title: Transcriptional profile associated with human oocyte meiotic maturation

city: Barcelona

first: Montse

last: BARRAGAN

state: Select One

address: Baldiri Reixac, 15

institute: Clinica EUGIN

summary: The transition from a transcriptionally active state (GV) to a transcriptionally inactive state (mature MII oocytes) is one of the requirements for the acquisition of oocyte developmental competence. After maturation, oocytes are mostly transcriptionally quiescent, and developmental competence prior to embryonic genome activation (EGA) relies on maternal RNA and proteins. The landscape of expressed genes at the MII stage could be mostly driven by post-transcriptional mechanisms, such as alternative splicing (AS). With the development of single cell transcriptome analysis, genome wide AS analysis becomes technically feasible and available to fully characterize the AS patterns in human oocytes. Profiling spliced mRNA isoforms might provide novel information on the molecular mechanisms driving early development, and might be a source of potential biomarkers of oocyte quality. The goal of the present study is to perform a transcriptomic analysis in oocytes at different stages of maturation, to identify the profiles of alternative spliced isoforms produced in both oocyte’ stages.

overall_design: A total of 12 in vivo matured (MII) and 4 non-matured (GV stage) oocytes from 16 women undergoing oocyte donation were included in this study, processed and analyzed individually. Average women age was 28 ± 4.7 years (range 21-34), with a mean antral follicle count (AFC) of 21 ± 10.7 follicles (range 5-43). Oocytes were divided in 4 experimental groups (4 oocytes in each group) according to their maturation stage, and the age and AFC of the women (mean ± SD): GV oocytes from women up to 30 years old with high AFC (GV group; 26±4.1 years old and 27±13 follicles), MII oocytes from women up to 30 years old with high AFC (H-MII group; 26±4.6 years old and 24±3 follicles), MII oocytes from women with low AFC (L-MII group; 27±5.4 years old and 7±1 follicles) and MII oocytes from women above 31 years old with high AFC (O-MII group; 32.8±1.5 years old and 27±6 follicles). Total RNA from each oocyte independently was isolated, amplified, labeled, and hybridized on HTA 2.0 arrays (Affymetrix).

first: Montserrat

last: Barragán

first: David

last: Cornet-Bartolomé

first: Filippo

last: Zambelli

first: Anna

last: Ferrer-Vaquer

first: Gustavo

last: Tiscornia

first: Rita

last: Vassena


title: Transcriptome-wide mapping of MARF1-bound mRNAs

status: Public on Jun 16 2020

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

type: Expression profiling by high throughput sequencing

summary: To comprehensively identify MARF1-associated mRNAs, we performed iCLIP using  engineered HEK293 cells stably expressing a doxycycline (Dox)-inducible FLAG-tagged MARF1 that lacks RNAse activity. Our iCLIP analysis of MARF1 in HEK293 cells identified 108 mRNAs bound by MARF1 and demonstrates that MARF1 binds to the majority of these mRNAs via their 3’UTRs.

overall_design: UV cross-linking with immunoprecipitation using FLAG antibody, followed generating a library of MARF1-protected RNA fragments.

first: William

middle: R

last: Brothers

first: Steven

last: Hébert

first: Marc

last: Fabian


title: Concentration-dependent regulation by Rbfox enabled by motifs of intermediate affinity

city: Cambridge

first: Bridget

middle: E

last: Begg

state: MA

address: 31 Ames St

department: Biology

country: USA

institute: Massachusetts Institute of Technology

summary: The Rbfox family of splicing factors regulate alternative splicing during animal development and in disease, impacting thousands of exons in the maturing brain, heart, and muscle. Rbfox proteins have long been known to bind to the RNA sequence GCAUG with high affinity, but just half of Rbfox CLIP peaks contain a GCAUG motif. We incubated recombinant RBFOX2 with over 60,000 mouse and human transcriptomic sequences to reveal significant binding to several moderate-affinity, non-GCAYG sites at a physiologically relevant range of RBFOX concentrations. We find that many of these “secondary motifs” bind Rbfox robustly in cells and that several together can exert regulation comparable to a GCAUG in a trichromatic splicing reporter assay. Furthermore, secondary motifs regulate RNA splicing in neuronal development and in neuronal subtypes where cellular Rbfox concentrations are highest, enabling a second wave of splicing changes as Rbfox levels increase.

overall_design: nsRBNS at 5 concentrations with one replicate (121nM), two 0 nM controls, and two input controls.

first: Christopher

middle: B

last: Burge


title: RNA-binding Protein PCBP1/hnRNP E1 is an Intracellular Checkpoint for Balancing Effector versus Regulatory T Cells

city: Columbus

first: Zihai

last: Li

state: OH

address: 460 W 12th Ave

department: Institute for Immuno-Oncology

institute: Ohio State University

summary: Distinct lineages of T cells can act in response to various environmental cues to either drive or restrict immune-mediated pathology. Immunotherapy involving the block of cell surface immune checkpoints CTLA-4 and PD-1/PD-L1 has revolutionized cancer treatment across a wide spectrum of malignancies. However, additional immune regulatory mechanisms remain to be discovered, and will facilitate development of next generation agents to overcome resistance to current therapies. We now report that the RNA-binding protein, PCBP1, is critical for stabilizing effector T cell functions by limiting expression of T effector cell-intrinsic Treg-commitment programs and subverting expression of immune-suppressive signals. Indeed, T cell-specific deletion of Pcbp1 increased Treg development, enlisted multiple inhibitory checkpoint molecules including PD-1, TIGIT and VISTA on TILs, and thwarted anti-tumor immunity. Our results demonstrate a critical role for PCBP1 as an intracellular checkpoint for balancing effector versus Treg cells and also suggest PCBP1 as a novel target for cancer immunotherapy.

overall_design: Spleen mRNA profiles of 6-8 weeks old wild type (WT) and Pcbp1f/fCD4-Cre male mice were generated by deep sequencing, in quadruplicate, using Illumina HiSeq3000.

first: Dongjun

last: Chung

first: Ephraim

last: Ansa-Addo


title: Genome-wide screening and characterization of genes involved in response to high dose of ciprofloxacin in Escherichia coli

city: Harbin

first: Rui

last: Sui

address: Department of Microbiology, Harbin Medical University, 194 Xuefu Road, Nangang District, Harbin, China, 150086

department: Microbiology

country: China

institute: Harbin medical University

summary: Background: Antibiotic resistance is an urgent threat to public health. Prior to the evolution of antibiotic resistance, bacteria frequently undergo response and tend to develop a state of adaption to the antibiotic. Ciprofloxacin is a broad-spectrum antibiotic by damaging DNA. With the widespread clinical application, the resistance of bacteria to ciprofloxacin continues to increase. This study aimed to investigate the transcriptome changes under the action of high concentration of ciprofloxacin in Escherichia coli.  Results: We identified 773 up-regulated differentially expressed genes (DEGs) and 645 down-regulated DEGs in ciprofloxacin treated cells. Enriched biological pathways reflected the up-regulation of biological process such as DNA damage and repair system, toxin/antitoxin systems, formaldehyde detoxification system, peptide biosynthetic process and cellular protein metabolic process. With KEGG pathway analysis, up-regulated DEGs of kdsA and waa operon were associated with “LPS biosynthesis”. rfbABC operon was related to “streptomycin biosynthesis” and “polyketide sugar unit biosynthesis ”. Down-regulated DEGs of thrABC and fliL operons were associated with “flagellum-dependent cell motility” and “bacterial-type flagellum” in GO terms, and enriched into “biosynthesis of amino acids” and “flagellar assembly” in KEGG pathways. After treatment of ciprofloxacin, bacterial lipopolysacchride (LPS) release was increased by two times, and the mRNA expression level of LPS synthesis genes, waaB, waaP and waaG were elevated (P < 0.05).   Conclusions: Characterization of the gene clusters by RNA-seq showed high dose of ciprofloxacin not only lead to damage of bacterial macromolecules and components, but also induce protective response against antibiotic action by up-regulating the SOS system, toxin/antitoxin system and formaldehyde detoxification system. Moreover, genes related to biosynthesis of LPS were also upregulated by the treatment indicating that ciprofloxacin can enhance the production of endotoxin on the level of transcription. These results demonstrated that transient exposure of high dose ciprofloxacin is double edged. Cautions should be taken when administering the high dose antibiotic treatment for infectious diseases.

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

overall_design: E. coli K12 strain MG1655 and strains treated with 2 μg/mL ciprofloxacin

last: Sun

first: Yingmei

last: Fu

first: Fengmin

last: Zhang


title: BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility [ATAC-Seq]

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Mouse naive and primed pluripotent stem cells, ESC and EpiSC, represent two distinct stages of pluripotency. Here we report that BMP4 drives primed to naive transition or PNT by reprogramming chromatin accessibility. ATAC-seq reveals that a short pulse of BMP4 triggers EpiSCs to close 26409 and open 6428 loci to reach an intermediate state that continue to open 18744 and close 7042 loci under 2iL until reaching a naive state, following with a dramatic reactivation of the silenced X chromosome. Among loci opened by BMP4 are those encoding Id1, Tfap2c/2a and Zbtb7b that synergistically drive PNT without BMP4. Tfap2c-/- ESCs or EpiSCs self-renew normally, while the former capable of differentiating to the latter but the latter fails to undergo PNT, a defect rescuable by exogenous Tfap2c. Our results link BMP4 to PNT through a binary logic of chromatin closing and opening, revealing the intrinsic power of extracellular factors to reorganize nuclear architecture in development.

overall_design: We analyzed the transcriptome expression profiles (RNA-seq) and chromation accessibility (ATAC-seq) during PTN


title: Amelioration of Brain Histone Methylopathies by Balancing a Writer-Eraser Duo KMT2A-KDM5C [ChIP-seq]

city: Ann Arbor

first: Christina

middle: N

last: Vallianatos

state: MI

address: 1241 East Catherine

institute: University of Michigan

summary: We describe a methyl histone writer-eraser double-mutant animal that corrects phenotypes of single-mutants KMT2A and KDM5C.

overall_design: We performed H3K4me3 ChIP-Seq from adult male mouse amygdala tissue.

first: Robert

middle: S

last: Porter

first: Shigeki

last: Iwase


title: Amelioration of Brain Histone Methylopathies by Balancing a Writer-Eraser Duo KMT2A-KDM5C [RNA-seq]

overall_design: We performed RNA-seq from adult male mouse amygdala and hippocampus tissue.

first: Katherine

last: Bonefas


title: Amelioration of Brain Histone Methylopathies by Balancing a Writer-Eraser Duo KMT2A-KDM5C

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

overall_design: Refer to individual Series


title: BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility [RNA-Seq]


title: RNAseq data for de novo assembly of the Vuilleminia comedens transcriptome as it grows on wood

city: Swansea

first: Daniel

last: Eastwood

address: Singleton Park

country: United Kingdom

institute: Swansea University

summary: Vuilleminia comedens is a basidiomycete pioneer species in attached angiosperm branches, especially beech (Fagus sylvaticus), initiating decomposition of lignocellulose. Pioneer species exert priority effects on subsequent colonisers influencing community structure. Wood decay is an essential part of the carbon cycle, underpinning forest ecosystem processes, but despite its clear importance, remarkably little is known about the pioneer species which begin the process of lignocellulose decomposition. This work studied the transcriptome and proteome of V. comedens growing in inoculated beech wood blocks in the laboratory. Our analysis focused on nutrient acquisition by decomposition of lignocellulose, and the specialised metabolic processes utilised by the fungus to mitigate against the effects of both plant defence compounds and the toxic derivatives produced as a result of lignin breakdown. Our results show that V. comedens expresses transcripts encoding a large range of enzymes associated with lignocellulose decomposition and metabolism of carbohydrate-based compounds, suggesting a broad-based approach to nutrient acquisition. Furthermore, the transcriptome included an array of genes for specialised metabolism and xenobiotic mitigation, some of which were highly expressed, suggesting that the chemical environment that V. comedens inhabits during wood decay is a significant challenge to successful growth. The proteomic data support the importance of lignin decomposition and xenobiotic mitigation to V. comedens.

overall_design: Total RNA was extracted from three independent biological replicates, grown on separate wood blocks, to inform transcriptome assembly.

first: Suzy

middle: C

last: Moody


title: Analysis of tumor-bearing Farnesoid X Receptor and Small heterodimer Partner double knockout and control WT mice in both sexes

status: Public on Jun 15 2020

city: Houston

first: Yun Seong

last: Jeong

state: TX

address: 6565 MD Anderson Blvd.

institute: MD Anderson Cancer Center

summary: Mice were aged to a year and their livers were collected and analyzed at the end of the experiment. All the mice used in this study are on C57/B6 background.

overall_design: Since double knockout of Fxr and Shp develop spontaneous liver tumors by one year of age only in the male mice, we decided to examine their transcription profile and compare it to the female livers. WT male and female mice were used as controls.

first: Sayee

last: Anakk

first: Kangho

last: Kim

first: Ju

last: Lee

first: Yun

first: Sung

middle: H


title: Total poly(A)+ RNA sequencing

city: Oxford

first: Adrien

last: Birot

address: South Parks Rd

department: Departement of Biochemistry

institute: University of Oxford

summary: Nuclear 3’ to 5’ nuclease RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given the large number of RNA species and intervening RNA processing factors. Here we analysed changes in the poly(A)+ RNA proteins interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. Our data demonstrate a functional connection between Rrp6 and Mtl1 in controlling processing and levels of multiple protein-coding and non-coding transcripts. Furthermore, we show that exosome mutants accumulate components of U1 and U2 snRNPs and show depletion of NTC components from RNA suggesting that the stage prior to the activation of the spliceosome represents a critical quality control step. We have also identified potential new RNA binding factors involved in exosome regulation, including a zinc-finger protein called Mub1 that controls levels of selected transcripts encoding for proteins implicated in stress response. Collectively, our data have provided a global view of RNA metabolism alterations in exosome deficient cells and revealed RNA binding proteins that may act as novel exosome cofactors.

overall_design: 4 samples in triplicates

first: Cornelia

last: Kilchert


title: RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

summary: We performed cryosectioning of oocytes along the animal-vegetal axis (first developmental axis, section A (first animal) to section E (last vegetal), followed by RNA-Seq to determine the localization profiles of coding and noncoding RNAs. The method allowed for a complete view on RNA localization. We found that nearly all RNAs are localized, but only a small percentage is actively transported during oogenesis.

overall_design: RNA profiles (mRNA, lncRNA, other RNA) were generated by deep sequencing, in biological triplicates (each oocyte divided into five segments), using Illumina HiSeq.

last: Sindelka

first: Ravindra

last: Naraine

first: Pavel

last: Abaffy


title: BMP4 Resets Primed to Naive Pluripotency by Reprogramming Chromatin Accessibility

first: Jiangping

last: He


title: Transcriptional survey of peripheral blood links lower oxygen saturation during sleep with reduced expressions of CD1D and RAB20 that is reversed by CPAP therapy

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Sleep Disordered Breathing (SDB) is associated with a wide range of physiological changes, likely due in part to the influence of hypoxemia during sleep on gene expression. We studied gene expression in peripheral blood mononuclear cells in association with three measures of SDB: the Apnea Hypopnea Index (AHI); average oxyhemoglobin saturation (avgO2) during sleep; and minimum oxyhemoglobin saturation (minO2) during sleep. We performed discovery analysis in two community-based studies: the Multi-Ethnic Study of Atherosclerosis (MESA; N = 580) and the Framingham Offspring Study (FOS; N=571). Associations with false discovery rate (FDR) q-value<0.05 in one study were considered to have replicated if a p-value<0.05 was observed in the other study. Associations that replicated between cohorts, or with FDR q-value<0.05 in meta-analysis of the two studies, were carried forward for gene expression analysis in the blood of 15 participants from the Heart Biomarkers In Apnea Treatment (HeartBEAT) trial who had moderate or severe obstructive sleep apnea (OSA) and were studied before and after three months of treatment with continuous positive airway pressure (CPAP). We also performed Gene Set Enrichment Analysis based on all trait and cohort analyses. We identified 22 genes associated with SDB traits in both MESA and FHS. Of these, lower CD1D and RAB20 expressions were associated with lower avgO2 in MESA and FHS, and CPAP treatment increased their expression in HeartBEAT. Immunity and inflammation pathways were up-regulated in subjects with lower avgO2, i.e. in those with a more severe SDB phenotype (MESA),  whereas immuno-inflammatory processes were down-regulated in response to CPAP treatment (HeartBEAT).

overall_design: The Heart Biomarker Evaluation in Apnea Treatment (HeartBEAT) study is a randomized, 4-site single-blind clinical trial that investigated the efficacy of OSA therapy in reducing cardiovascular disease risk for patients with moderate-severe OSA (ClinicalTrials.gov NCT01086800). Of HeartBEAT participants randomized to the CPAP treatment group, a subsample of 15 individuals who also adhered to CPAP therapy (defined by at least 4 hours of CPAP use over the 3-month intervention period) participated in a gene expression study.  Venous blood was collected following an overnight fast in 8 mL heparinized Cell Prep Tubes containing Ficoll Hypaque (Becton Dickinson #362753) in order to separate peripheral blood mononuclear cells.  The tubes were centrifuged fresh at room temperature for 15 minutes at 2000 G to isolate the buffy coat, which was pelleted, resuspended in Millipore S-002-10F freezing medium, and cryopreserved at -80C.

first: Tamar

last: Sofer

middle: J

last: Gottlieb


title: Transcriptome profile of Primary Human Lung Fibroblasts (Cystic Fibrosis vs. Non-Cystic Fibrosis) [2D]

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: The transcriptomic profile of cystic fibrosis human lung fibroblasts was compared to normal human lung fibroblasts.

overall_design: Total RNA was extracted from Cystic Fibrosis and Non-Cystic Fibrosis fibroblasts grown in 2D to about 100% confluency.

first: R

first: G

last: Imparato


title: Transcriptome and 5mC/5hmC of Trophoblast Stem Cells

city: Shanghai

first: Shaorong

last: Gao

address: Siping Road NO.1239

institute: Tongji University

type: Methylation profiling by high throughput sequencing


title: Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [MeDIP-seq]

summary: RNA-seq of WT, Tet2-het and Tet2-KO mTSCs in stem-state, RNA-seq of WT and Tet2-KO mTSCs in vitro differentiation, (h)MeDIP of WT and Tet2-KO mTSCs in stem-state

overall_design: RNA-seq and (h)MeDIP-seq profiles , generated by deep sequencing in diplicate, using HiSeq 2500. Paired-end 125-bp sequencing was applied.

first: Linfeng

last: Zhang

first: Wenchao

last: Xiu


title: A Drosophila Model of Pontocerebellar Hypoplasia Reveals a Critical Role for the RNA Exosome in Neurons

city: Atlanta

first: Derrick

middle: Jerone

last: Morton

state: GA

address: 1510 Clifton Rd NE

institute: Emory

summary: RNA-sequencing analysis reveals increased steady-state levels of key neuronal genes in Rrp40 mutant flies

overall_design: Examination of Rrp40 missense mutantions modeled in Drosophila

first: Anita

last: Corbett


title: Xist Repeats A and B account for two distinct phases of X-inactivation establishment

city: hopkinton

first: barry

middle: A

last: kesner

state: ma

address: 1 chamberlain street

institute: molecular biology

summary: X-chromosome inactivation (XCI) is a global silencing mechanism by which XX and XY mammals equalize X-linked gene dosages. XCI begins with an establishment phase during which Xist RNA spreads and induces de novo heterochromatinization across a female X chromosome, and is followed by a maintenance phase when multiple epigenetic pathways lock down the inactive X (Xi) state. Involvement of Polycomb repressive complexes 1 and 2 in XCI has been intensively studied, but with conflicting conclusions regarding their recruitment and role in Xi silencing. Here we reveal that establishment of XCI has two phases and reconcile the roles that Xist Repeats A and B play in gene silencing and Polycomb recruitment. Repeat A initiates both processes, whereas Repeat B bolsters or stabilizes them thereafter. Once established, XCI no longer requires Repeat A during maintenance. These findings integrate disparate studies and present a unified view of Xist?s role in Polycomb-mediated silencing.

overall_design: RNAseq, H3K27me3 ChIP-seq, H2AK119ub ChIP-seq in WT and RepB ES cells during differentiation timecourse; H3K27me3, H2AK119ub ChIP-seq in RepA MEF

first: D

last: Colognori

first: H

last: Sunwoo

last: Wang

first: C

first: J

middle: T

last: Lee


title: Changes in relative transcript amounts caused by hydrogen sulfide treatment, deletion of BigR, and BigR mutant complement in Acinetobacter baumannii

city: Bloomington

first: David

middle: Peter

last: Giedroc

state: IN

address: 212 S. Hawthorne Drive

department: Chemistry

institute: Indiana University

summary: Acinetobacter baumannii is an opportunistic nosocomial pathogen that is the causative agent of several serious infections in humans. Here, we investigate the response of A. baumannii toward sodium sulfide (Na2S), known to be associated with some biofilms at oxic/anoxic interfaces, as a model for how this major human pathogen manages sulfide homeostasis. These results reveal that A. baumannii encodes two persulfide‑sensing transcriptional regulators, a primary sigma54‑dependent transcriptional activator (FisR), and a secondary system controlled by the persulfide‑sensing repressor biofilm growth‑associated repressor (BigR) both of which regulate operons encoding for sulfide detoxification or transportation. In addition, sulfide induces an alternative cytochrome bd oxidase which is refractory to inhibition by H2S and represses importers of alternate sulfur sources. Lastly, our results suggest additional genes regulated by BigR beyond sulfide detoxification including genes associated with assembly of type 1 chaperone-usher pilus.

overall_design: RNA for the sulfide experiment was prepared from cultures of wild-type and ΔbigR and ΔbigR mTn7(bigRC34A/C100A) strains of Acinetobacter baumannii 17978 grown exponentially in LB media at 37°C to OD600=0.2. At this point Na2S was added to treated cultures at a ﬁnal concentration of 0.2 mM for a 10 min exposure, then samples were collected from all treated and untreated conditions. Three independent biological replicates of RNA were prepared for each strain or condition. cDNA libraries were sequenced and the sequencing results were used as the data base for differential expression analysis.

first: Brenna

last: Walsh

first: Jiefei

first: Katherine

last: Edmonds

first: Lauren

middle: D

last: Palmer

first: Yixiang

first: Jonathan

last: Trinidad

first: Eric

middle: P

last: Skaar


title: Single cell RNAseq of male and female peritoneal macrophages

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

summary: Determine the heterogeneity of peritoneal macrophages obtained from unmanipulated male and female C57BL/6J mice

overall_design: CD11b+ SiglecF-, CD19-, CD3-, Ly6G- peritoneal cells from unmanipulated mice were FACS-purified and processed using the 10X Genomics platform

first: Pieter

last: Louwe

first: Calum

last: Bain

first: Victor

last: Huici

first: Katerina

last: Boufea

first: Stephen

last: Jenkins


title: Gene expression profiles in fetal human liver sinusoidal endothelial cells (LSEC)

city: Bronx

first: Sanjeev

last: Gupta

state: NY

address: 1300 Morris Park Ave.

department: Medicine

institute: Albert Einstein College of Medicine

summary:
Understanding molecular fingerprints of specific cell types is central for defining lineage development, progression, differentiation and pathophysiological perturbations. This study addressed gene expression profiles in freshly isolated fetal human LSEC as well as these LSEC after cell culture.
Comparisons with human umbilical vein endothelial cells (HUVEC) allowed determination of lineage-specific differences. Cell culture allowed identification of differences in phenotype regulation of cells under these conditions.

overall_design: Comparisons were made between freshly isolated LSEC (PP cells), LSEC after initial culture (P0 cells) and LSEC after passages (P2 or P3) from 3 donors each. Freshly isolated HUVEC served as controls for comparisons.

first: Sriram

last: Bandi

first: Tatyana

last: Tchaikovskaya


title: Transcriptome and 5mC/5hmC of Trophoblast Stem Cells [RNA-seq]

first: Shaorong

last: Gao

first: Linfeng

last: Zhang

first: Wenchao

last: Xiu


title: Quantitative analysis of transcriptomes in irradiated/unirradiated pancreatic cancer cells

status: Public on Jun 14 2020

first: Ling

last: Tian

state: Shanghai

address: No. 650, New Songjiang Road

department: Institute of Translational Medicine

institute: Shanghai General Hospital

summary: Irradiated dying tumor cells play crucial roles in tumor repopulation. However, the transcriptome changes in pancreatic cancer cells after radiation remains unknown. Here we performed RNA-sequencing in pancreatic cancer cell line SW1990 and PANC-1 that were 10Gy irradiated or unirradiated. Bioinformatic analysis revealed that the transcriptomes were significantly changed after radiation. Gene Ontology (GO) analysis revealed that the signaling concerning extracellular vesicles, especially exosomes, were significantly enriched. Further investigation revealed the vital role of irradiated dying tumor cells-derived exosomes in potentiating tumor repopulation.

overall_design: Examination of transcriptome changes after radiation in 2 cell types.


title: Fluctuations in sex hormones affect ex vivo HIV infection in cervical mucosa and mucosal immunity

city: New York

first: Natalia

last: Teleshova

address: 1230 York Avenue

institute: Population Council

summary: There is an ongoing debate whether sex hormones impact risk of HIV transmission. This study evaluated if serum estradiol (E2) and progesterone (P4) levels predict the ex vivo cervical tissue HIV infection, tissue immune environment and transcriptome. Cervical mucosa and peripheral blood samples were collected from subjects undergoing total hysterectomies. Tissue explants were challenged with HIV-1BaL and infection was monitored in the supernatants by HIV gag qRT-PCR. Serum E2 and P4 concentrations were measured by radioimmunoassay. Blood and tissue T cell phenotypes were characterized by flow cytometry. Tissue responses to HIV exposure were measured by Luminex. Tissue transcriptome in an unchallenged portion of mucosa was analyzed by RNAseq. We show that serum E2 concentrations inversely associated with cervical HIV-1BaL infection ex vivo and this association was independent of potential confounders (race, age, phase of the cycle, parakeratosis, metaplasia, histopathological signs of cervical inflammation, and HSV-2 status). E2 concentrations did not associate with T cell frequencies/phenotype in either tissues or blood. However, higher E2 concentrations predicted a mixed profile of pro-/anti-inflammatory genes expression and HIV-induced soluble mediators. In contrast, P4 concentrations or P4/E2 ratios did not associate with ex vivo tissue infection level, but increased P4 concentrations associated with high frequencies of a4b7+ and low LFA-1+ T cells and mainly pro-inflammatory responses to HIV. These data suggest inhibitory effect of E2 on local mucosal HIV amplification early post transmission, provide insights in the mechanism of E2-mediated anti-HIV activity and highlight P4-associated immune changes in the mucosa.

overall_design: Endocervical samples were derived from subjects with high (n=5; 205-599 pg/ml) vs. low-moderate (n=5; 27-109 pg/ml) estradiol concentrations. Ectocervical samples were derived from subjects with high (n=3; 277-599pg/ml) vs. low-moderate (n=4; 27-109 pg/ml) E2 levels.


title: Functional dissection of RanBP2 and Nup88/Nup214 subcomplex in nucleocytoplasmic transport

city: Bethesda

first: Alexei

last: Arnaoutov

state: MD

address: 49 Convent Dr, Bldg 49 Room 5A10

department: PCRM

institute: NICHD

summary: RNA-Seq was performed upon protein depletion to examine whether the loss of RanBP2, Nup88 or Nup214 contributes to transcriptional changes.

overall_design: Cytoplasmic nucleoporins were selectively depleted using the Auxin-degron system.  RNA-Seq analyses were performed for gene expression profiling.

first: H

last: Lee

first: S

last: Chen

first: A

first: M

last: Dasso


city: Amherst

first: Rilee

last: Zeinert

address: 240 Thatcher Way

institute: UMass Amherst

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) and transposon insertion mutagenesis (Tnseq) libraries of Lon deletions compared to wt Caulobacter crescentus.
Methods: See Methods section of The Lon protease links nucleotide metabolism with proteotoxic stress for information regarding methods or contact lead correspondence. Briefly, Samples for RNAseq were extracted from wt and lon deletion strains grown to mid exponential phase.
Methods: See Methods section of The Lon protease links nucleotide metabolism with proteotoxic stress for information regarding methods or contact lead correspondence. Briefly, Samples for Tnseq were generated by Eztn5 transposon mutagenesis.
Conclusions: Our study represents the first detailed analysis of lon deletion comparison to wt caulobacter transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: wt and lon deletion strains for both RNAseq and Tnseq

first: Chien

last: Peter

first: Zeinert

last: Rilee


title: Histone H1 distribution and epitope exposure within chromatin high-order structure

city: Colchester

first: Vladimir

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

summary: Within the cell nucleus, histone H1 is the most mobile histone.  Yet, it is regarded as key to the establishment and stability of chromatin higher-order structure.  The implication is that chromatin higher-order structure is dynamic, in part due to the mobility of H1.  Defining the positions of H1 on chromatin in situ, therefore, represents a challenge.  Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq) is traditionally the method for mapping histones onto DNA elements.  But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure.  A second formaldehyde fixation after antibody binding to intact in situ chromatin, but before sonication (xxChIP-seq), preserves this information and reveals which histone epitopes are inaccessible in situ.  In this study, the distribution of two histone H1 variants H1.2 and H1.5 is defined and compared by both xChIP-seq and xxChIP-seq in undifferentiated HL-60/S4 cells, illustrating the influences of preserved chromatin higher-order structure. We have found that xChIP and xxChIP signals are anticorrelated. H1.2 versus H1.5-enrichments were particularly distinct near bound Pol II, SMC3 proteins, as well as domains marked by H3K4me1, H3K9ac, H3K27ac and H3K36me3. H1.5-enriched regions have an average nucleosome repeat length NRL=184 bp, as opposed to 190 bp for H1.2-enriched regions. We have also studied the distribution of H1 variants with respect to DNA methylation. Most changes of DNA methylation during differentiation appear within ~60bp from the nucleosome entry/exit and are preferably associated with H1.2-bound nucleosomes, whereas H1.5 histones are depleted from CpGs. Our results suggest that different physical packing of nucleosomes may exist in H1.2- versus H1.5-enriched areas, characterized by differential H1 epitope exposure as assessed by xChIP and xxChIP.

overall_design: All ChIP-Seq experiments were performed on undifferentiated HL-60/S4 cells that were fixed, permeabilized and stored in cryovials (containing ~107 cells/cryovial) in liquid Nitrogen.  Cells had been harvested from growth medium at ~106 cells/ml, centrifuged and washed with PBS, fixed in 1% HCHO/PBS for 10 min at RT, stopped with 0.125 M glycine for 5 min, washed with PBS, followed by PBS + 0.1 M PMSF.  The fixed cells were permeabilized for 10 min at 4oC in a lysis buffer containing 25 mM HEPES buffer (pH 7.8), 1 mM MgCl2, 10mM KCl, 0.1% NP40, 1 mM DTT and 0.5 mM PMSF.  Following centrifugation and removal of supernatants, cell pellets were frozen in residual lysis buffer at liquid Nitrogen temperature. For both single-fixation and double-fixation ChIP (xChIP and xxChIP), chromatin was disrupted with a Covaris Focused Ultrasonicator M220.  In xChIP, each frozen cell pellet (1 cryovial) was dispersed in 130 µl of Covaris Sonication Buffer (1 mM EDTA, 10 mM Tris [pH 7.6], 0.1 % SDS), followed by sonication (20 min, 200 cycles, 75 Watts, Duty Cycle 20%, 7oC).  The sonicates were centrifuged at 18,000xg, 10 min, 40C and the supernatants recovered.  SDS was reduced in the supernatants to ~0.003% and replaced with 0.05% Tween-20, employing repeated dilution with PBST (PBS+0.05% Tween-20) and centrifugal concentration using a Centricon YM-50.  Six centrifugations of ~1/2 dilutions with PBST at 1000xg, 10 min resulted in ~0.5 ml of the final retentate with reduced SDS.  IgG-free BSA (Sigma A3294) was added to a final BSA concentration of 5%. In xxChIP, the once-fixed frozen cell pellets were dispersed in a buffer reminiscent of the permeabilizing buffer used in immunostaining reactions (0.1% Triton X-100, 0.1 mM PMSF plus Sigma Protease Inhibitor Cocktail [P8340]) for 20 min at RT.  After PBS washes, the permeabilized cells were suspended in PBST+5% IgG-free BSA (PBSTB) and rotated for 90 min at RT.  To 300 µl aliquots containing ~6x107 cells, the primary antibody was added: 30 µl anti-histone H1.2 (1 mg/ml) or 60 µl anti-histone H1.5 (0.5 mg/ml).  The cells plus antibody were rotated for 4 hours at RT.  Following antibody incubation, the cells were washed several times with PBS to remove unbound antibody.  They were made 1% HCHO/PBS for the second fixation and rotated 2.5 minutes at RT.  Fixation was stopped with 0.125 M glycine for 5 min, cells washed with PBS and dispersed in 1.0 ml of Covaris Sonication Buffer (1 mM EDTA, 10 mM Tris [pH 7.6], 0.1 % SDS), followed by sonication at optimized conditions (40 min, 400 cycles, 75 Watts, Duty Cycle 26%, 7oC).  The sonication buffer was replaced with PBST, employing centrifugal concentration, as described above. Of necessity, the immunoprecipitation (IP) protocols differed slightly, comparing xChIP to xxChIP.  The xChIP preparations in PBSTB buffer were incubated with control agarose (1 hour, with rotation) and recovered from the minicolumns by centrifugation at 4oC.  Samples of the “cleaned” sonicates were retained as “Input”.  Simultaneously, Protein A/G agarose minicolumns, equilibrated in PBSTB, were incubated 4-5 hours with 4 µg of rabbit anti-histone H1.2 or H1.5, rotating at RT, followed by washing with PBSTB.  The equilibrated and “cleaned” sonicates were incubated with the antibody-bound Protein A/G agarose minicolumns overnight, rotating at 4oC.  Subsequently, the sonicate-bound columns were washed 5 times with PBSTB and 2 times with PBST, to remove unbound chromatin.  Elution of the bound chromatin fragments was accomplished by addition of 50 µl of 100 mM NaHCO3 + 1% SDS, tumbling for 15 min at RT.  After centrifugal recovery, a second elution with 50 µl was performed, yielding ~100 µl of pooled eluate.  The IP eluates were digested with RNAse and proteinase K overnight at 65oC.  DNA was purified employing Sigma Gene Elute (NA1020-1KT).  By contrast, xxChIP preparations, having the anti-H1 antibodies already bound and crosslinked to the chromatin fragments and in PBSTB buffer, were “cleaned” on the control agarose minicolumns, an aliquot removed for “Input” and the remainder incubated with Protein A/G agarose minicolumns overnight, rotating at 4oC, followed by washing to remove unbound chromatin.  Elution of the bound chromatin fragments and DNA purification were similar to the xChIP procedures.

first: Travis

last: Gould

first: Christopher

last: Clarkson

first: Logan

last: Boyd

first: Naveed

last: Ishaque

first: Ada

last: Olins

first: Donald


title: Episignatures stratifying ADNP syndrome show modest correlation with phenotype [Methylation]

first: Michael

last: Breen

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

type: Methylation profiling by genome tiling array

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: Episignatures stratifying ADNP syndrome show modest correlation with phenotype

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

overall_design: Refer to individual Series


title: Analysis of exosomal miRNAs upon irradiation in pancreatic cancer cells

first: Ling

last: Tian

type: Non-coding RNA profiling by high throughput sequencing

summary: We used miRNA-seq and bioinformatics to analyze and annotate the expression profiles exosomal miRNAs in pancreatic cancer cells after radiation, compared with the unirradiated cells. A total of 481 miRNAs were identified, and 284 miRNAs were annotated in miRBase. There were 22 filtered differentially expressed miRNAs (9 for up-regulated and 13 for down-regulated, fold change > 2, p-value < 0.05). This study provides the results of exosomal miRNA change in pancreatic cancer cells after radiation.

overall_design: Examination of small RNA profiles of pancreatic cells-derived exosomes by NGS


title: Affymetrix CytoScan 750K data for validation of the BoBs/CNV-seq comparison study

status: Public on Jun 12 2020

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

summary: BACs-on-Beads (BoBs) assay and Copy Number Variation Sequencing (CNV-Seq) are two frequently used methods in today’s prenatal diagnosis. Several researches studies were conducted to investigate the performance of each approach, but they were never compared side by side. This dataset is intended to be used as the 'gold standard dataset' for the validation of BoBs/CNV-seq test reasults on 10 amniotic fluid samples with pathogenic fetal CNVs.

overall_design: CNV analysis using Affymetrix 750K  was performed on 10 samples to validate the results generated by BoBs assay and CNV-seq.

first: LiangPu

last: Xu

first: Chen


title: CD117hi expression identifies a human fetal hematopoietic stem cell population with high proliferation and self-renewal potential

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

summary:
We identified and characterized a CD34+CD38-CD45+CD117hi population of HSCs present all along human fetal liver development.
CD117hi (HSC) and CD117lo (HC) populations were sorted from first trimester (T1) and second trimester (T2) fetal livers to perform pair-wise comparison between HSCs and HCs.

overall_design: CD34+CD38-CD45+CD117hi (HSC) and CD34+CD38-CD45+CD117lo (HC) populations were sorted from T1 (n=4) and T2 (n=2) fetal livers and RNA was purified using RNeasy Plus Micro Kit (Qiagen). RNA concentration and integrity were evaluated with the Agilent Bioanalyzer 2100 and 2 ng of total RNA reverse transcribed following the Ovation Pico System V2 (Nugen). cDNA is then hybridized to GeneChip® HumanGene2.0ST (Affymetrix).

first: Michèle

last: Souyri

first: Loïc

last: Maillard

first: Sandra

last: Sanfilippo


title: Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase [RNA-Seq]

city: Dortmund

first: Richard

last: Cardoso da Silva

state: North Rhine Westfallen

department: Mechanistic Cell Biology

country: Germany

institute: Max Planck Institute of Mol Physiol

summary: Pch2 is an AAA+ protein that controls DNA break formation, recombination and checkpoint signaling during meiotic G2/prophase. Chromosomal association of Pch2 is linked to these processes, and several factors influence the association of Pch2 to euchromatin and the specialized chromatin of the ribosomal (r)DNA array of budding yeast. Here, we describe a comprehensive mapping of Pch2 localization across the budding yeast genome during meiotic G2/prophase. Within non-rDNA chromatin, Pch2 associates with a subset of actively RNA Polymerase II (RNAPII)-dependent transcribed genes. Chromatin immunoprecipitation (ChIP)- and microscopy-based analysis reveals that active transcription is required for chromosomal recruitment of Pch2. Similar to what was previously established for association of Pch2 with rDNA chromatin, we find that Orc1, a component of the Origin Recognition Complex (ORC), is required for the association of Pch2 to these euchromatic, transcribed regions, revealing a broad connection between chromosomal association of Pch2 and Orc1/ORC function. Ectopic mitotic expression is insufficient to drive recruitment of Pch2, despite the presence of active transcription and Orc1/ORC in mitotic cells. This suggests meiosis-specific ‘licensing’ of Pch2 recruitment to sites of transcription, and accordingly, we find that the synaptonemal complex (SC) component Zip1 is required for the recruitment of Pch2 to transcription-associated binding regions. Interestingly, Pch2 binding patterns are distinct from meiotic axis enrichment sites (as defined by Red1, Hop1 and Rec8). This suggests that although Pch2 is linked to axis/SC-directed recruitment and function, the chromosomal population of Pch2 described here is not directly associated with chromosomal axis sites. In line with this observation, interfering with the pool of Pch2 that associates with active RNAPII transcription does not lead to effects on the chromosomal abundance of Hop1, a known axial client of Pch2. We thus report characteristics and dependencies for Pch2 recruitment to meiotic chromosomes, and reveal an unexpected link between Pch2, SC formation, chromatin and active transcription.

overall_design: mRNA profile of yeast strains (ndt80 and ndt80pch2) undergoing meiosis (SPO medium) at 4h generated by deep sequencing in duplicate, using and Illumina HiSeq3000 instrument

last: da Silva

first: María

last: Villar-Fernández

first: Gerben

last: Vader


title: Gene expression changes following seviteronel (Sevi) treatment in HCI-009 PDXs

city: Aurora

first: Jessica

last: Christenson

state: CO

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: Triple-negative breast cancer (TNBC) is aggressive and difficult, and few targeted therapies are available to treat this patient population. The androgen receptor (AR) has emerged as a potential target in breast cancer. Newer generation AR inhibitors, such as Seviteronel (Sevi), are unique in their ability to inhibit AR both directly and by blocking upstream androgen synthesis. The purpose of this study was to investigate the pre-clinical activity of Sevi in TNBC and further explore the effectiveness of targeting both androgen biosynthesis and AR activity in combination with other downstream acting agents. AR overexpressing (AR+) TNBC cell lines, xenografts and androgen responsive patient-derived xenograft (PDX) models were using to show how effectively Sevi inhibits AR activity and cell/tumor proliferation. Single cell RNA-sequencing of the AR+ cell line MDA-MB-453 illustrated heterogeneity in AR levels and identified cell cycle pathway activation in ARHigh versus ARLow expressing cells. Combination treatment with the cell cycle CDK4/6 inhibitor abemaciclib and Sevi showed synergy in AR+ TNBC cells and increased effectiveness, compared to each drug alone, in an AR+ TNBC xenograft model. While cell cycle inhibitors have been approved for use in hormone-receptor positive breast cancer, our studies suggest that these drugs may be equally effective in AR+ TNBC cells, especially when combined with AR antagonists.    Implications. These data suggest that targeting AR signaling at multiple points throughout the pathway may be an effective was to treat patients with AR+ TNBC.

overall_design: HCI-009 is a TNBC PDX originally developed in the laboratory of Dr. Alana Whelm and propagated in immunodeficient NOD/SCID/gamma (NSG) mice. When tumors reached a size of approximately 100 mm3, mice were randomized and matched into treatment groups (n=4-5 mice per group). 150mg/kg/day Sevi was administered daily by oral gavage for 2 weeks.

first: Kathleen

middle: I

last: O'Neill

first: Michelle

middle: M

last: Williams

first: Nicole

last: Spoelstra

first: Kenneth

last: Jones

first: G

last: Trahan

first: Elaina

last: Van Patten

first: Joel

last: Eisner

first: Jennifer

middle: K

last: Richer


title: Regulons and protein–protein interactions of PRD-containing Bacillus anthracis virulence regulators reveal overlapping but distinct functions

status: Public on Jun 13 2020

city: Houston

first: Theresa

middle: Marie

last: Koehler

state: Texas

address: 6431 Fannin Street, MSB 1.508

department: Microbiology and Molecular Genetics

institute: McGovern Medical School

summary:
Purpose: Bacillus anthracis produces three regulators, AtxA, AcpA and AcpB, which control virulence gene transcription and belong to an emerging class of regulators termed ‘PCVRs’ (Phosphoenolpyruvate-dependent phosphotransferase regulation Domain-Containing Virulence Regulators). AtxA, named for its control of toxin gene expression, is the master virulence regulator and archetype PCVR. AcpA and AcpB are less well studied. Reports of PCVR activity suggest overlapping function. We used RNA-Seq to assess the regulons of the paralogous regulators in strains constructed to express individual PCVRs at native levels.
Methods: Cultures were incubated in toxin-inducing conditions, and expression of each PCVR in the atxAacpAacpB-null background strain was induced with an IPTG concentration that yielded native protein levels for each PCVR. RNA was extracted when cultures reached late-exponential phase using saturated acid phenol extraction, followed by RNA precipitation from the aqueous phase. Creation of libraries for NGS analysis used total RNA (1.0 μg). Samples were treated with Ribo-Zero (Epicentre) to remove ribosomal RNA prior to fragmentation using divalent cations and heat. Libraries were created using an Illumina TruSeq sample preparation kit following the protocol as recommended by the manufacturer. NGS sequencing was performed as a paired-end 50 base sequence using an Illumina HiSeq 1500 following the protocol recommended by the manufacturer.
Results: Plasmid and chromosome-borne genes were PCVR controlled, with AtxA, AcpA and AcpB having a ≥4-fold effect on transcript levels of 145, 130 and 49 genes respectively. Several genes were coregulated by two or three PCVRs. Of the 203 transcripts associated with pXO1, 15 were altered at least fourfold: 13 by AtxA and 2 by AcpA. No pXO1-derived transcripts were affected fourfold or greater by AcpB. Read maps revealed that many of the regulated transcripts from pXO1 were associated with the 35 kb region that lies within a larger 44.8 kb pathogenicity island (PAI) (Thorne, 1993). We detected transcripts for 110 genes on pXO2, of which 21 were regulated fourfold or greater by at least one of the three PCVRs. The highly regulated genes clustered within a 35.5 kb region of the plasmid, which includes the capsule biosynthetic operon capBCADE followed by the weakly co-transcribed acpB gene. A significantly smaller proportion of PCVR-regulated genes mapped to the chromosome. Of the 5593 transcripts, 198 were altered fourfold or greater by one or more PCVRs. Clustering of PCVR-regulated chromosome genes was not apparent. Among the most highly regulated chromosomal genes were many genes associated with branched chain amino acid (BCAA) synthesis and uptake. Of the 17 genes implicated in BCAA biosynthesis, expression of 13 of these genes is repressed by AtxA and AcpB. In this work, we have shown that the three PRD-containing virulence regulators of B. anthracis exhibit overlapping and divergent target gene specificities.
Conclusions: In this work, we show the relative activities of the PCVRs for specific and co-regulated genes. The results reveal the vast effects of the PCVRs on B. anthracis gene expression and indicate a high degree of functional similarity among the regulators. Our investigations provide insight into control of B. anthracis gene expression and expand our knowledge of structure and function of this emerging class of virulence gene regulators.

overall_design: We employed RNA-Seq to determine the independent functions of AtxA, AcpA and AcpB on the complete B. anthracis genome. We created an atxAacpAacpB-null mutant from the clinical pXO1+  pXO2+  Ames strain. Using the triple-null mutant as the background strain, we constructed strains carrying the individual PCVR-encoding genes in trans under the control of an IPTG-inducible promoter. We induced the expression of individual regulators and we employed RNA-Seq to determine regulons.

first: Malik

last: Raynor


title: AR heterogeneity in TNBC MDA-MB-453 cells

overall_design: TNBC androgen receptor (AR)-positive MDA-MB-453 cells were sequenced by single cell RNAseq to examine cell line heterogeneity, in particular differences in AR expression and genes associated with different levels of AR

middle: L

middle: R


title: Differentially expressed genes between the R-spodin2-overexpressing Huh-7 cell line and its negative control

city: Nanjing

first: CHANG

last: ZHENG

address: 22 Hankou Road

institute: Nanjing University

summary: To identify additional R-spodin2 target genes and the mechanisms behind its tumor-suppressive effect, we performed global microarray analysis of mRNA expression in a R-spodin2-overexpressing Huh-7 cell line and a negative control

overall_design: mRNAs in R-spodin2-overexpressing Huh7 cell line (n=2) and its negative control (n=2) by microarray using Agilent human 44k mRNA Microarray

first: Chang

last: Zheng

first: Fan

last: Zhou

first: Liang

last: Shi

first: Gui

middle: F

last: Xu

first: Bin

last: Zhang

first: Lei

last: Wang

first: Yu

middle: Z

last: Ge

first: Xiao

last: Zou

first: Yi


title: Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina

city: Dusseldorf

first: Anna

last: Sergeeva

address: Universitaetsstrasse 1

department: Institute of Botany

institute: Heinrich Heine University

summary: Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone ehxibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth.

overall_design: For mRNA profiling, 12 pep1-1 plants were grown per biological replicate. Three biological replicates were used for each examined sampling stage. Four different developmental stages were examined. Perennial stem samples were harvested from stages I_PZ (4 weeks old), II_PZ (5 weeks old), III_PZ (7 weeks old) and IV_PZ (30 weeks old). In addition, annual stem samples were harvested from 30 weeks old plants, termed IV_AZ_si and IV_AZ_if.

first: Petra

last: Bauer

first: Hans-Jörg

last: Mai


title: Pathogenesis of influenza A(H7N9) virus in aged non-human primates

city: Tokyo

first: Yoshihiro

last: Kawaoka

address: 4-6-1, Shirokanedai, Minato-ku

department: Department  of  Microbiology  and  Immunology

country: Japan

institute: University of Tokyo

summary: The avian influenza A(H7N9) virus has caused high mortality in humans, especially in the elderly; however, little is known about the mechanistic basis for this. In this study, we employed non-human primates to evaluate the effect of aging on the pathogenicity of A(H7N9) virus. We observed that A(H7N9) virus infection of aged animals (defined as 20–26 years) caused more severe symptoms than infection of young animals (defined as 2 3 years). In aged animals, lung inflammation was weak and virus infection was sustained. Although cytokine and chemokine expression in the lungs of most aged animals was lower than that in the lungs of young animals, one aged animal showed dysregulated proinflammatory cytokine and chemokine production, resulting in it being euthanized. These results suggest that attenuated or dysregulated immune responses in aged animals are responsible for the severe symptoms observed among elderly patients infected with A(H7N9) virus.

overall_design: Total RNA was extracted from lung samples and blood by using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. RNA was labeledwith Cy3 dye with the QuickAmplabelingkit(Agilent Technologies), and hybridized to the Rhesus Macaque Gene Expression Microarray (Agilent Microarray Design Identification Number 026806; Agilent Technologies), as previously described [22]. Individual microarrays were performed for each lung sample that was collected from naïve and infected animals. Statistical analysis was performed using the LIMMA package. The log2of the intensity of each probe was background corrected and normalized between arrays (using the quantile method). Duplicate probes were averaged.

first: Satoshi

last: Fukuyama

first: Kiyoko

last: Iwatsuki-Horimoto

first: Maki

last: Kiso

first: Noriko

last: Nakajima

first: Robert

middle: W

last: Gregg

first: Hiroaki

last: Katsura

first: Yuriko

last: Tomita

first: Tadashi

last: Maemura

first: Tiago

last: da Silva Lopes

first: Tokiko

last: Watanabe

first: Jason

middle: E

last: Shoemaker

first: Hideki

last: Hasegawa

first: Seiya

last: Yamayoshi


title: Expression data of miRNAs extracted from plasma [Affymetrix miRNA4.0]

city: nanjing

first: yu

last: chen

address: 264, Guangzhou Road

department: Department of Psychiatry

institute: The Affiliated Brain Hospital of Nanjing Medical University

summary: The symptoms of bipolar depression (BD) overlapping with unipolar depression (UD) makes it difficult to perform an accurate diagnosis. We aimed to investigate the potential of plasma miRNAs to distinguish BD from UD. In this study, we used the Affymetrix Genechip miRNA 4.0 Array to investigate the profiles of differentially expressed miRNAs (DEMs) in peripheral blood plasma. As a result, forty-two DEMs (17 with downregulation and 25 with upregulation) between UD and BD patients.

overall_design: Peripheral blood samples of 7 UD patients, 7 BD patients and 6 healthy individuals were collected fore the miRNA extraction and hybridization on Affymetrix microarrays. UD patients'code numbers include:825,835,849,541,516,456,628.BD patients'code numbers include:530,452,629,845,853,956,972.Meanwhile the healthy controls were coded as:704,613,577,568,566,564.

first: Yu

last: Chen


title: Exosomal miRNA sequencing of UVB-irradiated melanocytes and non-irradiated melanocytes

city: Hangzhou

first: Zeren

last: Shen

address: No. 79 Qingchun Road

institute: The First Affiliated Hospital, School of Medicine, Zhejiang University

summary: We report the exosomal miRNA expression profile of melanocytes with or without UVB treatment by miRNA sequencing.

overall_design: Examination of 2 different miRNome profiling in melanocytes.

first: Jiaqi

last: Sun

first: Jinghong

last: Xu


title: Inheritance Patterns of Leukocyte Gene Expression Under Heat Stress in F1 Hybrids Cattle and Their Parents

city: 重庆

first: Gongwei

last: zhang

address: 重庆市荣昌区学院路160号

institute: 西南大学

summary: This study aimed to investigate the heat tolerance and inheritance patterns of leukocyte transcriptomics in F1 hybrid cattle (AN♂ × DR♀) and their parents Red Angus (AN) and Droughtmaster (DR) under heat stress.

overall_design: Leukocyte transcriptomics in F1 hybrid cattle and their parents.

first: Gong

last: Zhang

first: Ling

last: Wang

first: Fuyuan

last: Zuo


title: Gene expression profile of TPT1  gene knock downed  human ES-NSC

city: Shinanomachi,Shinjukuku

first: Shigeki

last: Ohta

state: Tokyo

institute: Keio University

summary: To evaluate the function of TPT1 in human ES-derived neural stem cells (ES-NSCs), we knock downed TPT1 gene expression based on the lentivirus system expressing shTPT1 RNA with control. We isolated RNA from ES-NSCs 2 days after infection and subjected to RNA-seq analysis. In silico data analysis supported the function of TPT1 related to cell cycle regulation, consistent with in vitro experimental results.

overall_design: Examination of gene expression profile of  TPT1  gene knock downed  human ES-NSC


title: RNA-Sequencing Reveals the Changes of Gene Expression Profile in the Lipopolysaccharide-induced Immunoresponsed Uterine Body after the Immunosuppressant Cyclosporine A-treatment

city: Chengdu

last: xu

state: Sichuan

address: No. 211 Huimin road

department: College of animal science and technology

institute: Sichuan Agricultural University

summary: Infection of Gram-negative bacteria in female genital tract causes systematic immune-response and reproductive dysfunction. Immunosuppressor Cyclosporine A (CsA) is widely used in the treatment of genital tract immune response, however, the knowledge on the changes of transcriptome after CsA inhibiting lipopolysaccharide (LPS)-induced immune response still remains unknown.

overall_design: Twelve New Zealand white rabbits (n=12) were randomly divided into 4 groups. The rabbits in the control group were treated with normal saline, and CsA solvent was intramuscularly injected. The rabbits from LPS group were treated with LPS by intrauterine infusion, and 500 μL of CsA solvent was intramuscularly injected. In the CsA treatment group, the uterus was perfused with normal saline, intramuscularly injected with CsA; The rabbits of LPS and CsA co-treatment group (LPS+CsA) were treated with LPS by intrauterine infusion and CsA by intramuscular injection. After 3 hours of treatment, collect uterine body tissue, that subsequently rapidly frozen by liquid nitrogen and then stored at -80℃.

first: Yan

last: Zeng

first: Mutian

first: Yutian

first: Guangbin

last: Zhou

first: Changjun

first: Tianzhen

last: Song

first: Zuo

last: Zhicai

first: Ming


title: miRNA sequencing of  islet-drived exosomes  in HFD mice

first: Yi

address: Tianyuandong Road 818

institute: Nanjing medical university

summary: After isolation, islets were cultured in a serum-exosomes-free culture media for one week. Collected culture media were centrifuged first at 300g for 20 min to pellets cells and then at 10000g for 20 min to discard dead cells and cell debris. Exosomes were then isolated from the supernatant by ultracentrifugation at 110000g for 70 min. Exosomes were collected in a minimal volume of PBS,and added three times the volume of Trizol LS to extract exosomes RNA.

overall_design: miRNA profiles of islet-drived exosomes

first: Yunxia

last: Zhu

first: Xiao

last: Han


title: Identification of Lead Drug Candidates for COVID-19 based on Drug Screening Using Human Pluripotent Stem Cell-Derived Cells/Organoids

city: New York

first: David

last: Redmond

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary: We systematically probed which cell types are permissive to SARS-CoV-2 infection. Transcriptomic analysis following SARS-CoV-2 infection of hPSC-derived pancreatic and lung organoids revealed upregulation of chemokines but not type I/III interferon signaling, similar to what was seen in primary human COVID-19 pulmonary infection.

overall_design: Transcriptomic analysis of stem cell derived liver and pancreas organoids

first: Robert

last: Schwartz

first: Shuibing

first: Huanhuan

middle: J

first: Benjamin

last: tenOever


title: Transcriptomic signatures of spleen and liver CD4+ T cells from Leishmania donovani-infected C57BL/6J mice

city: Herston

first: Susanna

last: Ng

state: QLD

address: 300 Herston Road

department: Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

summary: This study was designed to investigate tissue-specific transcriptional changes in spleen and liver CD4+ T cells from C57BL/6J mice infected with L. donovani.

overall_design: A microarray was performed on RNA extracted from spleen and liver CD4+ T cells from naïve (n = 4 or 5) or L. donovani-infected (day 56; n = 5) C57BL/6J mice. Each naïve liver CD4+ T cell replicate consists of 5 mice, pooled.

first: Christian

last: Engwerda

middle: S


title: Conformation of sister chromatids in the replicated human genome

city: Vienna

first: Michael

last: Mitter

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

summary: The three-dimensional organization of the genome supports regulated gene expression, recombination, DNA repair, and chromosome segregation during mitosis. Chromosome conformation capture (Hi-C) has revealed a complex genomic landscape of internal chromosome structures in vertebrate cells yet how sister chromatids topologically interact in replicated chromosomes has remained elusive due to their identical sequences. Here, we present sister-chromatid-sensitive Hi-C (scsHi-C) based on nascent DNA labeling with 4-thio-thymidine. Genome-wide conformation maps of human chromosomes revealed that sister chromatid pairs interact most frequently at the boundaries of topologically associating domains (TADs). Continuous loading of a dynamic cohesin pool separates sister-chromatid pairs inside TADs and is required to focus sister chromatid contacts at TAD boundaries. We identified a subset of TADs that are overall highly paired, characterized by facultative heterochromatin, as well as insulated topological domains that form separately within individual sister chromatids. The rich pattern of sister chromatid topologies and our scsHi-C technology will make it possible to dissect how physical interactions between identical DNA molecules contribute to DNA repair, gene expression, chromosome segregation, and potentially other biological processes.

overall_design: Sister-chromatid sensitive Hi-C (scsHi-C) Method validation using DNAseq and analysis of chromatin structure by scsHi-C with and without protein depletion using the auxin-inducible degron (AID) systems.

first: Christoph

middle: C

last: Langer


title: Surfactant protein A (SP-A) variants and sex-specific regulation of gene expression networks in alveolar macrophages in response to Klebsiella pneumoniae-induced lung infection

city: hershey

first: Nithyananda

last: Thorenoor

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

summary: Surfactant protein A (SP-A) in addition to its surfactant-related functions interacts with alveolar macrophages (AM), the guardian cells of innate immunity, and regulates many of its functions under basal condition and in response to various insults, such as infection and oxidative stress. The human SP-A locus consists of two functional genes, SFTPA1 and SFTPA2, and one pseudogene.  The functional genes encode human SP-A1 and SP-A2 proteins, respectively, and each has been shown to have several genetic variants.  It has been shown that SP-A variants differ in their ability to regulate lung function mechanics and survival in response to bacterial infection.  Here, we investigated the effect of hSP-A variants on the AM gene expression profile in response to K. pneumoniae (Kp) infection.  We used four humanized transgenic (hTG) mice that each carried SP-A1 (6A2, 6A4) or SP-A2 (1A0, 1A3), and KO.  The gene expression profiling of AM was performed after 6 h post-infection.  We found: a) significant sex differences in the expression of AM genes between males and females; b) in response to infection, 858 (KO), 196 (6A2), 494 (6A4), 276 (1A0) and 397 (1A3) genes were identified (P < 0.05) and some of these were differentially expressed with ≥ 2 fold, specific to either males or females; c) significant gene-specific differences between the SP-A1 and SP-A2 variants; d) via Ingenuity Pathway Analysis (IPA) key pathways and molecules were identified that had direct interaction with TP53, TNF, and cell cycle signaling nodes; e) validation of key molecules exhibited significant differences in the expression between males and females; f) IPA for SP-A1 and SP-A2 variants and KO revealed, top diseases and bio-functions for males and females that contained a high number of genes involved in the inflammatory response, immunological disease, infectious diseases, respiratory diseases, cancer, and others.  These results reveal for the first time a large number of biologically relevant functional pathways influenced by sex and SP-A variant in response to K. pneumoniae infection.  These data may assist in studying molecular mechanisms of SP-A-mediated AM gene regulation and potentially identify novel therapeutic targets for K. pneumoniae infection.

overall_design: Humanized transgenic (hTG) mice that carried SP-A1 (6A2, 6A4), SP-A2 (1A0, 1A3) variant,  as well as SP-A knockout (KO) mice were used in this study.  They were 12 weeks old.  hTG mice were generated on the C57BL/6J SP-A (KO) background. The animals were exposed  to K. peumoniae for 6hrs.  A group of 4 animals (males, females) were exposed and alveolar macrophages (AM) were isolated after 6 h of recovery. Total RNA was extracted, RNA-seq libraries were generated followed by deep sequencing  to identiy mRNA expression. The differentially expressed miRNAs (DEG) between males and females were identified by using the edgeR and the TCC v1.14.0 R package  with false discovery rate (FDR) adjusted p value of 0.1 as a significance cutoff.

first: Joanna

last: Floros


title: Inhibition of BET proteins rescues neural defects in Rett syndrome [DNA methylation profile]

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

summary: Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder caused by mutations in the methyl-CpG binding protein 2 (MeCP2). Cellular heterogeneity in the brain confounds the understanding of RTT etiology. To date, how MeCP2 mutation affects defined cell types in human brain remains unclear, and effective therapeutics for RTT is lacking. Here we show that cell-type-specific transcriptome impairment and JQ1-mediated rescue in RTT cells from dorsal and ventral human forebrain organoids. We find that MeCP2 mutation severely impairs human cortical interneurons (INs). Dysregulation of MeCP2-BRD4 ChIP regulatory axis and three-dimensional genome architecture are critically involved in the abnormal transcription in RTT INs, and JQ1 strongly rescues RTT INs by resetting the aberrant chromatin binding of BRD4 ChIP. Finally, JQ1 alleviates RTT-like phenotypes in mice. These data demonstrate that BRD4 ChIP dysregulation is a critical driver for RTT etiology and targeting BRD4 ChIP is an effective therapeutic opportunity for RTT.

overall_design: DNA methylation profiles were generated by Reduced representation bisulfite sequencing (RRBS).

first: Yangfei

last: Xiang

first: Eriona

last: Hysolli

first: In-Hyun

last: Park


title: Discovery of CD80 and CD86 as recent activation markers on regulatory T cells by protein-RNA single-cell analysis

city: Oxford

first: Dominik

last: Trzupek

address: Roosevelt Drive

department: Wellcome Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre

institute: University of Oxford

summary:
Background: Traditionally, the transcriptomic and proteomic characterisation of CD4+ T cells at the single-cell level has been performed by two largely exclusive types of technologies: single-cell RNA-sequencing (scRNA-seq) and antibody-based cytometry. Here we present a multi-omics approach allowing the simultaneous targeted quantification of mRNA and protein expression in single-cells and investigate its performance to dissect the heterogeneity of human immune cell populations.
Methods: We have quantified the single-cell expression of 397 genes at the mRNA level and up to 68 proteins using oligo-conjugated antibodies (AbSeq) in 43,656 primary CD4+ T cells isolated from blood and 31,907 CD45+ cells isolated from blood and matched duodenal biopsies. We explored the sensitivity of this targeted scRNA-seq approach to dissect the heterogeneity of human immune cell populations and identify trajectories of functional T-cell differentiation.
Results: We provide a high-resolution map of human primary CD4+ T cells, and identify precise trajectories of Th1, Th17 and regulatory T-cell (Treg) differentiation in blood and tissue. The sensitivity provided by this multi-omics approach identified the expression of the B7 molecules CD80 and CD86 on the surface of CD4+ Tregs, and we further demonstrated that B7 expression has the potential to identify recently activated T cells in circulation. Moreover, we identified a rare subset of CCR9+ T cells in blood with gut-homing properties and expression of several immunomodulatory receptors, suggestive of a regulatory function at barrier sites.
Conclusions: This transcriptomic and proteomic hybrid technology provides a cost-effective solution to dissect the heterogeneity of immune cell populations, including more precise and detailed descriptions of the differentiation and activation of circulating and tissue-resident cells in response to therapies and in stratification of patients.

overall_design: Multi-omics characterisation of primary human CD4+ T cells (3 donors; resting and stimulated samples) and CD45+ cells (2 donors; paired blood and duodenal biopsies) by targeted scRNA-sequencing (BD Rhapsody and AbSeq)

first: Linda

last: Wicker

first: John

middle: A

last: Todd

first: Ricardo

last: Ferreira


title: PRMT1 differentially regulates gene expression in T47D-breast cancer cells

city: LYON 3EME ARRONDISSEMENT

first: Lucie

last: Malbeteau

address: 28 rue Laennec

department: Cancer Cell Plasticity

institute: Cancer Research Center of Lyon

summary: Using a genome-wide analysis, we demonstrated that PRMT1 is selectively required for progesterone-regulated expression of PR target genes, implicated in cell proliferation and migration.

overall_design: We examined whether PRMT1 is required for progesterone-induced expression of genes, by depleting PRMT1 in T47D breast cancer cells, using siRNA. We examined gene expression changes at 6 hours progesterone (R5020) treatment compared with ethanol treatment as a control. siRNA for a nonspecific sequence (siCT) followed by 6h of R5020 treatment was performed as control.

first: Coralie

last: Poulard

first: Laura

last: Corbo


title: Selective inhibition of HDAC3 targets synthetic vulnerabilities and activates immune surveillance in lymphoma

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: CREBBP mutations are highly recurrent in B-cell lymphomas and either inactivate its histone acetyltransferase (HAT) domain or truncate the protein. Herein, we show that these two classes of mutations yield different degrees of disruption of the epigenome, with HAT mutations being more severe and associated with inferior clinical outcome. Genes perturbed by CREBBP mutation are direct targets of the BCL6/HDAC3 onco-repressor complex. Accordingly, we show that HDAC3 selective inhibitors reverse CREBBP mutant aberrant epigenetic programming resulting in: a) growth inhibition of lymphoma cells through induction of BCL6 target genes such as CDKN1A and b) restoration of immune surveillance due to induction of BCL6-repressed IFN pathway and antigen presentation genes. By reactivating these genes, exposure to HDAC3-i restored the ability of tumor infiltrating lymphocytes to kill DLBCL cells in an MHC II and MHC I dependent manner, and synergized with PD-L1 blockade in a syngeneic model in vivo. Hence HDAC3-i represents a novel mechanism-based immune-epigenetic therapy for CREBBP mutant lymphomas.

overall_design:
Lymphoma B cell lines transfected with CRISPR gRNAs to induce CREBBP mutation
KDAC001 is an HDAC3 inhibitor.
KDAC005 is the control compound.

first: Patrizia

last: Mondello

first: Ari

last: Melnick

last: Green


title: Transcriptional signature of CD4+ T cells from visceral leishmaniasis patients

first: Susanna

last: Ng

summary: This study was designed to invesitgate changes in the transcriptional changes in CD4+ T cells from visceral leishmaniasis patients infected with L. donovani.

overall_design: Bulk RNA-sequencing was performed on CD4+ T cells isolated from the blood of visceral leishmaniasis patients (n = 11) upon presentation to the clinic (day 0), and 30 days after treatment with Ambisome (day 30). Day 0 and day 30 samples are paired.

first: Christian

last: Engwerda

first: Shyam

last: Sundar


title: Granulin expression effect on day 1 adults

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

summary: Analysis of day 1 adult animals expressing granulins 1, 2 and 3 in a progranulin null background. Results provide insight into a role for granulins in lysosome function and protein homeostasis.

overall_design: Total RNA was extracted from day 1 adults of the following strains: wildtype (N2E), pgrn-1(-), pgrn-1(-); granulin1(+); pgrn-1(-); granulin2(+) and pgrn-1(-); granulin3(+). Total RNA transcriptome from these samples was profiled by RNA seq.

first: Victoria

last: Butler

first: Fuying

last: Gao

last: Corrales

first: Wilian

last: Cortopassi

first: Benjamin

last: Caballero

first: Mihir

last: Vohra

first: Kaveh

last: Ashrafi

first: Ana

last: Cuervo

first: Matthew

last: Jacobson

first: Aimee

last: Kao


title: Single-cell RNA sequencing of human, macaque, and mouse testes uncovers primate-specific features of spermatogenesis

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

summary: Spermatogenesis is a highly regulated process that produces sperm which faithfully transmits genetic information to the next generation. Although extensively studied in mice, our current understanding of human and macaque spermatogenes is limited to known populations defined by state-specific markers developed from rodent data. As between-species differences have been reported in the process duration and cellular differentiation hierarchy, it remains unclear how molecular markersand cell states are conserved or have diverged from mice toman. To address this challenge, we employ single-cell RNA sequencing to identify transcriptional signatures of major germ and somatic cell-types of the testes in both human and macaques, and compared these data with mouse to characterize conserved and divergent features. This approach reveals differences in gene regulation throughout spermatogenesis, including differences in the stem/progenitor pool of spermatogonia, the expression timing of classical markers of differentiation, potential regulators of meiosis, the kinetics of RNA turnover during sperm maturation, and germ cell-soma communication. These datasets provide a rich foundation for future targeted mechanistic studies of germ cell development and in vitro gametogenesis.

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Drop-seq of cryopreserved adult human and macaque testes.

first: Saher

last: Hammoud


title: RNA-seq analysis of murine microglial BV2 cells treated with interferon-gamma (IFNγ)

city: St. Louis

first: Anthony

last: Orvedahl

state: Missouri

address: 425 S. Euclid Ave

institute: Washington University School of Medicine

summary: BV2 cells were treated with IFNγ. Wildtype cells were compared to cells made deficient for Atg5 via CRISPR/Cas9.

overall_design: Independent biological replicates for each condition were pooled in a single library.

first: Michael

last: McAllaster

first: Amy

last: Sansone

first: Bria

last: Dunlap

first: Chandni

last: Desai

first: Ya-Ting

last: Wang

first: Dale

last: Balce

first: Cliff

last: Luke

first: Sanghyun

last: Lee

first: Robert

last: Orchard

first: Maxim

middle: N

last: Artyomov

first: Scott

last: Handley

first: John

middle: G

last: Doench

first: Gary

last: Silverman

first: Herbert

last: Virgin


title: Inhibition of BET proteins rescues neural defects in Rett syndrome [RNA-seq]

first: Yoshiaki

last: Tanaka

department: Medicine

overall_design: RNA-seq were generated by deep sequencing

first: Yangfei

last: Xiang

first: In-Hyun

last: Park


title: Inhibition of BET proteins rescues neural defects in Rett syndrome [ChIP-seq]

overall_design: CTCF ChIP, BRD4 ChIP and MECP2 binding peaks were generated by deep sequencing


title: Inhibition of BET proteins rescues neural defects in Rett syndrome

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

overall_design: Refer to individual Series


title: Inhibition of BET proteins rescues neural defects in Rett syndrome [HiC-seq]

overall_design: 3D chromation interaction profiles were generated by deep sequencing

first: Benjamin

last: Patterson


title: Inhibition of BET proteins rescues neural defects in Rett syndrome [ATAC-seq]

overall_design: Open chromatin profile were generated by deep sequencing


title: R-loops Function as a Balance during Somatic Cell Reprogramming

city: Guangzhou

first: Yaoyi

last: Li

state: Guangdong province

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou National Laboratory

summary: R-loop induces genome instability and regulates gene expression. However, regulatory mechanism of R-loop in stem cell biology remains unclear. Here, we mapped the profiling of R-loops during reprogramming process and revealed that R-loops change prior to gene expression and are mainly accumulated and enriched at terminator of genes. Disrupting homeostasis of R-loops via RNaseH1 loss-of-function blocks reprogramming in a medium independent manner. Interestingly, Sox2 but not other Yamanaka factors overcomes the inhibitory effects of RNaseH1 loss on reprogramming. Sox2 forms a complex with Ddx5 and R-loop in cells and common targets for Sox2 and Ddx5 at R-loops are mainly associated with pluripotent genes. Furthermore, Sox2 inhibits the resolving activity of RNA helicase Ddx5 at R-loops to facilitate reprogramming. Together, these results indicate that the importance of R-loops balance for reprogramming and shed light on the regulation Sox2/Ddx5 on R-loops during reprogramming.

overall_design: Gene expression profiling of reprogrammed cells with OSKM at different time points. Gene expression profiling of reprogrammed cells with OSKM plus control/RNaseH1/RNaseH1(D209N) at different time points. R-loops mapping of reprogrammed cells with OSKM at different time points. R-loops mapping of reprogrammed cells with OSKM plus control/RNaseH1/RNaseH1(D209N) at different time points. Chromatin accessibility analysis of reprogrammed cells with OSKM plus control/RNaseH1/RNaseH1(D209N) at different time points. CLIP-seq to identify Ddx5-associated RNAs.

first: Wei

last: Xu

first: Yawei

last: Song

first: Qin

first: Kuan

first: Qianwen

last: Sun

first: Hongjie

last: Yao


title: Role of myelin-derived antigens in pain: a female connection

city: La Jolla

first: Andrei

last: Chernov

address: 9500 Gilman Dr

department: Anesthesiology

institute: University of California San Diego

summary: Intrasciatic injections of the MBP84-104-WT (wild type) peptide, MBP84-104-SCR (scramble) peptide and PBS carrier were conducted in female and male mice (n=6). In 7 days after the intrasciatic injection the specimens of sciatic nerves (SN), dorsal root ganglia (DRG) and dorsal spinal cord (DSC) were collected and the RNA-seq was conducted.

overall_design: Examination of gene expression in rodent peripheral and central nervous systems stimulated by myelin basic protein (MBP) fragment

middle: V

first: Alex

middle: Y

last: Strongin

first: Veronica

last: Shubayev


title: Inhibition of BET proteins rescues neural defects in Rett syndrome [scRNA-seq]

summary: Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder caused by mutations in the methyl-CpG binding protein 2 (MeCP2). Cellular heterogeneity in the brain confounds the understanding of RTT etiology. To date, how MeCP2 mutation affects defined cell types in human brain remains unclear, and effective therapeutics for RTT is lacking. Here we show that cell-type-specific transcriptome impairment and JQ1-mediated rescue in RTT cells from dorsal and ventral human forebrain organoids. We find that MeCP2 mutation severely impairs human cortical interneurons (INs). Dysregulation of MeCP2-BRD4 regulatory axis and three-dimensional genome architecture are critically involved in the abnormal transcription in RTT INs, and JQ1 strongly rescues RTT INs by resetting the aberrant chromatin binding of BRD4. Finally, JQ1 alleviates RTT-like phenotypes in mice. These data demonstrate that BRD4 dysregulation is a critical driver for RTT etiology and targeting BRD4 is an effective therapeutic opportunity for RTT.

overall_design: mRNA profiles of drug-treated hMGEOs and hCOs with single-cell level were generated by deep sequencing


title: Transcriptomic comparative analysis of uninfected and L. amazonensis-infected Bone Marrow-Derived Dendritic Cells

status: Public on Jun 11 2020

city: Paris

first: Hugo

last: Varet

address: 28 rue du Docteur Roux

institute: Institut Pasteur

summary: To determine the modulation of gene expression of mouse BMDCs in the presence of living intracellular Leishmania amazonensis amastigotes at 24 hr post infection.

overall_design: Dendritic cells were generated in vitro from bone marrow progenitors. Leishmania amazonensis amastigotes were purified from mouse cutaneous lesions and were added to DC cultures. After 24h, and following a sorting procedure using the FacsAria, only BMDCs housing living amastigotes were selected for total RNA extraction based on the expression of MHC class II (host cell) and DsRed2 (parasites) molecules. Transcriptome profiling was carried out using a one-color hybridization setting on Affymetrix GeneChip mouse genome 430 2.0 arrays.

first: Hervé

last: LECOEUR

first: Thibault

last: ROSAZZA

first: Kossiwa

last: KOKOU

first: Jean-Yves

last: COPPEE

last: VARET

first: Arezou

last: LARI

first: Pierre-Henri

last: COMMERE

first: Robert

last: WEIL

first: GuangXun

last: MENG

first: Geneviève

last: MILON

first: Gerald

last: SPÄTH

first: Eric

last: PRINA


title: Integrated Analysis of mRNA-seq and miRNA-seq to Identify c-MYC, YAP1 and miR-3960 as Major Players in the Anticancer Effects of Caffeic Acid Phenethyl ester in Human Small Cell Lung Cancer Cell Line

first: Ya

last: Luo

address: 17, 3rd Section, Renmin South Road

institute: Sichuan University

summary: Small-cell lung cancer H446 cells were treated with CAPE. The regulation mediated by miR-3960 after CAPE treatment was explored and the altered signaling pathways were predicted in a bioinformatics analysis.CAPE decreased the expression of yes-associated protein 1 (YAP1) and cellular myelocytomatosis oncogene (c-MYC) protein. Moreover, the upregulation of miR-3960 by CAPE contributed to CAPE-induced apoptosis. The knockdown of miR-3960 decreased the CAPE-induced apoptosis.

overall_design: H446 cells were harvested for RNA extraction after 8 h of CAPE treatment at a concentration of 40 µM. The cells incubated with the same volume of DMSO as the CAPE (40 μM)-treated group were used as the control. There are three samples in CAPE-untreated and treated groups.

first: Fei

last: Mo

first: Dian

last: Fan

first: Hao

last: Zeng

first: Jinen

last: Song

first: Yunuo

last: Zhao

first: Meng

first: Xuelei

last: Ma


title: Myocardial Infarction accelerates breast cancer progression via innate immune reprogramming (RNA-seq: sham vs LAD ligation)

first: Emily

last: Brown

state: NY

address: 435 E 30th St

institute: NYU Langone

summary: Breast cancer patients have increased risk of myocardial infarction (MI), but whether these events impact cancer pathogenesis is not known.  In mouse models of breast cancer, MI increased circulating Ly6Chigh monocytes and their recruitment to tumors, accelerating cancer progression and metastasis. Analysis of the bone marrow reservoir revealed that MI epigenetically reprogrammed Ly6Chigh monocytes to an immunosuppressive phenotype that was maintained in monocytes in the circulation and tumor at the transcriptional level.  Depletion of Ly6Chigh monocytes abrogated MI-induced cancer progression and increased activated cytotoxic T cells in the tumor.  In early-stage breast cancer patients, post-diagnosis incident cardiovascular events, such as MI, increased the risk of recurrence and cancer-specific mortality, highlighting the clinical relevance of our findings. Collectively, our results indicate that MI induces cross-disease communication that accelerates breast cancer progression.

overall_design: Bulk RNA sequencing of five sham samples and 3 LAD ligation samples. Bone marrow monocytes were isloated from mice 9 days following LAD ligation or sham surgery.

first: Graeme

last: Koelwyn

first: Emma

middle: M

last: Corr

first: Coen

last: van Solingen

first: Kathleen

middle: B

last: Albers

first: Milessa

last: Afonso

first: P

last: Schlegel

first: Monika

last: Sharma

first: Lianne

last: Shanley

first: Tessa

last: Barrett

first: Karishma

last: Rahman

first: Valeria

last: Mezzano

first: Edward

last: Fisher

first: Jonathan

middle: D

last: Newman

first: Daniela

last: Quail

first: Erik

last: Nelson

first: Bette

last: Caan

first: Lee

last: Jones

first: Kathryn

last: Moore


title: Chromatin landscape changes of regenerating wing imaginal discs

city: Tempe

first: Robin

last: Harris

state: AZ

address: 427 E Tyler Mall LSE 229

department: School of Life Sciences

institute: Arizona State University

summary: We report the changes in chromatin accessibility associated with regeneration in wing imaginal discs at two developmental timepoints during L3. Wing discs were ablated using tissue-specific expression of the pro-apoptotic gene eiger at an early timepoint (day 7) when the discs retain high regenerative capacity and at a late time point (day 9) when regenerative capacity has significantly declined. ATAC-seq was performed on these discs after 40 hr of ablation and compared to identically staged unablated discs. We detect 14,142 open chromatin peaks after merging overlapping peaks from 3 biological repeats of all 4 conditions. Of these, 349 change significantly (log2fc>0.5, p<0.1) either opening or closing upon damage in early L3 discs, while only 55 open or close in late L3 discs. We describe two consequential groups of peak changes, those that are damage responsive (DR) in early L3 (222 peaks) and those that are maturity silenced (MS), open in early damaged L3 and closed in late damaged L3 (729 peaks). 28 peaks fall in the overlap of these two groups.

overall_design: Wing discs from early L3 (day 7@18'C) and late L3 (day 9 @18'C) unablated or ablated with egr for 40hrs (4 samples x 3 biological replicates each)

first: Iswar

middle: K

last: Hariharan

first: Daniel

last: McKay


title: Immunomodulation of Intracranial Melanoma in Response to Blood-Tumor Barrier Opening with Focused Ultrasound - Bulk RNA seq

status: Public on Jun 10 2020

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

summary: Activating microbubbles (MBs) with focused ultrasound (FUS) for blood-brain (BBB) and blood-tumor barrier (BTB) opening permits targeted therapeutic delivery. While the effects of FUS-mediated BBB opening have been investigated for normal brain tissue, no such studies exist for intracranial tumors. As this technology advances into clinical immunotherapy trials, it will be crucial to understand how FUS modulates the tumor immune microenvironment. Here, bulk RNA sequencing revealed that FUS BTB/BBB opening (1 MHz, 0.5 MPa peak-negative pressure) of intracranial B16F1cOVA tumors increases the expression of genes related to proinflammatory cytokine and chemokine signaling, pattern recognition receptor signaling, and antigen processing and presentation. Flow cytometry revealed increased maturation (i.e. CD86) of dendritic cells (DCs) in the meninges and altered antigen loading of DCs in both the tumor and meninges. For DCs in tumor draining lymph nodes, FUS had no effect on maturation and elicited only a trend towards increased presentation of tumor-derived peptide by MHC. Neither tumor endothelial cell adhesion molecule expression nor homing of activated T cells was affected by FUS. In conclusion, FUS-mediated BTB/BBB opening elicits signatures of inflammation; however, the response is mild, transient, and unlikely to elicit a systemic response independent of administration of immune adjuvants.

overall_design: Groups of 3-4 tumor bearing mice were treated with sham or FUS-mediated BBB disruption for harvest at both 6 h and 24 h post treatment, for a total of 4 groups. At either 6 or 24 hours following FUS activation of MB, B16F1cOVA brain tumors harvested and processed for bulk mRNA sequencing followed by bioinformatics analyses.

first: Colleen

middle: T

last: Curley

first: Richard

last: Price


title: Myocardial Infarction accelerates breast cancer via innate immune reprogramming

first: Emily

last: Brown


title: Impact of BHLHE40-AS1 over expression in MCF10A cells

city: Rensselaer

first: Sridar

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary: BHLHE40-AS1 was cloned into pBABE-Puro. Empty vector and pBABE-BHLHE40-AS1 were used to generate retrovirus and infect MCF10A cells. Transduced cells were selected with 1ug/mL puromycin for 2 weeks.

overall_design: 2x10^5 MCF10A-pBABE and MCF10A-BHLHE40-AS1 cells were plated in a 6 well dish. Total RNA was extracted 48 hours post plating. Three independent biological replicates were collected to check reproducibility.

first: Rebecca

last: DeVaux

first: Jason

last: Herschkowitz


title: Single cell analysis of iNKT cells from murine epididymal adipose tissue and spleen

city: Dublin

first: Lydia

last: Lynch

address: Trinity Biomedical Sciences Institute 152-160 Pearse St

country: Ireland

institute: Trinity College Dublin

summary:
We confirm previous findings that adipose iNKT cells are transcriptionally distinct from canoncial splenic iNKT cells and we demonstrate that the adipose iNKT cell population is hetergeneous, containing two major functional subsets which can be segregated by expression of the surface marker NK1.1 (Klrb1c).
Both of these adipose iNKT cell subsets play a role in the regulation of adipose tissue tissue homeostasis, including NK1.1+ iNKT cells, which produce IFNγ and induce adipose NK cell-mediated killing of adipose tissue macrophages.

overall_design: Unbiased single cell sequencing of sorted whole murine iNKT cells from epidiymal adipose tissue (one sample) and spleen (two samples hashed together, one sample from untreated mice and one sample from mice treated with 1μg aGalactosylCeramide)

first: Nelson

last: LaMarche

first: Harry

last: Kane

first: Ayano

last: Kohlgruber

first: Michael

last: Brenner


title: Genomic CpG methylation profiles of peripheral blood mononuclear cells in childhood AD patients and control subjects

city: Kaohsiung

first: Kuang-Den

last: Chen

address: 123, Ta-Pei Rd., Niao-Sung Dist.

department: Translational Research Center in Biomedical Sicences

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

summary:
Peripheral blood samples were taken from a total of 48 individuals (24 AD patients and 24 controls) and subjected to access DNA CpG methylation state using Infinium HumanMethylation450 BeadChips. This array consists of probes to determine the site-specific methylation status of more than 450K CpG loci across the human genome.
Approximately 500 ng of bisulfate-converted DNA (BCD) was used per BeadChip for hybridization in accordance with the protocol and instructions of Infinium HD methylation. After completing the whole-genome amplification step and then controlled enzymatic end-point fragmentation, BCD samples were precipitated and re-suspended for hybridization for 16 h at 48C. During this process, the DNA molecules are annealed to two bead types with methylated loci (C)-specific and unmethylated loci (T)-specific oligomers. Afterward, the non-hybridized or mis-hybridized DNA was washed away, followed by single-base extension using 2,4-dinitrophrnol- and biotin-labeled ddNTPs and the annealed BCD as templates.

overall_design: Bisulfite converted DNA from 48 PBMC samples (with 24 control subjects and 24 AD patients) was hybridized to the Illumina Infinium HumanMethylation450 BeadChip array.

first: Ho-Chang

last: Kuo