subcutaneously in castor oil.

first: Marine

last: Adlanmerini

first: Jean-François

last: Arnal

first: Françoise

last: Lenfant

first: Pascal

middle: G

last: Martin

first: Claire

last: Naylies

first: Yannick

last: Lippi


title: Episignatures stratifying ADNP syndrome show modest correlation with phenotype [RNA-seq]

city: New York

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

summary: We conducted an independent study on 24 individuals with ADNP syndrome and replicated the existence of the two mutation-dependent ADNP episignatures. To probe whether the two distinct episignatures correlate with clinical outcomes, we used deep behavioral and neurobiological data from two prospective cohorts of individuals with a genetic diagnosis of ADNP syndrome.

overall_design: Examination of genome-wide methylation and gene expression, with deep clinical phenotypes from individuals with ADNP mutations.

first: Silvia

last: De Rubeis


title: N6 methyladenoside sequencing of T cells

city: Chciago

first: Chuan

last: He

state: IL

address: 929 E 57 th St

institute: University of Chicago

summary: N6 methyladenoside (m6A) sequencing was performed on induced Treg cells, Tnaive cells, CD4+ T cells from germ-free mice and CD4+ T cells from specific pathogen free mice. We found that there are 465 genes with increased m6A levels and 4083 genes with decreased m6A levels in iTregs compared to Tnaïve cells. We found that there are 291 genes with increased m6A levels and 344 genes with decreased m6A levels in germ-free CD4+ T-cells compared to T cells from specific pathogen free mice

overall_design: mRNA profiles of induced Treg, Tnaive, and CD4 T cells from germ-free mice and specific-pathogen-free mice.

first: Thomas

middle: X

last: Lu

first: Linda

last: Zhang


title: Examination of mouse heart cell expression changes after myocardial Infarction

status: Public on Jun 10 2020

city: Los Angeles

first: Feiyang

last: Ma

state: CA

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

department: Molecular Biology Institute

institute: UCLA

summary: The mammalian heart possesses a poor ability to regenerate after acute ischemic cardiac injury and lost cardiac muscle is replaced by scar tissue. Multiple clinical studies demonstrate that the size of scar tissue following myocardial infarction is an independent predictor of cardiovascular outcomes, yet little is known about factors that regulate the size of scar after ischemic cardiac injury. In this report, we demonstrate that collagen V, a fibrillar collagen and a minor constituent of heart scars regulates the size of heart scars after ischemic cardiac injury. Depletion of collagen V in heart scars in two independent animal models led to a significant and paradoxical increase in post infarction scar tissue size with worsening of heart function. A systems genetics approach analyzing genes versus traits across 100 in-bred strains of mice independently demonstrated that collagen V is a critical driver of post injury heart function. We show that collagen V deficiency alters the ultra-structure and mechanical properties of scar tissue that make it more vulnerable to expansion. There is altered reciprocal feedback between matrix and cells that induce expression of specific mechanosensitive integrins which drive fibroblast activation and increased ECM gene expression. Scar size increases. Administration of cilengitide, an inhibitor of specific integrins, completely rescues the phenotype of increased post injury scarring, myofibroblast formation and cardiac dysfunction in collagen V deficient mice. These observations demonstrate that collagen V, a structural constituent of heart scar tissue regulates scar size in an integrin dependent manner.

first: Tomohiro

last: Yokota

first: Arjun

last: Deb

first: Matteo

last: Pellegrini


title: Landscape of G-quadruplex DNA structural regions in breast cancer

city: Manchester

first: Angela

last: Simeone

address: 200 Hathersage Rd

institute: Genomic Services QIAGEN

summary: Response and resistance to anticancer therapies vary due to inter- and intra-tumour heterogeneity. Here, we developed and applied a quantitative chromatin immunoprecipitation sequencing methodology to map differentially enriched G-quadruplex (G4) DNA structure-forming regions (∆G4Rs) in 22 breast cancer patient-derived tumour xenograft (PDTX) models. ∆G4Rs are significantly more associated with the promoter of highly amplified and expressed genes, and with somatic single-nucleotide variant mutations. Specific ∆G4Rs associate with certain patterns of breast cancer TF occupancy, revealing 7 distinct transcription factor programs with differential activities across PDTXs. Collectively, ∆G4Rs report on the genomic, transcriptomic and regulatory architecture of breast cancer. ∆G4R abundance and locations stratify PDTXs into at least three G4-based subtypes. ∆G4Rs of the majority of PDTXs (14/22) associated with more than one distinct breast cancer subtype, which we also call an integrative cluster (IC). This suggests the frequent coexistence of multiple breast cancer states within a PDTX model; the majority, in contrast to expectation, displaying aggressive triple-negative IC10. Short-term cultures of PDTX models with increased ∆G4R levels are more sensitive to small molecules targeting G4 DNA. Thus, G4 DNA structural landscapes revealed additional IC-related intra-tumour heterogeneity in PDTX biopsies, improving their cancer stratification and potentially new treatment strategies.

sample_organism:
Drosophila melanogaster
Homo sapiens
Mus musculus

overall_design: Examination of 22 different PDTX breast cancer models by quantitative G4-ChIP-seq.

first: Robert

last: Hänsel-Hertsch

first: Abigail

last: Shea

first: W

middle: I

last: Hui

first: Katherine

last: Zyner

first: Giovanni

last: Marsico

first: Oscar

last: Rueda

first: Alejandra

last: Bruna

first: Alistair

first: Xiaoyun

first: Santosh

last: Adhikari

first: David

last: Tannahill

first: Carlos

last: Caldas

first: Shankar

last: Balasubramanian


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility [40-K562 RNA-seq]

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: We report a new technology for the parallel bimodal analysis of RNA-seq and ATAC-seq within a single-cell, known as ASTAR (Assay for Single-cell Transcriptome and Accessibility Regions).

overall_design: ASTAR-RNAseq libraries were prepared from K562

first: Q

last: Xing

first: C

first: Y

last: Zeng

first: H

last: Li

last: Loh


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility [40-K562_ATAC]

overall_design: ASTAR-ATACseq libraries were prepared from K562


title: Rapamycin and dexamethasone during pregnancy prevents tuberous sclerosis complex associated cystic kidney disease

city: Jerusalem

first: Morris

last: Nechama

state: Israel

address: Hadassah Medical Center, Ein Karem

department: Pediatric

country: Israel

institute: Hadassah Hebrew University Medical Center

summary: Chronic kidney disease is the main cause of mortality in patients with tuberous sclerosis complex disease (TSC). The mechanisms underlying TSC cystic kidney disease remain unclear with no available interventions to prevent cyst formation. Using targeted deletion of TSC1 in nephron progenitor cells, we showed that cysts in TSC1 null embryonic kidneys originate from injured proximal tubular cells with high mTOR complex 1 activity. Injection of rapamycin to pregnant mice inhibited the mTOR pathway and tubular cell proliferation in kidneys of TSC1 null offspring. Rapamycin also prevented renal cystogenesis and prolonged the life span of TSC newborns. Gene expression analysis of proximal tubule cells, identified sets of genes and pathways that were modified secondary to TSC1 deletion and rescued by rapamycin administration during nephrogenesis. Inflammation with mononuclear infiltration was observed in the cystic areas of TSC1 null kidneys. Dexamethasone administration during pregnancy decreased cyst formation not only by inhibiting the inflammatory response but also by interfering with the mTORC1 pathway. These results reveal novel mechanisms of cystogenesis in TSC disease and suggest new interventions prior to birth to ameliorate cystic disease in offspring.

overall_design: RNA expression profile of proximal tubule cells extracted at E18.5 from WT, Six2 Cre Tsc1 Fl/Fl  and Six2 Cre Tsc1 Fl/Fl mice subjected to Rapamycin treatment during embryogenesis. Each condition had three replicates.

first: Oded

last: Volovelsky


title: Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma [RNA-Seq]

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

summary: CD4+ helper T cells (TH) and regulatory T cells (Treg) that respond to common allergens play an important role in driving and dampening airway inflammation in patients with asthma. Until recently, direct, unbiased molecular analysis of allergen-reactive TH and Treg cells has not been possible. To better understand the diversity of these T cell subsets in allergy and asthma, we analyzed the single-cell transcriptome of ~50,000 house dust mite (HDM) allergen-reactive TH cells and Treg cells from asthmatics with HDM allergy and from three control groups: asthmatics without HDM allergy and non-asthmatics with and without HDM allergy. Our analyses show that HDM allergen-reactive TH and Treg cells are highly heterogeneous, and certain subsets are quantitatively and qualitatively different in subjects with HDM-reactive asthma. The number of interleukin (IL)-9 expressing HDM-reactive TH cells is greater in asthmatics compared with non-asthmatics with HDM allergy, and display enhanced pathogenic properties. More HDM-reactive Th and Treg cells expressing the interferon-response signature (THIFNR and TregIFNR) are present in asthmatics without HDM allergy compared with those with HDM allergy. In cells from these subsets (THIFNR and TregIFNR), expression of TNFSF10 was enriched; its product, TRAIL, dampens activation of TH cells. These findings suggest that the THIFNR and TregIFNR subsets may dampen allergic responses, which may help explain why only some people develop TH2 responses to nearly ubiquitous allergens.

overall_design: Bulk and single-cell RNA-seq were performed from pure populations of HDM-reactive memory TH and Treg cells were isolated ex vivo from asthmatics with HDM allergy (n = 6) and from three control groups: asthmatics without HDM allergy (n = 6) and non-asthmatics with (n = 6) and without HDM allergy (n = 6)

first: Grégory

last: Seumois

first: Ciro

last: Ramírez-Suástegui

first: Benjamin

middle: J

last: Schmiedel

first: Shu

last: Liang

first: Bjoern

last: Peters

first: Alessandro

last: Sette


title: Characterization of a Novel Compound that Stimulates STING-Mediated Innate Immune Activity in an Allele-Specific Manner

city: Beaverton

first: Victor

last: DeFilippis

state: OR

address: 505 N.W. 185th Avenue

department: Vaccine and Gene Therapy Institute

institute: Oregon Health & Science University

summary: A small molecule termed M04 behaves as a novel agonist of human STING. Importantly, we find that the molecule exhibits a differential ability to activate STING based on the allelic variant examined. Furthermore, while M04 is inactive in mice, expression of human STING in mouse cells rescues reactivity to the compound. Using primary human cells in ex vivo assays we were also able to show that M04 is capable of simulating innate responses important for adaptive immune activation such as cytokine secretion, dendritic cell maturation, and T cell cross-priming. Collectively, this work demonstrates the conceivable utility of a novel agonist of human STING both as a research tool for exploring STING biology and as an immune potentiating molecule.

overall_design: PBMCs from two healthy human donors were obtained and treated with DMSO vehicle, M04, cGAMP, or the TLR4/TRIF agonist LPS. RNA sequencing was then used to measure individual transcript levels in each sample and comparisons to vehicle-treated cells were made. Reads were aligned to the Homo_sapiens.GRCh38 genome in Ensembl along with its corresponding annotation, release 84. The program STAR (v020201) was used to align the reads to the genome. Two-pass mode was used with default parameters. Since STAR utilizes the gene annotation file, it calculated the number of reads aligned to each gene.

first: Jinu

last: Abraham

first: Sara

last: Botto

first: Nobuyo

last: Mizuno

first: Kara

last: Pryke

first: Bryan

last: Gall

first: Dylan

last: Boehm

first: Tina

last: Sali

first: Haihong

last: Jin

first: Aaron

last: Nilsen

first: Michael

last: Gough

first: Jason

last: Baird

first: Marita

last: Shaktoura

first: Caroline

last: Subra

first: Lydie

last: Trautmann

first: Elias

middle: K

last: Haddad


title: Choroid plexus organoids predict CNS drug permeability and reveal human CSF proteins produced by specialized cell types

first: Paula

last: Freire Pritchett

address: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus

institute: Medical Research Council

summary: The choroid plexus (ChP) is a protective epithelial barrier that filters blood and secretes cerebrospinal fluid (CSF), an important fluid for nutrient maintenance in the brain and transport of signalling molecules. Here, we establish human ChP organoids with a selective epithelial barrier that secrete CSF-like fluid in self-contained compartments. We show that this in vitro barrier exhibits the same selectivity to small molecules as the in vivo counterpart, and that ChP-CSF organoids can predict CNS permeability of novel compounds. Characterization of the transcriptomic signature of ChP organoids and the proteomic make-up of the CSF-like fluid demonstrate a high degree of similarity to the in vivo counterpart. We leverage the fact that these organoids represent the tissue in isolation to examine their cellular make-up, and explore the specialized epithelial subtypes involved in de novo production of key CSF components. This reveals the presence of heterogeneous epithelial ChP populations, including a newly identified myoepithelial cell type, and uncovers human-specific factors secreted by these specialized cell types.

overall_design: 3 samples of 2 pooled human choroid plexus organoids each along with 1 sample of 2 pooled telencaphalic organoids were dissociated with Accumax and run through the 10X pipeline and then analysed in Seurat and compared with existing in vivo datasets (available through the USCS cell browser: cortex-dev.cells.ucsc.edu and mouse-organogenesis.cells.ucsc.edu).

first: Madeline

last: Lancaster

first: Laura

last: Pellegrini

first: Claudia

last: Bonfio

first: Jessica

last: Chadwick

first: Farida

last: Begum

first: Mark

last: Skehel


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Mouse single cell ATAC-seq)

first: Chadi

last: El Farran

summary: We report a new technology for the parallel bimodal analysis of  RNA-seq and ATAC-seq within a single-cell, known as STAR (Single-cell Transcriptome  and Accessibility Regions).

overall_design: Single-cell ATAC-Seq libraries prepared from 96 E14 mES Cells and 96 2i mouse ES cells.

first: Qiaorui

last: Xing

first: C

last: EL Farran

first: Hu

last: Li

first: Yuin-Han

last: Loh


title: ZBTB38 is dispensable for hematopoiesis and antibody responses.

city: Tucson

first: Deepta

last: Bhattacharya

state: Arizona

address: 1656 E. Mabel Street, MRB 217

department: Department of Immunobiology

institute: University of Arizona

summary: We performed RNA-sequencing of ZBTB38-sufficient and -deficient germinal center B cells. Very few genes were dysregulated by the absence of ZBTB38.

overall_design: RNA-seq of ZBTB38 KO and WT germinal center B cells.

first: Rachel

last: Wong


title: Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma

first: Pandurangan

last: Vijayanand

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

overall_design: Refer to individual Series


title: Host-pathogen transcriptomics of Mucor circinelloides NCRIP deficient spores phagocytosed by mouse macrophages

city: Murcia

first: Carlos

last: Pérez-Arques

state: Murcia

address: Campus Universitario Espinardo, Facultad de Biología

department: Genética y Microbiología

institute: Universidad de Murcia

summary: Here in this work, we uncovered the role of NCRIP in regulating virulent processes and transposable movements through key components of the pathway, RdRP1 and R3B2. Mutants in these genes are unable to launch a proper virulent response to macrophage phagocytosis, resulting in a decreased virulence potential. The transcriptomic profile of rdrp1Δ and r3b2Δ mutants revealed a pre-exposure adaptation to the stressful phagosomal environment even when the strains are not confronted by macrophages.

overall_design:
8 samples are provided and analyzed, comprising 2 replicates (blank and R) for each coculture interacting samples and each single culture, which are as follows: Mucor r3b2 mutant strain cocultured with mouse macrophages (cell line J774A.1) for 5h, Mucor rdrp1 mutant strain co-cultured with mouse macrophages (cell line J774A.1) for 5h, Mucor r3b2 mutant strain (R7B) single-cultured in cell media for 5h, and Mucor rdrp1 mutant strain singlecultured in cell media for 5h.

Libraries were prepared with Illumina TruSeq strand-specific mRNA kits and sequenced with an Illumina HiSeq 2500 system to generate 50-bp, first-strand (or reverse) and single-end reads.

last: Perez-Arques

first: Maria-Isabel

last: Navarro-Mendoza

first: Victoriano

last: Garre

first: Francisco-Esteban

last: Nicolas


title: Effective treatment of immune checkpoint blockade-resistant tumors by pharmacological activation of estrogen receptor beta

city: Chengdu

first: Shengtao

last: Zhou

address: #17, Renmin South Road

department: Department of Obstetrics and Gynecology

institute: West China Second Hospital, Sichuan University

summary: In this study, we examined the differential RNA profile of LY500307 plus PD-1-treated 4T1 cells and PD-1-treated 4T1 cells compared with control 4T1 cells

overall_design: We used RNA sequencing to compare the differential RNAs of LY500307 plus PD-1-treated 4T1 cells and PD-1-treated 4T1 cells compared with control 4T1 cells


title: Acetylation of cytidines by NAT10 enhances HIV-1 replication through stabilization of viral RNA

city: Taipei

first: Kevin

last: Tsai

address: 128 Sec. 2, Academia Rd. Nankang

department: Institute of Biomedical Sciences

country: Taiwan

institute: Academia Sinica

summary: As obligate parasites, viruses need to navigate a variety of cellular regulatory systems while infecting and replicating in the host cell. Post-transcriptional modifications have recently emerged as an important layer of regulation of viral RNA function. For example, our lab and others have shown that the RNA modification N6-methyladenosine (m6A) can enhance the replication of multiple viruses in cis, including Human Immunodeficiency virus 1 (HIV-1), Influenza A virus, SV40 and Kaposi's sarcoma-associated herpesvirus (KSHV). Recent reports have revealed the presence of another RNA modification, N4-acetylcytidine (ac4C) on cellular mRNAs and have shown that ac4C can enhance mRNA stability and translation. Here, we demonstrate that ac4C is present at multiple sites on HIV-1 mRNAs and on the viral genomic RNA. Through ac4C RNA immunoprecipitation (RNA-IP) and RNA-seq, we found ac4C on HIV-1 mRNAs as well as the virion genomic RNA, with ac4C sites in the coding regions of the pol, env, nef genes, and the trans-activation response (TAR) hairpin. Phenotypically, we observe that increasing the expression level of the ac4C acetyltransferase NAT10 leads to an increase in viral replication that is dependent on the RNA binding and enzymatic domains of NAT10. Moreover, both CRISPR-depletion of NAT10 (ΔNAT10) and treatment with the small molecule NAT10 inhibitor Remodelin, diminishes HIV-1 replication in T cells. Lastly, silent mutations introduced to prevent ac4C deposition on the viral genome indeed diminished HIV-1 replication. Our data suggest that HIV-1 has evolved to incorporate ac4C in essential viral gene coding regions and regulatory RNA structures, and that NAT10-dependent ac4C addition enhances HIV-1 replication.

overall_design: PA-ac4C-seq on poly(A)+ RNA from mock-infected or HIV-1-infected CEM-SS and CEM cells; PA-ac4C-seq on RNA extracted from HIV-1 infected CEM-SS, SupT1, and CEM cells; PA-ac4C-seq validation of ac4C depletion in virions produced from control or NAT10-depleted CEM cells; GFP (control) or NAT10 PAR-CLIP on HIV-1-infected CEM cells.

first: Bryan

middle: R

last: Cullen


title: Parallel Bimodal Single-cell Sequencing of Transcriptome and Chromatin Accessibility (Human single cell ATAC-seq)

overall_design: ASTAR scATAC libraries prepared from BJ, K562, JK1 and Jurkat Human Cell Lines