title: Aggressive PDACs show hypomethylation of repetitive elements and the execution of an intrinsic IFN program linked to a ductal cell-of-origin

city: Heidelberg

first: Elisa

last: Espinet

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

type: Methylation profiling by high throughput sequencing

summary: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer embedded in an extensive desmoplastic stroma. Since this challenges the molecular analyses of bulk tumor samples, we FACS-purified epithelial cells from PDAC and healthy human pancreas and performed genome-wide transcriptome and DNA methylome analyses. Clustering based on DNA methylation revealed two distinct groups of PDAC with different methylation levels at genomic regions encoding repeat elements. Methylationlow tumors showed higher expression of endogenous retroviral (ERV) transcripts and a strong engagement of the dsRNA sensing machinery. This results in the cell intrinsic activation of an interferon response signature (IFNsign), leading to the reprogramming of stromal cells towards a pro-tumorigenic microenvironment and poor patient outcome. Methylationlow/IFNsignhigh and Methylationhigh/IFNsignlow PDAC cells harbored distinct lineage traits specific for normal ductal or acinar pancreatic epithelial cells at the methylation and transcriptional level. Moreover, ductal-cell-derived KrasG12D/Trp53-/- mutant mouse PDACs showed higher expression of IFNsign compared to tumors initiated by the same drivers in acinar cells. Collectively, our data point to two distinct origins and etiology of human PDACs, with the aggressive Methylationlow/IFNsignhigh tumor subtype potentially targetable by agents blocking cell intrinsic IFN-signaling.

overall_design:
WGBS analysis of the epithelial cells  isolated from 7 human PDAC tumors and 6 normal distal adjacent pancreas tissue. Epithelial cells were isolated from the human tissue  using flow cytometry and defined as EpCAM+/CD45-. Data were processed as previously described (Wang et al. Nat Protocol, 2013): Sequencing reads were aligned using BWA with human reference genome version hg19/GRCh37. Duplicate reads were discarded. Methylation calling was performed as previously (Delacher and Imbusch et al. Nat Immunology, 2017). The raw counts of methylated and unmethylated reads for each CpG site from different libraries were merged for each sample.
*** Submitter declares that the raw data is deposited in the European Genome-phenome Archive (EGA) due to patient privacy concerns. EGA accession number is EGAS00001004660. ***

first: Andreas

last: Trumpp

first: Charles

last: Imbusch

first: Zuguang

last: Gu


title: KIF20A promotes the development of soft tissue sarcoma by activating the PI3K-AKT signaling pathway

status: Public on Nov 23 2020

city: Changchun

first: zhenhua

last: zhu

address: Xinmin  Street 71#

country: China

institute: The First Hospital of Jilin University

type: Expression profiling by high throughput sequencing

summary: Soft tissue sarcoma (STS) is a group of malignancies that can appear in any part of the body. The prognosis of STS patients remains unsatisfactory, mainly due to metastasis and recurrence. Upregulation of KIF20A is associated with poor prognosis of STS patients, but its downstream mechanism is unknown. In the present study, we found that downregulation of KIF20A in the STS cell line HT-1080 inhibits cell proliferation, migration, and invasion and induced cell apoptosis and G2/M arrest in vitro. In addition, downregulation of KIF20A in HT-1080 repressed tumorigenesis of STS in a xenograft mouse model. Pathway analysis showed, that downregulation of KIF20A led to suppression of downstream PI3K-AKT and NF-κB pathways. Specifically, the phosphorylation of AKT at Ser473 was inhibited. Taken together, our results indicate that KIF20A plays an important role in the development of STS by inhibiting cell proliferation, migration, invasion via the PI3K-AKT signaling pathway. Therefore, KIF20A is a potential therapeutic target in STS.

overall_design: Three KIF20A knockdown HT1080 cell lines and three control HT1080 cell lines.

first: Zhenhua

last: Zhu

first: Dahui

last: Sun


title: Genome-wide analysis of t(14;18)-negative/BCL2 expression-negative FL

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

country: Spain

institute: Hospital Clínic

summary: A subset of FL in adults are negative for t(14;18) translocation and BCL2 expression The tumor shows low grade cytology and lack both BCL2 expression and t(14;18) translocation. The genetic alterations involved in the pathogenesis of FL without t(14;18)-negative translocation and BCL2 expression are not well known.

overall_design: The aim of this study was to perform a complete genetic characterization of t(14;18)-negative FL. Fifty-seven cases with consensus diagnosis of FL and absense of t(14;18) by fluorescence in situ hybridization and without BCL2 expression by immunohistochemistry, were analyzed by copy number (CN) array and targeted sequencing analyses of genes associated with FL pathogenesis.

first: Inga

last: Muller

first: Joan

middle: E

last: Ramis Zaldivar

first: Julia

last: Salmerón Villalobos

first: Leticia

last: Quintanilla-Martinez


title: Overexpression of A kinase interacting protein 1 attenuates myocardial ischemia / reperfusion injury, but does not influence heart failure development

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

summary:
Aims A kinase interacting protein 1 (AKIP1) stimulates physiological growth in cultured cardiomyocytes and attenuates ischemia / reperfusion (I/R) injury in ex vivo perfused hearts. We aimed to determine whether AKIP1 modulates the cardiac response to acute and chronic cardiac stress in vivo.
Methods and results Transgenic mice with cardiac-specific overexpression of AKIP1 (AKIP1-TG) were created. AKIP1-TG mice and their wild type (WT) littermates displayed similar cardiac structure and function. Likewise, cardiac remodeling in response to transverse aortic constriction or permanent coronary artery ligation was identical in AKIP1-TG and WT littermates, as evidenced by serial cardiac magnetic resonance imaging and pressure-volume loop analysis. Histological indices of remodeling, including cardiomyocyte cross-sectional diameter, capillary density and left ventricular fibrosis were also similar in AKIP1-TG mice and WT littermates. When subjected to 45 minutes of ischemia followed by 24 hours of reperfusion, AKIP1-TG mice displayed a significant 2-fold reduction in myocardial infarct size and reductions in cardiac apoptosis. In contrast to previous reports, AKIP1 did not co-immunoprecipitate with or regulate the activity of the signaling molecules NF-κB, protein kinase A or AKT. AKIP1 was, however, enriched in cardiac mitochondria and co-immunoprecipitated with a key component of the mitochondrial permeability transition (MPT) pore, ATP-synthase. Finally, mitochondria isolated from AKIP1-TG hearts displayed markedly reduced calcium induced swelling, indicative of reduced MPT pore formation.
Conclusions In contrast to in vitro studies, AKIP1 overexpression does not influence cardiac remodeling in response to chronic cardiac stress. AKIP1 does, however, reduce myocardial I/R injury through stabilization of the MPT pore. These findings suggest that AKIP1 deserves further investigation as a putative treatment target for cardioprotection from I/R injury during acute myocardial infarction.

overall_design: 4 groups, 8 mouse SHAM (4 WT and 4 AKIP_TG) and 8 mouse IR (4 WT and 4 AKIP1_TG) where ischemia / reperfusion (I/R) injuried

first: H

middle: G

last: Booij

last: Yu

first: R

middle: A

last: de Boer

first: C

middle: W

last: van de Kolk

first: B

last: van de Sluis

first: J

middle: M

last: van Deursen

first: W

middle: H

last: van Gilst

last: Silljé

middle: D

last: Westenbrink


title: Evolved differences in cis and trans regulation between the maternal and zygotic mRNA complements in the Drosophila embryo

status: Public on Nov 24 2020

city: Davis

first: Susan

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

country: USA

institute: University of California, Davis

summary: During embryogenesis in animals, initial developmental processes are driven entirely by maternally provided gene products that are deposited into the oocyte. The zygotic genome is transcriptionally activated later, when developmental control is handed off from maternal gene products to the zygote during the maternal to zygotic transition (MZT). The MZT is highly regulated and conserved across all animals, and while some details change across model systems where it has been studied, most are too evolutionarily diverged to make comparisons as to how this process evolves. There are differences in maternal gene products and their zygotic complements across Drosophila species, so here we used hybrid crosses between sister species of Drosophila (D. simulans, D. sechellia, and D. mauritiana) and transcriptomics to determine how gene regulation changes in early embryogenesis across species. We find that regulation of maternal transcript deposition and zygotic transcription evolve through different mechanisms. Changes in transcript levels occur predominantly through differences in trans regulation for maternal genes, while changes in zygotic transcription occur through a combination of regulatory changes in cis, trans, and both cis and trans. We find that patterns of transcript level inheritance in hybrids relative to parental species differs between maternal and zygotic transcripts; maternal transcript levels are more likely to be conserved but both stages have a large proportion of transcripts showing dominance of one parental species. Differences in the underlying regulatory landscape in the mother and the zygote are likely the primary determinants for how maternal and zygotic transcripts evolve species.

sample_organism: Drosophila sechellia x Drosophila mauritiana

sample_organism: Drosophila simulans x Drosophila mauritiana

sample_organism: Drosophila simulans x Drosophila sechellia

sample_organism: Drosophila mauritiana x Drosophila simulans

sample_organism: Drosophila mauritiana x Drosophila sechellia

overall_design: Crosses between D. simulans, D. sechellia, and D. mauritiana, reciprocally where possible, were performed, for 5 total crosses. Embryos were collected from two developmental stages, stage 2 where all transcripts present are maternal in origin, and late stage 5, after zygotic genome activation. Stage 2 embryos were collected from F1 hybrid mothers, late stage 5 embryos were F1 hybrids themselves (collected from a between-species cross). mRNA-Seq was performed on RNA extracted from single staged embryos, 3 replicates per cross for stage 2, and 6 replicates per cross for stage 5 (3 female and 3 male embryos), for a total of 45 hybrid embryo samples.

first: Emily

middle: L

last: Cartwright


title: Change in circulating miRNA at two weeks after anti-TNF therapy predicts response at 14 weeks: a pilot study

status: Public on Nov 22 2020

city: Boston

first: Ilya

last: Korsunsky

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital

summary: Circulating microRNA were collected from RA patients before and 2, 4, and 14 weeks after anti-TNF (Golimumab) treatment. Changes in expression from baseline to 2 weeks are predictive of response, whereas changes to 4 and 14 weeks are not. This study suggests the importance of collecting early biomarker samples post-treatment to evaluate efficacy and guide therapy.

overall_design: 120 samples of Plasma microRNA from 30 subjects across 4 timepoints were assayed.


title: Development of specialized sensory neurons engages a nuclear receptor required for functional plasticity

city: New York

first: Mary

last: Rossillo

state: ny

address: 550 1st ave

institute: NYU Langone

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Behavioral and neurogenomic responses to acoustic and visual sexual cues are correlated in female torrent frogs

city: Chengdu

first: Longhui

last: Zhao

address: No. 9 Section 4, Renmin South Road

institute: Chengdu Institute of Biology, Chinese Academy of Sciences

summary: Diverse animal species use multimodal communication signals to coordinate reproductive behavior. Despite active research in this field, however, the brain mechanisms underlying multimodal communication remain poorly understood. Although anuran amphibians rely on acoustic communication some anurans like humans and many mammalian species, often produce auditory signals accompanied by conspicuous visual signals (e.g. vocal-sac inflation). In this study, we used video playbacks to determine the role of vocal-sac inflation in little torrent frogs (Amolops torrentis). The results showed that auditory cues (i.e. male advertisement calls) as well as visual cues are attractive to female torrent frogs, although the auditory cue was more attractive than the visual cue. Moreover, females preferred simultaneous bimodal cues to unimodal cues. Then we exposed females to blank, visual, auditory and audiovisual stimuli and analyzed whole brain tissue gene expression changes using RNA-seq. The hierarchical clustering of differentially expressed genes (DEGs) showed that samples from the same behavioral stimulus category were more aggregative than those from different behavioral categories nearly forming a cluster, and implying a strong relationship between neurogenomic states and momentarily expressed sexual signals. We also found that the Gene Ontology (GO) terms and KEGG pathways involved in energy metabolism were mostly enriched in blank contrast versus visual, acoustic or audiovisual stimuli, suggesting that brain energy use plays a key role in the perception of these stimuli. Moreover, analyses of immediate early genes (IEGs) showed that only the c-fos gene was differently expressed in response to different stimuli. These results increase our understanding of how neurogenomic states reflect brain mechanisms mediating female preferences for different sexual cues.

overall_design: Brain mRNA profiles of perceiving multimodal cues were generated by deep sequencing, in triplicate, using Illumina X-ten PE150

first: Jianguo

last: Cui


title: Transcriptome analysis of TACI-deficient and WT naïve T cells

city: Singapore

first: Alison

middle: P

last: Lee

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

summary: TACI (transmembrane activator and calcium modulator and cyclophilin ligand interactor) plays critical roles in B cells by promoting immunoglobulin class-switching and plasma cell survival. However, its expression and function in T cells remain controversial. In this study, we found that TACI deficiency in mice results in expansion of TH17 and Treg populations. To understand the mechanisms underlying increased frequencies and numbers of TH17 cells correlated with more severe colitis in TACI-/- mice, microarray-based transcriptome analysis was conducted to identify genes that were differentially expressed in TACI-/- vs WT naive CD4+ T cells.

overall_design: Naive CD4+ T cells were FACS-sorted from pooled spleens and lymph nodes of TACI-/- and WT mice (n = 2 each).

first: Andy

last: Tan

first: K-P

last: Lam


title: mRNAseq of wild type and ets-5 mutant C. elegans BAG neurons

summary: comparative transcriptomics of wild type and ets-5 mutant C. elegans BAG neurons

overall_design: BAG neurons were isolated from embryonic preps of wild type and ets-5 mutants using FACS. mRNA for two biological replicates were sequenced using Illumina Hi seq 2500. Fastq files were aligned to ws243 using STAR. Quantification was performed using HTSeq, and differential expression analysis was performed using DESeq2.

first: Niels

last: Ringstad


title: ChIP-seq of wild type and ets-5-gfp worms

summary: We performed ChIP-seq on worms expressing gfp-tagged ets-5 and wild type worms as a control.

overall_design: TF ChIP-seq in experimental and control strains


title: Self-renewing Endometrial Epithelial Organoids of the Human Uterus [single-cell RNA-seq data]

city: Columbia

first: Thomas

last: Spencer

state: MO

address: 920 East Campus Drive

department: Animal Sciences

institute: University of Missouri

summary: The inner lining of the human uterus, termed the endometrium, is replete with glands that are hypothesized to be important for establishment of pregnancy through interactions with other endometrial cells and the embryo. A three-dimensional culture system was utilized to establish and generate endometrial epithelial organoids from normal human endometrium that display long-term expandability, can be cryopreserved, and are hormone responsive. Here, single cell RNA-seq was used to create a high-resolution gene expression atlas of the endometrial epithelial organoids and to define responsiveness to reproductive hormones.

overall_design: In order to investigate the roles of uterine glands in first trimester human pregnancy, we used an established protocol of Matrigel and WNT-activating conditions to generate three-dimensional human uterine gland organoid (HUGO) cultures from endometrial biopsies. The HUGO expand long-term, are genetically stable, differentiate following treatment with reproductive hormones, and can be cryopreserved. After passage, HUGO were grown for 4 days in expansion medium and then treated with estrogen (E2) for 2 days and then either nothing (Control), E2 and medroxyprogesterone acetate (MPA) or E2+MPA+cAMP for a further 6 days (n=3 replicates per patient and treatment). Total RNA was extracted from the organoids using a standard TRIzol-based protocol and Direct-zol RNA MiniPrep Plus isolation kit (Zymo Research, R2070). RNA quality and concentration was determined by a Fragment Analyzer (Advanced Analytical Technologies). RNA library preparation and sequencing was conducted by Illumnia platform by Novogene, California.

first: Harriet

middle: C

last: Fitzgerald

first: Pramod

last: Dhakal

first: Susanta

middle: K

last: Behura

first: Daniel

middle: J

last: Schust


title: Transciptomic analysis of human aortic smooth muscle cells (HASMCs) with BAF60a knockdown

status: Public on Nov 21 2020

city: Ann Arbor

first: Haocheng

last: Lu

state: Michigan

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

summary: We used NGS-derived transcriptome profiling (RNA-seq) to compare the transcriptional difference between human aortic smooth muscle cells (HASMCs) transfected with 30nM siRNA targeting BAF60a (siBAF60a) or non-targeting siRNA (siControl)

overall_design: mRNA profiles of HASMCs transfected with 30nM siControl or siBAF60a (RNA was extracted 72h after transfection) were generated by RNA sequencing, with 4 replicates in each group.

first: Ziyi

last: Chang

first: Jifeng

last: Zhang


title: Porphyromonas gingivalis  affect gene expression in skeletal muscle, tibialis anterior muscle.

city: Tokyo

first: Sayaka

last: Katagiri

country: Japan

institute: Tokyo Medical and Dental University

summary: To further development of our gene expression we have employed microarray expression  to identify genes.  The mice were randomly divided into a control group and a group receiving oral injection of sonicated P. gingivalis twice a week  for 6 weeks. Skeletal muscle in mice was extracted.

overall_design: Porphyromonas gingivalis induced gene expression in mice skeletal muscle was measured  after oral administration.

first: Kazuki

last: Watanabe


title: Altered microRNA expression: Control vs. Intracranial Aneurysmal Tissues

city: Bengaluru

first: Supriya

last: M

state: India

address: Hosur road

country: India

institute: NIMHANS

summary: High throughput miRNA microarray screening approach, we compared the miRNA expression pattern in ruptured aneurysm tissues obtained during surgery from patients with aneurysmal subarachnoid hemorrhage (aSAH) with control tissues. Aim was to determine miRNA signature in aneurysmal tissues.

overall_design: Case-Control Study.  Total RNA was isolated from aneurysm tissue and controls. RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively and The Hy3™-labeled samples and Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th Gen from Exiqon.

first: Rita

last: Christopher

first: Manjunath

last: Supriya

first: Bhagavatula

middle: I

last: Devi

first: Dhananjaya

last: Bhat

first: Dhaval

last: Shukla


title: RNA-sequencing of adipose-derived stem cells in 0 or direct-current electric field

city: Shenyang

first: Mingzhu

last: Jin

address: 155N Nanjing Street, Heping District

institute: The First Hospital of China Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The circRNA, lncRNA, miRNA, and mRNA levels of both the direct-current electric field and control groups of adipose-derived stem cells were obtained by RNA sequencing.

overall_design: Examing 2 conditions, 3 replicates each.

first: Xinghua

last: Gao


title: Transciptomic analysis of human aortic smooth muscle cells (HASMCs) with BAF60a overexpression

summary: We used NGS-derived transcriptome profiling (RNA-seq) to compare the transcriptional difference between human aortic smooth muscle cells (HASMCs) infected with 20MOI adenovirus encoding human BAF60a (AdBAF60a) or GFP (AdGFP)

overall_design: mRNA profiles of HASMCs transfected with 20MOI AdGFP or AdBAF60a (RNA was extracted 48h after infection) were generated by RNA sequencing, with 3 replicates in each group.


title: Genome-wide maps of chromatin state changes in BAF60a deficient human aortic smooth muscle cells (HASMCs)

summary: We compared BRG1 binding and histone modification states between siControl and siBAF60a transfected human aortic smooth muscle cells (HASMCs) through ChIP sequencing.

overall_design: Examination of BRG1 and 2 different histone modifications in siControl or siBAF60a transfected HASMCs.


title: Porphyromonas gingivalis affects gene expression in skeletal muscle, soleus muscle

overall_design: Porphyromonas gingivalis induced gene expression in mice skeletal muscle was measured  after oral administration (Pg).  Control mice (Co) were given saline only.


title: The global map of Rio1 activity in Saccharomyces cerevisiae

city: Milan

first: Peter

last: De Wulf

address: via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

type: Genome variation profiling by genome tiling array

summary: In Saccharomyces cerevisiae, the kinase Rio1 regulates rDNA transcription and segregation, pre-rRNA cleavage, and 40S ribosomal subunit maturation. Other roles are unknown. Human orthologue RIOK1; which is frequently overexpressed in malignancies, drives tumor growth and metastasis. Again, also RIOK1 biology is poorly understood. In this study, we charted the global activity of Rio1 in budding yeast. By producing and systems-integrating its protein-interaction, gene-transcription, and chromatin-binding maps we generated Rio1's multi-layered activity network, which controls protein synthesis and turnover, metabolism, growth, proliferation, and genetic stability. Rio1 regulates itself at the transcriptional level, and manages its network both directly and indirectly, via a battery of regulators and transcription factors, including Gcn4. We experimentally confirmed the network and show that Rio1 commands its downstream circuit depending on the growth conditions encountered. We also find that Rio1 and RIOK1 activities are functionally equivalent. Our data suggest that pathological RIOK1 expression may deregulate its network and fuel promiscuous transcription and ribosome production, uncontrolled metabolism, growth, proliferation, and chromosomal instability; well-known contributors to cancer initiation, maintenance and metastasis.

overall_design: ChIP-on-chip analyses were carried out as described in Bermejo R. et al., Meth. Mol. Biol. 582: 103-18 (2009). Labelled probes were hybridized to Affymetrix S.cerevisiae Tiling 1.0 (P/N 900645) arrays and processed with TAS software.


title: The Effects of UAB126 on Liver Gene Expression

city: Birmingham

first: Jeonga

last: Kim

state: Alabama

institute: University of Alabama at Birmingham

summary: We report the gene expression profiles in the livers from mice fed high fat diet with or without UAB126

overall_design: C57BL/6 mice were fed a high fat diet (60% fat) with or without UAB126 (1.2 g/kg diet) for 12 weeks


title: Single-cell atlas of major haematopoietic tissues in the mouse embryo

city: Monterotondo

first: nicolas

last: descostes

address: via Ramarini 32

department: Bioinformatics

institute: EMBL

summary: The aim of this experiment was to compare by single-cell RNA sequencing the aorta-gonad-mesonephros (AGM) region and yolk sac (YS), the two major sites of embryonic hematopoietic, between 9.5 and 11.5 days of mouse embryonic development.

overall_design: AGM and Yolk Sac from E9.5 and E11.5 C57Bl/6 mouse embryos were isolated and single cell suspensions were generated. Cells were stained with the anti-VE-Cadherin antibody and 7AAD. Cells were analyzed and sorted by flow cytometry. After doublet exclusion, single live 7AAD- cells were bulk sorted into 15ml tubes as VE-CadPos endothelial cells and VE-CadNeg microenvironment cells, and taken for dispensing on ICELL8 chip (Takara). There was two ICELL8 chips in total (one for E9.5 and another for E11.5). Single cells from each population were selected on the ICELL8 machine. Sequencing libraries were generated and were later sequenced together on the Illumina Next Seq 500 sequencer.

first: Maya

last: Shvartsman

first: Polina

middle: V

last: Pavlovich

first: Kerstin

last: Ganter

first: Artem

last: Adamov

first: Konstantin

last: Chukreev

first: Nicolas

last: Descostes

first: Andreas

last: Buness

first: Christophe

last: Lancrin


title: Nanoparticle Internalization Promotes the Survival of Primary Macrophages

city: Newark

first: Catherine

last: Fromen

state: DE

address: 150 Academy St, 209 Colburn Lab

institute: University of Delaware

summary: Macrophages have emerged as promising therapeutic targets for regulating immune microenvironments. However, tissue-isolated macrophages are plagued by poor survival, which limits the therapeutic efficacy and prevents thorough drug screening and model development. Therefore, developing strategies aimed at prolonging primary macrophage survival is imperative for realizing macrophage therapies and understanding macrophage behavior. We discovered that nanoparticle dosing significantly enhances ex vivo survival of primary macrophages, which is attributed to suppression of apoptosis and is linked to downstream phagocytosis and lysosomal signaling. We report that macrophage survival because of phagocytosis of nanoparticles fabricated with immunologically inert materials does not alter macrophage polarization or lead to aberrant activation. These findings provide a framework for extending the lifespan of primary macrophages ex vivo for drug screening, vaccine studies, and cell therapies.

overall_design: We investigate two groups of bone marrow-derived macrophages (BMMs) with 4 replicates each: 1. Treated with 100 ug/ml polyethylene glycol-based nanoparticles and 2. Untreated

first: Bader

last: Jarai


title: Transciptome analysis of human aortic smooth muscle cells (HASMCs) with 2-hydroxypropyl-β-cyclodextrin (HPbCD) treatment

first: Haocheng

last: Lu

summary: HASMCs were treated with HPbCD (10mg/kg) for 24 hours and harvest for RNA sequence.

overall_design: HASMCs mRNA profiles of control or HPbCD treatment were generated by RNA sequencing, in 4 replicates.

first: Yanbo

last: Fan


title: Harnessing TFEB to treat abdominal aortic aneurysm

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

overall_design: Refer to individual Series


title: BAF60a Deficiency in Vascular Smooth Muscle Cells Prevents Abdominal Aortic Aneurysm Formation by Attenuating Vascular Inflammation


title: RNA sequencing analysis of organoids and their parental tissues

city: ShenZhen

first: Jiang

last: Shengwei

address: No.1001 Xueyuan Avenue, Nanshan District

institute: Tsinghua University

summary: We  assessed whether organoids maintained the gene expression signatures of their parental healthy tissues and tumors. We performed transcriptomic analysis by bulk RNA sequencing (RNA-seq) across 3 mice,  3 patients and different periods iPSCs.  Total RNA of organoids and their parental tissues were extracted at day 7 and day 0, respectively. Total RNA of iPSCs were extracted at day 0, day 1 and day 4. The results show that the organoids are able to replicate the inter-patient heterogeneity, which determines their feasibility on personalized therapy evaluation.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA sequencing analysis of  3 mice(lung, liver and kidney organoids and their parental tissues),  3 patients(organoids and their parental tissues) and  iPSCs at day 0, day 1 and day 4

first: Shaohua

last: Ma

first: Laiqiang

last: Huang

first: Shengwei

last: Jiang

first: Jiaqi

last: Wang


title: Targeted single-cell RNA sequencing data of residual TIM-3+ leukemic stem cells post-SCT

city: Fukuoka

first: Teppei

last: Sakoda

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

summary: Since AML is hierarchically organized by self-renewing LSCs with heterogeneous sub-populations, we employed single-cell RNA sequencing to evaluate the changes in AML heterogeneity in terms of gene expression profiling, throughout the clinical course.

overall_design: Purified CD34+ BM cells of the diagnostic, CR, and relapse phases, from identical patients, were subjected to BD Rhapsody Single-Cell Analysis System, and the expression of originally customized 435 target genes was quantified

first: Yuichiro

last: Semba


title: Next-generation sequencing analysis of macrophage engulfing control or STC1-OE tumor corpses related transcriptomes

status: Public on Nov 20 2020

city: ANN ARBOR

first: Shasha

last: Li

state: MI

address: 1109 Maiden Ln, ct apt 104

summary: Purpose: To explore the transcriptomes changes in macrophage during long term engulfment of control or STC1-OE tumor corpses.

overall_design: Methods: Macrophages were loaded with STC1OE or control B16F-F10 corpses at 1 to 5 ratios. After culture for 20 hours, unbound tumor corpses were washed away. Total RNA was isolated using the Direct-zol RNA Miniprep Plus kit (Zymo Research) and mRNA libraries were prepared using the Illumina TruSeq technology. Libraries were then sequenced using an Illumina NovaSeq sequencer at 150 bp, paired end reads with approximately 30 million reads per sample. Four independent experiments were sequenced for each condition.

first: Heng

last: Lin

first: Weiping

last: Zou


title: Identity transcript factor EB (TFEB) target genes in human aortic smooth muscle cells (HASMCs)

summary: Using ChIP-Seq technology, we identitied novel target of TFEB in HASMCs.

overall_design: Examination of TFEB binding site in genome


title: RNA seq of Gnas mutant subcutaneous progenitor cells

first: Qian

last: Cong

address: 188 Longwood Ave

department: Harvard School of dental medicine

institute: Harvard University

summary: The Gnas mutant mice driver by AdCre injection showed heterotopic osssification. In order to understand the underlying mechanism, we performed RNA seq experiments using total RNA from the control and Gnas mutant subcutaneous progenitor cells.

overall_design: Isolation subcutaneous progenitor cells from Gnas flox mice with AfCre/GFP infection, than cultured for 7 days with osteogenic medium

first: Yingzi

last: Yang

first: Yuchen

last: Liu

first: Yaxing

last: Zhou


title: Microarray analysis of TFEB-regulated genes in vascular smooth muscle cells

summary:
Transcription factro-EB (TFEB) is a master gene for autophagy and lysosome biogenesis
We used microarrays to detail the gene expression in TFEB-overexpressing vascular smooth muscle cells identified distinct classes of TFEB-regulated genes.

overall_design: Human aortic smooth muscle cells (HASMCs) overexpressing control LacZ or TFEB were used for RNA extraction and hybridization on Affymetrix microarrays.


title: The landscape of accessible chromatin in bovine oocytes and early embryos

city: Gainesville

first: Zongliang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

summary: ATAC sequencing of bovine oocytes and early embryos revealed a genome-wide map of accessible chromatin of bovine early embryo development, highlighting the critical features of chromatin landscape and epigenetic reprogramming during bovine preimplantation embryo development.

overall_design:
GV, MII oocytes and differental developmental stages embryos (2-, 4-, 8-, 16-cell, morula, blastocyst, day 14 elongating embryo) were pooled for ATAC sequencing analysis.

**Please note that Peaks in individual samples from the same development stage were merged and the resulting peak data is linked to the corresponding first *A sample records.

first: Hao

last: Ming


title: Unravelling the genome-wide contributions of specific 2-alkyl-4-quinolones and PqsE to quorum sensing in Pseudomonas aeruginosa

city: Rome

first: Emanuela

last: Frangipani

address: Viale G. Marconi 446

department: Department of Sciences

institute: University of Roma Tre

summary:
Pseudomonas aeruginosa pathogenicity mainly relies on its ability to finely control the expression of virulence determinants via multiple quorum sensing (QS) systems. Despite the relevant role of the pqs QS system in controlling the expression of key virulence factors and biofilm formation in P. aeruginosa, our understanding of the molecular mechanisms governing this QS circuit, which employs 2-alkyl-4-quinolones (AQs) as signal molecules, is still preliminary, probably due to its complexity.  Multiple genes are required for the synthesis of the primary AQs, 2-heptyl-4-hydroxyquinoline (HHQ), 2-heptyl-3-hydroxy-4-quinolone (PQS), and 2-heptyl-4-hydroxyquinoline N-oxide (HQNO). These include the pqsABCDE operon, required for the synthesis of HHQ, which in turn is oxidized to PQS via the action of the monooxygenase PqsH. The monooxygenase PqsL is required for HQNO synthesis together with the pqsABCD genes. The fifth gene of the pqsABCDE operon, pqsE, is also required for the production of major virulence factors and for biofilm formation, and exerts a homeostatic effect on AQs synthesis by repressing the transcription of the pqsABCDE operon. The pqs system is subject to positive autoregulation, with the PqsR regulator promoting pqsABCDE transcription upon binding to HHQ or PQS. However, the individual contributions and relative importance of HHQ, PQS, HQNO and PqsE to AQ-dependent signalling is not fully apparent, because of the overlapping and interdependent nature of the factors involved in this complex QS network.
We used microarrays to detail the global response of a P. aeruginosa mutant strain unable to synthesise or convert AQs, and to express PqsE to exogenously provided AQs or IPTG (to induce pqsE expression).

overall_design: The Δ4AQ mutant strain of P. aeruginosa was grown to an OD600 of 1.5 in LB medium (EF_1A, EF_1B), or in LB supplemented with 40 μM HHQ (EF_2A, EF_2B), 40 μM PQS (EF_3A, EF_3B), 40 μM HQNO (EF_4A, EF_4B), or 1 mM IPTG (EF_5A, EF_5B), for RNA extraction and hybridization on Affymetrix microarrays.

first: Giordano

last: Rampioni

first: Marilena

last: Falcone

first: Stephan

last: Heeb

first: Matthew

last: Fletcher

first: Jean-Francois

last: Dubern

first: Paolo

last: Visca

first: Livia

last: Leoni

first: Miguel

last: Camara

first: Paul

last: Williams


title: Fully defined human PSC-derived microglia and tri-culture system reveals cell type specific potentiation of complement C3 production in a model of Alzheimer’s disease

city: New York

first: Sudha

last: Guttikonda

state: New York

address: 430 E 67th St

department: Developmental Biology

institute: MSKCC


title: Integrated multiomic analysis identifies functional epigenetic signatures regulating nucleotide excision repair (meRIP-seq)

city: Guangzhou

first: Yuming

last: Wang

state: Guangdong

address: Room 512, Anatomy Building

department: School of Basic Medical Science

institute: Guangzhou medical university

summary: Transcription-coupled nucleotide excision repair (TC-NER) is promptly triggered by 'local' elongating RNAP II molecules encountering DNA adducts such as cyclobutane pyrimidine dimers (CPD) induced by ultraviolet light and speeds up removing and repair in transcribed loci. Genome-wide measurements have revealed a dramatic shutdown of global transcription with a few exceptions of individual genes that are consequently highly upregulated by DNA damage. Deciphering the underlying mechanisms of the multifaceted transcriptional response always comprises one of the most fascinating frontiers in DNA repair research. Recent reports have revealed that persistent RNAP II initiation at the transcription start site of active regulatory regions with the continuous synthesis of start-RNAs guarantee sufficient scanning and repair of the whole transcribed genome, although transcription elongation drastically slows down shortly after genotoxic stress. Furthermore, a recent study found that RNA is extremely rapidly m6A methylated by METTL3 in response to UV irradiation which is crucial for recruitment of Pol k to DNA damage sites and subsequently mediates TC-NER. Together, these findings substantiate the molecular processes underlying the transcription-coordinated cellular response upon genotoxic stress might be more complex than previously believed. Unfortunately, all these findings merely focused on the early phase of recovery (within 4 hr after DNA damage). It remains to be determined how accessible chromatin reconfigures and regulates transcriptional programs in UV-induced DNA damage repair. It is also unclear whether the dynamics of gene expression are associated with other epigenomic reconstruction events such as global DNA methylation and demethylation. Moreover, the roles of internal messenger RNA modifications like N6-methyladenosine in TC-NER are poorly understood. Our integrative analyses provide a comprehensive view of the spatio-temporal chromatin configuration and epigenetic characterizations that accompanies TC-NER.

overall_design: MRC5 cells were either left untreated as control or treated with 12J/m2 of UV-C irradiation, followed by recovery for 30 minutes, 3 or 24 hours. Two biological replicates were performed for each sample.

first: Jiena

first: Yingying

last: Xu

first: Lingyun


title: Murine Tooth Embryoic Molar Germ; E11, 12, 16, 18

city: Kobe

first: Masato

last: Nakagawa

state: Hyogo

address: Minatojima Minamimachi, 2-2-3

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

summary: Transcriptional profiling of mouse E14 tooth molar germ comparing E11, 12, 16, 18 tooth molar germ. Goal was to identify unknown genes involved in tooth development,

overall_design: E14 vs E11, 12, 16, 18 tooth molar germ.

first: Takashi

last: Tsuji


title: Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis [scBS-seq]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

summary: Advancing maternal age causes a progressive reduction in fertility. The decline in developmental competence of the oocyte with age is likely to be a consequence of multiple contributory factors. Loss of epigenetic quality of the oocyte should be considered as one factor, as epigenetic errors could impair early developmental events or programme adverse outcomes in offspring that manifest only later in life. Here, we undertake joint profiling of the transcriptome and DNA methylome in individual oocytes from reproductively young and old female mice. We find reduced complexity as well as increased variance in the transcriptome in oocytes from aged females. This heterogeneity is reflected in the identification of discrete sub-populations of oocytes, including those with a transcriptome characteristic of oocytes with immature chromatin configuration, as well as those with a young-like transcriptome. Oocytes from older females had on average reduced CpG methylation, but the characteristic bimodal methylation landscape of the oocyte was preserved. Germline differentially methylated regions of imprinted genes were appropriately methylated irrespective of age. For the majority of differentially expressed transcripts, the absence of correlated methylation changes suggests a post-transcriptional basis for most age-related effects on the transcriptome. However, we did find differences in gene-body methylation at which there were corresponding changes in gene expression, indicating age-related effects on transcription that translate into methylation differences. Interestingly, oocytes varied in expression and methylation of these genes, which could contribute to variable competence of oocytes or penetrance of maternal age-related phenotypes in offspring.

overall_design: Fully-grown germinal vesicle (GV) oocytes were collected from the ovaries of C57BL/6Babr virgin females aged 12 weeks (young, n=39) or 44-54 weeks (old, n=41)

first: Juan

last: Castillo-Fernandez

first: Erika

middle: Y

last: Herrera-Puerta

first: Hannah

last: Demond

first: Stephen

last: Clark

first: Courtney

last: Hanna

first: Myriam

last: Hemberger

first: Gavin

last: Kelsey


title: Integrated multiomic analysis identifies functional epigenetic signatures regulating nucleotide excision repair (RRBS-seq)

last: Liu


title: Integrated multiomic analysis identifies functional epigenetic signatures regulating nucleotide excision repair (ATAC-seq)

overall_design: MRC5 cells were either left untreated as control or treated with 12J/m2 of UV-C irradiation, followed by recovery for 30 minutes, 3 or 24 hours.


title: Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis


title: Inhibition of the hepatic vitamin B12-dependent methionine-salvage pathway by trichloroethylene metabolites accounts for the formic aciduria in the rat

city: Manchester

first: Kate

last: Bloch

address: Alderley Park, Alderley Edge

institute: Manchester University

summary: The industrial solvent trichloroethylene (TCE) produces a marked formic aciduria in male and female F344 rats and in male C57Bl mice following single or multiple dosing. The two major metabolites of TCE formed by cytochromes P450 metabolism also produce formic aciduria. The quantity of formic acid excreted was about 2-fold higher following trichloroacetic acid (TCA) compared to trichloroethanol (TCE-OH) or TCE, at similar doses of 16mg/kg/day for 3 days. Prior treatment of male F344 rats with 1-aminobenzotriazole a cytochrome P450 inhibitor, followed by TCE, completely prevented the formic aciduria but had no effect on formic acid excretion produced by TCA, suggesting TCA is the proximate metabolite producing this response. Metabolism of formic acid is largely controlled by the vitamin B12 –dependent methionine salvage pathway. Transcriptomic analysis on the liver of rats dosed with 16mg/kg/day TCE for three days when compared to control liver showed nine differentially expressed genes, of particular interest was the down regulation of  LMBRD1   involved in the conversion of vitamin B12 into one of two molecules, methylcobalamin (CH3Cbl) or S-adenosylcobalamin (AdoCbl). Administration of CH3Cbl or hydroxocobalamin for 3 days to rats given a single dose of TCE, lead to a reduction in formic acid in their urine. Similarly, rats given TCE followed by L-methionine for 3 days excreted less formic acid in their urine. These findings suggest an effect on the vitamin B12 –dependent methionine salvage pathway. This was supported by the finding that hepatic methionine synthase, which converts homocysteine to methionine, was inhibited following three large daily dose of TCE. We propose that TCE metabolites interact with the vitamin B12 -dependent methionine salvage pathway leading to tetrahydrofolate deficiency and increased excretion of formic acid in rat urine.

overall_design: All animal procedures were performed in accordance with a license issued under the animals (Scientific Procedures) Act, 1986. Wistar-derived rats where bred in the Life Science Support Unit at Liverpool John Moores University. The rats were housed in plastic cages in a room maintained at 20 °C ± 2 °C and a relative humidity of 50% ± 5% with a 12 h light-dark cycle starting at 04.00 h. Rats were allowed food (rat expanded diet), and water ad libitum. Male rats (190–240 g) 7–9 weeks of age were used. Three rats being dosed orally with TCE body weight on in corn oil. Three control animals were dosed orally daily for 3 days with corn oil at. Rats were placed individually in metabolic cages after dosing for the collection of urine, on days 1, 2 and 3 and given food and water ad libitum. Urine was collected from each rat into a container which had 0.1 ml of 10% sodium azide to prevent bacterial growth. Urine volume was determined and the pH measured using a pH meter. Twenty four hours after the last dose all rats were killed by a rising concentration of carbon dioxide. A portion about 50 mg of liver and renal-cortex were quickly harvested and immersed in RNAlater.Rats were dosed orally for 3 days with TCE in corn oil at 16mg/kg/day at 5ml/kg. Controls received corn oil alone.

first: Katarzyna

first: Noreen

last: Yaqoob

first: Andrew

middle: R

last: Evans

first: Edward

last: Lock


title: Integrated multiomic analysis identifies functional epigenetic signatures regulating nucleotide excision repair

first: Yuming

last: Wang


title: Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis [scRNA-seq]

overall_design: Fully-grown germinal vesicle (GV) oocytes were collected from the ovaries of C57BL/6Babr virgin females aged 12 weeks (young, n=42) or 44-54 weeks (old, n=46)

middle: E


title: Genome-wide profiling of the cardiac transcriptome identifies novel heart specific long non-coding RNAs involved in pathogenesis of Arrhythmogenic Cardiomyopathy

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University


title: Integrated multiomic analysis identifies functional epigenetic signatures regulating nucleotide excision repair (RNA-seq)

first: Jiena

first: Yingying

last: Xu

first: Lingyun


title: RNAseq for non-disease heart RV

summary: Arrhythmogenic cardiomyopathy (AC) is an inherited cardiomyopathy characterized by fibrofatty replacement predominantly involved in right ventricle and clinically by ventricular arrhythmias.In this study, we set out to characterize the cardiac novel long-noncoding RNAs using deep RNA sequencing data from human heart tissues. Particularly, we identified AC specific novel lncRNAs that contribute to AC pathophysiology by comparing the lncRNAs transcripts of nine AC explanted hearts (RV), five non-diseased donor hearts (RV), four non-AC failing hearts (dilated cardiomyopathy, RV). To dissect the roles of novel lncRNAs in ARVC from LV, we also include six non-diseased donor hearts (LV) and six ARVC explanted hearts (LV) in the analysis. In the identified novel AC lncRNAs, a large part of them are derived from enhancer regions and acting as cis- elements to potentially regulate lipogenesis or lipid metabolism related genes. Finally, we validated several of these AC specific novel lncRNAs and their potential targets in independent patient samples. Collectively, we identified high-confidence AC specific novel lncRNAs from human samples and suggest their potential roles as cis- elements in AC pathology. Further study of these novel AC lncRNAs could provide new opportunities for diagnosis and therapeutic intervention.

overall_design: RNAseq for non-disease heart RV

first: Liang

last: Zhang

first: Deqiang

last: Sun

first: Jiangping

last: Song

first: Shengshou

last: Hu


title: RNA sequence analysis to compare MMTV-PyMT tumor cells with and without Dll1

city: Philadelphia

first: Rumela

last: Chakrabarti

state: PA

address: 380 S University Ave

institute: University of Pennsylvania School of Veterinary Medicine

summary: Several cell cycle genes were altered between Dll1+ and Dll1- population of tumor cells

overall_design: Examination of MMTV-PyMT, Dll1-GFP+ (n=2) and  MMTV-PyMT, Dll1-GFP-(n=2) tumors; MMTV-PyMT, Dll1-mCherry+ (n=2) and  MMTV-PyMT, Dll1-mCherry-(n=2) tumor cells

first: John

last: Tobias


title: RNAseq for non-disease heart LV

overall_design: RNAseq for non-disease heart LV


title: Lifelong Reduction in Complex IV Induces Tissue Specific Metabolic Effects But Does Not Reduce Lifespan or Healthspan in Mice

city: Saint Louis

first: Wilson

middle: Chun Yim

last: Fok

address: 660 S Euclid Ave

department: Hematology

institute: Washington University in St. Louis

summary: Loss of SURF1, a Complex IV assembly protein, was reported to increase lifespan in mice despite dramatically lower cytochrome oxidase (COX) activity.  Consistent with this, our previous studies found advantageous changes in metabolism (reduced adiposity, increased insulin sensitivity and mitochon-drial biogenesis) in Surf1-/- mice.  The lack of deleterious phenotypes in Surf1-/- mice is contrary to the hypothesis that mitochondrial dysfunction contributes to aging.  We found only a modest (non-significant) extension of lifespan (7% median, 16% maximum) and no change in healthspan indices in Surf1-/- vs Surf1+/+ mice despite substantial decreases in COX activity (22-87% across tissues). Dietary restriction (DR) increased median lifespan in both Surf1+/+ and Surf1-/- mice (36 and 19%, respectively).  We measured gene expression, metabolites and targeted expression of key metabolic proteins in adi-pose tissue, liver and brain in Surf1+/+ and Surf1-/- mice.  Gene expression was differentially regulated in a tissue specific pattern. We found that many proteins and metabolites are downregulated in Surf1-/- adipose tissue and reversed by DR, while in brain most metabolites that changed were elevated in Surf1-/- mice.  Finally, mitochondrial unfolded protein response (UPRmt)-associated proteins were not uniformly altered by age or genotype, suggesting the UPRmt is not a key player in aging or the response to reduced COX activity.  While the changes in gene expression and metabolism may represent com-pensatory responses to mitochondrial stress, the important outcome of this study is that lifespan and healthspan are not compromised in Surf1-/- mice, suggesting that mitochondrial deficiencies may not be a critical determinant of lifespan.

overall_design:
Total RNA extracted from liver, fat (white adipose tissue), and brain (cortex) of Surf1+/+ and Surf1-/- mice
Number of samples total: 44: with 16 samples in Liver (8 WT, 8 Surf1 KO), 12 samples in Fat (6 WT, 6 Surf1 KO), and 16 samples in Brain (8 WT, 8 Surf1 KO)

first: Sathyaseelan

middle: S

last: Deepa

first: Gavin

last: Pharaoh

first: Michael

last: Kinter

first: Vivian

last: Diaz

first: Kaitlyn

last: Riddle

first: Daniel

last: Pulliam

first: Shauna

last: Hill

first: Kathleen

last: Fischer

first: Vanessa

last: Soto

first: Constantin

last: Georgescu

first: Jonathan

last: Wren

first: Carlo

last: Viscomi

first: Arlan

last: Richardson

first: Holly

last: Van Remmen


title: ATAC sequence analysis to compare MMTV-PyMT tumor cells with and without Dll1

first: Rumela

last: Chakrabarti

summary: Several genes like Nfkb, Npy and Dll1 showed altered enrichment peaks between Dll1+ and Dll1- population of tumor cells.

overall_design: Examination of MMTV-PyMT, Dll1-mCherry+ (n=3) and MMTV-PyMT, Dll1-mCherry- (n=4) tumor cells.


title: Quantitative Analysis of ERR gamma-driven pancreatic acinar cell transcriptome

status: Public on Nov 19 2020

city: Daegu

first: Dipanjan

last: Chanda

address: Chilgok

country: South Korea

institute: Kyungpook National University Hospital

summary: The goal of this study is to compare NGS-derived pancreatic acinar cell-based transcriptome profiling (RNA-seq) to evaluate ERR gamma-driven transcriptional program

overall_design: Gene expression profiling upon ERR gamma overexpression in pancreatic acinar cells

first: In-Kyu

last: Lee


title: Characterization of FOXA1 mutations in breast cancer (ATAC-seq KnockIn)

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

summary: Invasive Lobular Carcinoma (ILC) is the second most frequent breast cancer (BCa) type and encompasses 10-15% of BCa cases. FOXA1 specific mutations are enriched in this subtype of BCa, however their role in breast cancer pathogenesis is still ill-defined. FOXA1, together with estrogen receptor (ER), is a key transcription factor for the correct activation of estrogen-dependent gene expression and, consequently, for mammary gland development and BCa identity. FOXA1 has the capability to bind to and de-compact heterochromatin to render it accessible for other nuclear proteins, such as ER, and allow activation of their transcriptional programs upon estrogen stimulation. In this project, we aim to elucidate the role of FOXA1 missense mutations in altering its binding to DNA, chromatin accessibility, ER-dependent transcription and their implication in limiting the sensitivity to standard-of-care anti-hormonal therapy, commonly used in ER-positive BCa patients. To this end, we have generated BCa cell lines expressing these FOXA1 mutations and we will employ ATAC-Seq, RIME assays, ChIP-Seq and RNA-Seq to ascertain their effect on DNA accessibility, DNA binding capability, as well as binding of transcriptional coregulators, such as ER, to chromatin. We will extend our analyses to our internal BCa patient datasets with detailed clinical annotation to study the correlation between presence of FOXA1 mutations and response to anti-hormonal therapy of ER-positive BCa patients. The results of this project will allow to understand how the different mutations in the Forkhead domain can alter FOXA1 and ER function, transcriptional regulation and response to anti-hormonal therapy in ER-positive BCa patients.

overall_design: ATAC-seq analysis of MCF7 cells with knockin of either FOXA1 wild-type (WT) or a FOXA1 mutant (SY242CS) construct.

first: Amaia

last: Arruabarrena-Aristorena

first: Jesper

last: Maag


title: Development of a 3D functional assay and identification of biomarkers, predictive for response of high-grade serous ovarian cancer (HGSOC) patients to poly-ADP ribose polymerase inhibitors (PARPIs) - targeted therapy

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

summary: Epithelial ovarian cancer (EOC) is the most serious of all gynecological cancers, mainly due to its asymptomatic nature and the resulting lack of early diagnosis. Cells with defects in DNA repair accumulate genetic abnormalities and may progress to become malignant. However, this DNA repair deficiency makes tumor cells vulnerable to further compromise by therapeutic targeting of other associated pathways, using agents such as poly-ADP ribose polymerase (PARP) inhibitors (PARPIs). A major challenge facing the use of PARPIs is the paucity of functional assays/biomarkers to identify HGSOC patients who may benefit from these agents, in particular the subgroup with non-BRCA-mutant, HR-deficient cancers. Our study presents a predictive tool which may help identify sporadic HGSOC patients, most likely to respond to PARPIs therapy. We have successfully developed and employed a functional 3D assay to test PARPIs sensitivity in EOC based on ascites-derived primary cell cultures (AsPCs) from EOC patients. Our data showed that this approach can better mimic primary tumor response to PARPIs treatments. We have successfully grown 42 AsPCs, and have prepared spheroid cultures from AsPCs using 3D-Biomatrix technology. We were able to monitor the cytotoxic effect on AsPCs spheroids of each of the drugs olaparib (Astra- Zeneca) and niraparib (Tesaro, licensed from Merck). Our results showed that AsPCs appear to be much more sensitive to niraparib compared to olaparaib.   The cytotoxic effect observed by the two drugs was confirmed by analysis of γH2AX foci formation. Data demonstrated γH2AX foci to significantly increase in cell lines that are sensitive to the drug treatments. Consecutively, epithelial-to-mesenchymal transition (EMT) was also assessed in resistant vs. sensitive cell lines. Our results indicate that PARP inhibition can inhibit the acquisition of an EMT phenotype in sensitive cell lines, but not in resistant cell lines.   Moreover, global gene and microRNA expression profiling of PARPI-R and PARPI-S spheroid cultures identifies gene/mRNA biomarkers, associated with PARPI sensitivity. We believe our predictive tool has helped classify genes that can be clinically relevant in identifying PARP inhibitor sensitivity in ovarian cancer.

overall_design: Gene expression comparison of PARP-inhibitor sensitive AsPC vs resistant AsPC


title: Characterization of FOXA1 mutations in breast cancer (ChIP V5)

overall_design: ChIP-seq analysis of MCF7 cells overexpressing either FOXA1 wild-type (WT) or FOXA1 mutant (F266L) constructs.


title: Molecular detection of maturation stages in the developing kidney

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

summary: To identify maturation-dependent genes, we here performed single cell RNA sequencing (scRNA-seq) analysis using developing kidneys at different stages in the mouse, followed by highly sensitive in situ hybridization. We identified multiple genes expressed abundantly in newborn kidneys, but minimally at embryonic day 15.5. We then applied these maturation markers to the transplanted embryonic kidneys and found that the maturation process did not occur equally throughout nephron segments upon transplantation: glomeruli and proximal renal tubules became more mature than the other nephron segments. Thus, our scRNA-seq data at multiple stages of kidney development and identified maturation-dependent genes will serve as useful bases for assessing maturation of the developing kidney, and eventually of kidney organoids.

overall_design:
Kidney mRNA profiles of embryonic day 15.5, 17.5 and postnatal day 0 mice were generated by deep sequencing, using Illumina 10x
E12.5 embryonic kidneys were transplanted into the epididymis fat of NOD immuno deficient mice for 12 days

first: Hidekazu

last: Nagamuma

first: Koichiro

last: Miike

first: Akio

last: Kobayashi

first: Ryuichi

last: Nishinakamura


title: Two interacting ethylene response factors regulate heat stress response in Arabidopsis

city: La Jolla

first: Joanne

last: Chory

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Biology Laboratory

institute: Salk Institute for Biological Studies

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

overall_design: Refer to individual Series


title: Single-cell sequencing from the same pool of cells (identical barcodes) to generate short and long reads.

city: Berlin

first: Nikolaus

last: Rajewsky

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

summary: To understand gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level.

overall_design: An exponentially growing fixed human cell line was used for droplet-based single-cell mRNA transcriptome profiling in order to get gene expression levels and isoform diversity at the single-cell level.

first: Salah

last: Ayoub

first: Jonathan

last: Alles

first: Nikos

last: Karaiskos

first: Seung

last: Kim


title: The transcriptome dynamics of single cells during the cell cycle.

summary: We used the dataset to perform in-silico sorting of single cell transcriptomes along the cell cycle and thus being able to investigate gene expression dynamics along the mammalian cell cycle.

overall_design: An exponentially growing fixed human cell line was used for droplet-based single-cell mRNA transcriptome profiling in order to perform a posteriori in-silico sorting of single cell transcriptomes along the cell cycle and investigation of gene expression dynamics along the mammalian cell cycle.

first: Sara

last: Formichetti

first: Valerio

last: Fulci

first: Christine

last: Kocks


title: Transcriptome response study of arabidopsis wild type (Col-0), ERF95 and ERF97 overexpression lines to basal heat stress

summary: Analysis of transcriptome response of heat treated or untreated 7-day old whole seedlings with genotypes: Col-0 (wild type), p35S:ERF95 overexpression line and p35S:ERF97 overexpression line.  ERF95 and ERF97 are involved in heat stress response. Results provide insight into the nuclear genes expression profile under heat treatment in Col-0, the nuclear genes expression profile regulated by either ERF95 and ERF97 overexpression before and after heat treatment, and the regulation similarity between ERF95 and ERF97 overexpression lines.

overall_design: Total RNA samples were isolated from 7-day old whole seedlings with genotypes Col-0 (wild type), ERF95 and ERF97 overexpression lines grew under 16 h/8 h light/dark cycle condition with 100 µmol.m-2.s-1 light intensity at 22 °C following with or without 43 °C 22 min heat treatment. mRNA expression profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

first: Jianyan

last: Huang

first: Xiaobo

last: Zhao


title: Single-cell RNA-sequencing analysis for the molecular taxonomy of primate amygdala

city: shanghai

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: We thus isolated amygdala from rhesus macaques and performed single-cell RNA-sequencing analysis. The scRNA-Seq libraries were generated using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V2 Reagent Kits (10X Genomics, Pleasanton, USA). Briefly, cells nuclei were concentrated to 1000 nuclei/μL and approximately 15000 nuclei were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), which results into expected mRNA barcoding of 9000 single nucleus for each sample.

overall_design: One group, three samples were included.

first: Lei

last: Zhang


title: Impact of cadmium stress on the transcriptome of Streptococcus pneumoniae

city: Melbourne

first: Stephanie

last: Neville

state: Victoria

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: The University of Melbourne

summary: This study reports the impact of cadmium toxicity on the transcriptome of S. pneumoniae. The most transcriptionally-responsive pathways were found to be carbon source metabolism, fatty acid biosynthesis, cellular metal homeostasis and competence. This data provides a global overview of how the pneumococcus responds to metal ion intoxication, and subsequently, how it maintains viability during this stress.

overall_design: Purified RNA from four biological replicates of untreated S. pneumoniae D39 and S. pneumoniae D39 treated with 30 µM cadmium were pooled for RNA sequencing. Data was used to compare gene expression in the untreated cells to cadmium-treated cells.

first: Bart

middle: A

last: Eijkelkamp


title: Differential transcription in E. coli WT vs. fum null mutants in response to DNA damage induction

city: Jerusalem

first: Ophry

last: Pines

address: Ein Kerem Campus

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew university of Jerusalem

summary: The objective was to study the transcriptional profiles of fum null mutants vs the WT strain via RNA-seq, in order to find differentially expressed genes (DEGs, up or down regulated) in the WT strain in response to MMS treatment (0.35% [v/v],30 min), and more importantly in response to MMS+α-KG (0.35% [v/v], 30 min +25mM α-KG when indicated), compared to the mutant strains.

overall_design: 15 samples (with three biological replicates=overall 45 samples), refrece sample is the WT (BW25113) trated and untreated

first: Silas

last: Yardena

first: Pines

last: Ophry


title: Transcriptional analysis of the effect of monoamine oxidase A (MAOA) in human prostate cancer enzalutamide (ENZ)-resistant C4-2B (C4-2B ENZR) and LNCaP cells

city: Spokane

first: Boyang

last: Wu

state: Washington

address: 412 E. Spokane Falls Blvd

institute: Washington State University

summary: The overall goal of this study was to compare gene expression profiles in control and MAOA-knockdown prostate cancer cells.

overall_design: Stable silencing of MAOA in two human prostate cancer cell lines C4-2B ENZR and LNCaP was established using shRNA-expressing lentiviral infection followed by antibiotic selection. Four samples were analyzed by RNA-Seq.


title: Characterization of FOXA1 mutations in breast cancer (RNA-seq)

city: New York

first: Richard

last: Koche

overall_design: RNA-Seq analysis of MCF7 cells overexpressing either empty vector (EV),  FOXA1 wild-type (WTNS) or FOXA1 mutant (SY242CS, H247Y, S250F, F266L) constructs, in triplicates.

first: Amaia

last: Arruabarrena-Aristorena

first: Jesper

last: Maag


title: PRDM9 activity depends on HELLS and promotes 5-Hydroxymethylcytosine enrichment

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

summary: Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) at specific genomic locations that correspond to PRDM9-binding sites. The molecular steps occurring from PRDM9 binding to DSB formation are unknown. Using proteomic approaches to find PRDM9 partners, we identified HELLS, a member of the SNF2-like family of chromatin remodelers. Upon functional analyses during mouse male meiosis, we demonstrated that HELLS is required for PRDM9 binding and DSB activity at PRDM9 sites. However, HELLS is not required for DSB activity at PRDM9-independent sites. HELLS is also essential for 5-hydroxymethylcytosine (5hmC) enrichment at PRDM9 sites. Analyses of 5hmC in mice deficient for SPO11, which catalyzes DSB formation, and in PRDM9 methyltransferase deficient mice reveal that 5hmC is triggered at DSB-prone sites upon PRDM9 binding and histone modification, but independent of DSB activity. These findings highlight the complex regulation of the chromatin and epigenetic environments at PRDM9-specified hotspots.

overall_design:
5hMeDiP-seq and DMC1-SSDS experiments were performed on testis from different mouse lines
Please note that each processed data was generated from merged replicates and is linked to the corresponding *replicate 1 sample records.

first: Yukiko

last: Imai

first: Mathilde

last: Biot

last: Clément

first: Mariko

last: Inagaki

first: Serge

last: Urbach

first: Thomas

last: Robert

first: Frédéric

last: Baudat

first: Corinne

last: Grey

first: Bernard

last: de Massy


title: Characterization of FOXA1 mutations in breast cancer (ChIP-seq)

overall_design: ChIP-Seq analysis of MCF7 cells overexpressing either empty vector (EV),  FOXA1 wild-type (WTNS) or FOXA1 mutant (SY242CS, H247Y, S250F, F266L) constructs, in duplicates.


title: Two interacting ethylene response factors regulate heat stress response in Arabidopsis [ChIP-seq]

first: Joanne

last: Chory

summary: Analysis the binding targets of ERF95 and ERF97 with and without basal heat stress treatment using 7-day-old whole seedlings. Results provide insight into the binding targets of ERF95 and ERF97 before and after basal heat stress treatment, and the common targets between ERF95 and ERF97.

overall_design: We performed whole-genome chromatin immunoprecipitation with sequencing (ChIP-seq) analysis on 7-day-old Col-0, ERF95ox and ERF97ox seedlings with and without basal heat stress treatment.

first: Jianyan

last: Huang

first: Xiaobo

last: Zhao

first: Marco

last: Bürger

first: Yurong

last: Wang


title: A transcriptional switch in a novel non-canonical, ßcatenin dependent Wnt pathway controls axon midline decisions

city: San Joan d'Alacant

first: Eloísa

last: Herrera

address: Av Ramon y Cajal s/n

department: Instituto Neurociencias Alicante

institute: CSIC-UMH

summary: During the establishment of neuronal connections, axons must correctly navigate long pathways to find their targets. By focusing on the guidance of visual axons at the midline, we describe for the first time that a switch in a novel branch of the Wnt pathway, which is not the canonical or the non-canonical, that controls axonal directionality. This finding conciliates the current debate about the participation of the Wnt pathways in axon pathfinding.  We then identify the transcription factor (TF) Zic2 as the regulator of this switch and describe the entire set of genes regulated by it. Also, although previous genome-wide approaches have not retrieved the binding motif for this TF, we report here a de novo Zic2 binding motif that is located in promoter and intragenic regions. In addition, we find that the tyrosine kinase EphB receptor, which is one of the genes induced by Zic2, interferes with the Wnt pathway by phosphorylating betacatenin at the growth cone and inducing its asymmetric detachment from the membrane to promote axon steering.

overall_design: RNA-seq of Retinal ganglion cells (RGC) expressing GFP or Zic2, ChIP-seq of Zic2 in spinal cords and retina.

first: Maria

middle: T

last: López-Cascales

first: Cruz

last: Morenilla Palao

first: Jose

last: López-Atalaya

first: Luis

last: Calvo Diaz

first: Ángel

last: Barco Guerrero

first: Eloisa

last: Herrera González de Molina


title: Characterization of FOXA1 mutations in breast cancer (ATAC-seq)

first: Richard

last: Koche

overall_design: Omni-ATAC analysis of MCF7 cells overexpressing either empty vector (EV),  FOXA1 wild-type (WTNS) or FOXA1 mutant (SY242CS, H247Y, S250F, F266L) constructs, in duplicates

first: Amaia

last: Arruabarrena-Aristorena

first: Jesper

last: Maag


title: The RSC (Remodels the Structure of Chromatin) complex of Candida albicans shows compositional divergence and plays distinct roles in regulating pathogenic traits

city: Mumbai

first: Santanu

last: Ghosh

state: Maharashtra

address: Lab 303, BSBE Dept, IIT Bombay, Powai

department: Biosciences and Bioengineering

institute: IIT Bombay

summary: Regulation of gene expression programs is crucial for the survival of microbial pathogens in host environments and for their ability to cause disease. Here we investigated the epigenetic regulator RSC (Remodels the Structure of Chromatin) in the most prevalent human fungal pathogen Candida albicans. Biochemical analysis showed that CaRSC comprises 13 subunits and contains two novel non-essential members, which we named Nri1 and Nri2 (Novel RSC Interactors) that are exclusive to the CTG clade of Saccharomycotina. Genetic analysis showed distinct essentiality of C. albicans RSC subunits compared to model fungal species suggesting functional and structural divergence of RSC functions in this fungal pathogen. Transcriptomic and proteomic profiling of a conditional mutant of the essential catalytic subunit STH1 demonstrated global roles of RSC in C. albicans biology, with the majority of growth-related processes affected, as well as mis-regulation of genes involved in morphotype switching, host-pathogen interaction and adaptive fitness. We further assessed the functions of non-essential CaRSC subunits, showing that the novel subunit Nri1 and the bromodomain subunit Rsc4 play roles in filamentation and stress responses; and also interacted at the genetic level to regulate cell viability. Consistent with these roles, Rsc4 is required for full virulence of C. albicans in the murine model of systemic infection. Taken together, our data builds the first comprehensive study of the composition and roles of RSC in C. albicans, showing conserved and distinct features compared to model fungal systems, and illuminating how C. albicans uses RSC-dependent transcriptional regulation to respond to environmental signals and drive fitness and virulence in mammals.

overall_design: We investigated the global functions of RSC in C. albicans by analyzing the changes in the transcriptome of cells lacking the catalytic subunit Sth1. A conditional mutant harboring a doxycycline (dox)-repressible allele of STH1 (sth1∆/pTetO-STH1-MYC) was analysed in the presence or absence of 20 µg/ml dox. To assess the effect of dox alone on gene expression a near-isogenic sth1∆/STH1-MYC strain was also analysed. Three biological replicates per condition were analyzed.

first: Vinutha

last: Balachandra

first: Jiyoti

last: Verma

first: Madhu

last: Shankar

first: Timothy

middle: M

last: Tucey

first: Ana

last: Traven

first: Ralf

middle: B

last: Schittenhelm


title: Skeletal muscle gene expression changes one year following Roux-en-Y gastric bypass (RYGB) surgery

status: Public on Nov 18 2020

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

summary: We used gene expression microarray to understand the gene expression changes in skeletal muscle one year follow RYGB weight loss surgery.

overall_design: Vastus Lateralis samples were taken prior to and one year follow RYGB surgery. We sought to explore skeletal muscle gene expression profiles following surgical weightloss.

first: Barberio

last: Matthew

first: Hubal

last: Monica


title: Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL

city: Granada

first: Pedro

last: Medina Vico

state: Granada

address: Avenida de Fuente Nueva, s/n

department: Biochemistry and Molecular Biology I

institute: University of Granada

summary: Mutations in genes encoding the various subunits of the SWI/SNF chromatin remodeling complex are frequently observed in different human cancers. In diffuse large B-cell lymphoma (DLBCL), genetic changes in BCL7A, a subunit of the SWI/SNF complex, have been recently reported but the functional role of such genetic changes remains unknown. BCL7A mutations concentrate at the first exon and the most frequently mutated hotspot is the splice donor site of the first intron. By using in vitro and in vivo analyses, we show that restoration of BCL7A drives a tumor suppressor-like phenotype. Further, we found that splice site mutations block the tumor suppressor phenotype and prevent BCL7A from binding to the SWI/SNF complex. Finally, we identified that the SWI/SNF complex accumulates mutations in a third of DLBCL tumors, especially in the GCB subtype. These discoveries highlight the tumor suppressor role of BCL7A mutations in DLBCL, and suggest that the SWI/SNF complex is involved in DLBCL pathogenesis.

overall_design: Two DLBCL cell lines were used: OCI-LY1 and VAL. For each cell line, three conditions were tested: empty vector, wild type BCL7A overexpression, and splice site mutant BCL7A overexpression (delta27-BCL7A). Two biological replicates per condition were obtained.

first: Alvaro

last: Andrades

first: Carlos

last: Balinas-Gavira

middle: P

last: Medina


title: Role of hNABP2 (hSSB1) in transcriptional regulation

city: Saskatoon

first: Yuliang

last: Wu

state: Saskatchewan

address: Rm 4D01.1, HSB, 107 Wiggins Road

department: BMI

institute: University of Saskatchewan

summary: Use Global Run-On assay (GRO)-seq, chromatin immunoprecipitation (ChIP)-seq, and DNA: RNA immunoprecipitation (DRIP)-seq to investigate whether and how hNABP2 (hSSB1) regualte transcription.

overall_design: Global Run-On assay (GRO)-Seq: nascent RNA was pulled down by anti-BrDU conjugated beads, the RNA extracted from the GRO reaction was converted into cDNA, and library was prepared using the NEBNext Ultra II directional library prep kit (E7760, NEB). ChIP-Seq: chromatin was crosslinked with formaldehyde, DNA was sheared by sonication, and hNABP2-bound DNA was pulled down by hNABP2 antibod. the ChIPed DNA was end repaired using NEBNext Ultra II End Prep buffer and Enzyme mix, adaptor-ligated, cleaned with 0.9× AMPure beads. The adaptor ligated DNA was then amplified using four (Index 17, 24, 26 and 28) NEBNext Multiplex Oligos for Illumina and universal primers (E7335, NEB) for the two independent experiments. DNA: RNA immunoprecipitation (DRIP)-Seq: The DNA:RNA immunoprecipitation was performed DNA was incubated with S9.6 antibody  The RNA was extracted from the DRIP samples using Monarch RNA extraction kit (T2010, NEB). The libraries were constructed using directional RNA library prep kit.

first: Venkatasubramanian

last: Vidhyasagar

first: Shizhuo

last: Yang

first: Daniel

last: Hogan

first: Manhong

last: Guo

first: Ravi

last: Singh

first: Manisha

last: Yadav

first: Anthony

last: Kusalik

first: Peter

middle: C

last: Stirling

first: Franco

last: Vizeacoumar


title: A bioisostere of Dimebon/Latrepirdine delays the onset and slows the progression of pathology in FUS transgenic mice

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

summary: Despite intensive studies that improved our understanding of the disease mechanisms and multiple clinical trials, amyotrophic lateral sclerosis (ALS) remains an uncurable disease. Riluzole and Edaravone, two currently approved drugs, provide limited quality-of-life improvements in ALS patients. This emphasises the importance of searching for new drugs and therapeutic approaches that might be used, most probably in combination, for efficient treatment of ALS. A neuroprotective ability of certain gamma-carbolines, including Dimebon/Latrepirdine and its derivates, has been demonstrated in several models of neurodegeneration, suggesting that these compounds have a potential as components of a multiplex disease-modifying therapy of ALS. In this study we showed that a chronic treatment with a novel Dimebon bioisostere, DF402, delays the onset and slows the progression of pathology in the transgenic model of motor neuron disease caused by expression of pathogenic truncated form of human FUS protein. By using CatWalk gait analysis we have revealed parameters of transgenic animal gait that display changes before manifestation of clinical signs of pathology and parameters that are changed at the pre-symptomatic stage in response to DF402 treatment. RNAseq was used to compare the spinal cord transcriptomes of wild type, untreated and DF402-treated FUS transgenic mice. We found that at the early pre-symptomatic stage a limited number of genes significantly change expression in the spinal cord of transgenic mice and demonstrated that for 60% of these genes DF402 treatment causes the reversion of expression towards levels typical for expression of these genes in the spinal cord of wild type animals.

overall_design: Deep RNA sequencing of thoracic and lumbar regions of spinal cord

first: A


title: circRNAs, miRNAs and mRNAs expression profiling in rBMSCs affected by Ta-modified Ti surface or simple Ti surface

city: Shanghai

first: junyu

last: shi

address: 639 zhi-zao-ju road

department: Department of Implant Dentistry

institute: Shanghai Ninth People’s Hospital

summary: We have employed  circRNAs, miRNAs and mRNAs expression profiling as a discovery platform to identify genes with the potential to distinguish rBMSCs affected by Ta-modified Ti surface or simple Ti surface

overall_design: The rBMSCs were cultured on Ta-modified surface for 7 days, gene expression in  rBMSCs was measured.  Three independent experiments were performed in each group.


title: Interdependencies of Intratumoral Genetic Heterogeneity and the Immune Microenvironment in Chronic Lymphocytic Leukemia

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

summary: The tumor microenvironment (TME) and somatic mutations drive progression of chronic lymphocytic leukemia (CLL). Integrated bulk and single-cell RNA sequencing (RNA-seq) of paired peripheral blood (PB) and lymph node (LN) samples from patients with treatment naïve CLL showed upregulation of oncogenic processes in LN attributable to a minor population of activated tumor cells. A 10-gene activated tumor signature was positively correlated with activated CD4+ T cells and M2 macrophages in the TME. Whole exome sequencing of paired PB and LN samples showed subclonal expansion in LN in some patients. In remaining patients with clonal stability between PB and LN, a T-cell inflamed TME was detected by RNA-seq. These data connect the TME with molecular events in the pathogenesis of CLL.

overall_design: Single cell RNA sequencing (scRNA-seq) of paired peripheral blood and lymph node (n = 5 patients).

first: Clare

last: Sun

first: Yun-Ching

last: Chen

first: Adrian

last: Wiestner


title: Profile analysis of circRNAs in osteoclasts infected by intracellular Staphylococcus aureus

city: 苏州

first: haifang

last: zhang

address: 苏州

institute: 苏州大学附属二院

summary: This study aims to compared differential expression circRNA between normal and intracellular Staphylococcus aureus infection in osteoclast

overall_design: 6 samples were analyzed including 3 samples of control groups and intracellular Staphylococcus aureus infection group.

first: Zhihao

first: Xi

last: Wang

first: Liubing

last: Li


title: The miR-23a~27a~24-2 microRNA cluster promotes inflammatory polarization of macrophages

city: South Bend

first: Richard

last: Dahl

state: IN

address: Harper Hall 227, 1234 Notre Dame Ave.

institute: Indiana University School of Medicine, South Bend

summary:
Purpose: RNA-sequencing was performed to identify gene expression changes between bone marrow derived macrophages isolated from wildtype and mirn23a-/- (Mirc11-/-) mice that were either M1 or M2 polarized.
Results: Diferential gene expression was examined between wildtype and mirn23a-/- M1 polarized macrophages and wildtype and mirn23a-/- M2 polarized macrophages. The number of genes with significant (p<0.05) 2-fold changes in our M1 dataset is 4-fold higher than the 2-fold changed genes in our M2 dataset. 43 unique genes were differentially expressed over 2-fold in M1 mutant macrophages compared to wildtype with 29 upregulated and 14 downregulated. 10 genes (8 downregulated/ 2 upregulated)were differentially expressed in mirn23a-/- M2 macrophages by at least 2-fold compared to wildtype.

overall_design: Wildtype and mirn23a-/- (Mirc11-/-) bone marrow derived macrophage gene expression profiles after 24h of polarization (M1 or M2 conditions).

first: Sridhar

last: Rao

first: Kirthi

last: Pulakanti

first: Austin

last: Boucher


title: Gene expression of Mirc11-/- hematopoietic myeloid progenitors

summary: Compared gene expression between Lin-Sca1-cKit+ myeloid progenitors isolated from the bone marrow of 6-8 week old wildtype and Mirc11-/- mice. Previously observed that overexpression of Mirc11 in hematopoietic progenitors increased myeloid differentiation whereas loss of Mirc11 decreased myeloid differentiation. Performed RNA-seq to identify potential genes involved in myeloid differentiation regulated by Mirc11.  Gene expression analysis of Mirc11 deficient myeloid progenitors revealed a decrease in Toll like receptor and interferon signaling. This anti-inflammatory phenotype was further observed in mature cells as Mirc11-/- bone marrow derived macrophages (BMDMs) have an attenuated response to inflammatory lip-opolysaccharide (LPS).

overall_design: Sequenced total RNA obtained from Lin-Sca1-cKit+ bone marrow cells obtained from cohorts of wildtype and Mirc11 deleted mice.


title: Bone marrow-derived myeloid progenitors in the leptomeninges of adult mice

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

country: Switzerland

institute: University of Bern

summary: We describe a heterogeneous population of myeloid progenitors in the leptomeninges of adult C57BL/6 mice. This cell pool included common myeloid, granulocyte/macrophage, and megakaryocyte/erythrocyte progenitors. Accordingly, it gave rise to all major mye

overall_design: Single cell RNA profile of meningeal/brain surface cell preparation collected from five C57BL/6 WT mice (pooled) and enriched for KIT/CD117+ cells

first: Tobias

last: Königer

first: Luisa

last: Bell

first: Anika

last: Mifka

first: Michael

last: Enders

first: Valentin

last: Hautmann

first: Subba

last: Mekala

first: Arif

last: Ekici

first: Christian

last: Schulz

first: Stine

last: Mencl

first: Christoph

last: Kleinschnitz

first: Süleyman

last: Ergün

first: Stefanie

last: Kürten


title: Mirc11 role in myeloid differentiation

first: Richard

last: Dahl

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

overall_design: Refer to individual Series


title: single cell RNA sequencing of transplanted mouse hematopoietic stem cells

city: los angeles

first: Du

last: Jiang

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

summary: transcriptome analysis of mouse hematopoietic stem cells four months post transplantation at single cell resolution

overall_design: barcoded GFP+ HSCs were FACS-sorted from four independent recipient mice 4 months post transplantation, then subjected to processed using the Chromium Single-cell 3′ v2 Library Kit (10× Genomics, Pleasanton, CA) following the manufacturer’s instructions

first: Adnan

last: Chowdhury


title: Dermacentor marginatus female adults transcriptome

city: Urumqi

first: Ercha

last: Hu

state: Xinjiang

address: Nongda east Rd311

department: College of Veterinary

country: China

institute: Xinjiang Agricultural University

summary: The Ixodidea tick Dermacentor marginatus is a vector of many pathogens wide spread in Eurasia. Study of gene targets of the tick species provides insight to find novel tick protective antigen for drug development and vaccine targets. To obtain a broader picture of gene sequences and changes in expression level, we aimed to characterize the whole body transcriptome in D. marginatus adult female after engorgement and long-term starvation using RNA-seq. We have assembled and analyzed transcriptome of D. marginatus females 5 days after ecdysis, 24 h after a blood meal, and 6 months under controlled experimental conditions. Sequencing produced 30251 unigenes, of which 32% were annotated using Trinity. Gene expression was compared among groups differed by status as newly molted, starved and engorged female adult ticks. Nearly 1/3 of the unigenes in each group were differentially expressed compared to the other two group, and we found that the most numerous were proteins involved in catalytic and binding activities and apoptosis. Selected up-regulated differentially expressed genes in each group associated to protein, lipids, carbohydrate and chitin metabolism. Blood feeding and long-term starvation also caused genes differentially expressed in the defense response and antioxidant response. Finding the sequence information and expression pattern would be helpful in understanding molecular physiology of D. marginatus, and provides information for anti-tick vaccine and drug development.

overall_design: Nine samples are prepared for sequencing

first: Bayin

last: Chahan

first: Hu

last: Ercha

first: Meng

last: Yuan

first: Song

last: Ruiqi

first: Ma

last: Ying

last: Zhengxiang

first: Li

last: Min

first: Hao

last: Yunwei


title: Retinal transcriptome analysis of Rbfox2 deficient animals

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: Rbfox proteins regulate alternative splicing, mRNA stability and translation. These proteins are involved in neurogenesis and have been associated with various neurological conditions. We generated expression profile in adult and developing mouse retinas which lacks in Rbfox2 expression by RNA sequencing. The goals of this study is to identify the affected pathways in Rbfox2 KO mouse retina as well as potential splicing targets of Rbfox2.

overall_design: Retinal transcriptome of Rbfox2-/- (n=4) and control (n=4) animals was analyzed with RNA-seq.

first: Natik

last: Piri

first: Lei

last: Gu


title: Expression data from chemoresistant human non-small cell lung cancer

city: Shiyan

first: Fuyun

last: Ji

state: Hubei

address: South Renmin Road

department: Department of Medical Biology, School of Basic Medical Science

institute: Hubei University of Medicine

summary: Chemoresistance induced by cisplatin application hinders the clinical outcomes of chemotherapy and needs resolving, hence we sought to find its modulating role in tumorogenesis or drug resistance between  human lung adenocarcinoma cancer cell line A549 and its chemoresistant cell line A549/DDP.

overall_design: RNA extraction and hybridization on Affymetrix microarrays was utilized to evaluate the global differentiated gene expression profile  between A549 and A549/DDP.

first: Shilong

last: Yu


title: Characterization of simplified brain organoids (simBOs) derived from primitive neural stem cells (pNSCs)

city: Daejeon

first: Jeongmin

last: Ha

address: 125, Gwahak-ro, Yuseong-gu

department: Stem Cell Research Center

institute: Korea Research Institute of Bioscience and Biotechnology

summary: We established simplified brain organoids (simBOs), composed of mature neurons and astrocytes from expandable hPSC-derived primitive neural stem cells (pNSCs) that can be rapidly generated in 2 weeks and have more homogeneous properties. Transcriptome analysis revealed that three-dimensional (3D) differentiation facilitates the conversion of pNSCs to mature neuronal systems compared to a two-dimensional environment in the context of neurotransmitter release, synaptic vesicle formation, ion channels, calcium signaling, axonal guidance, extracellular matrix organization, and cell cycle. This was correlated with the translocation of YAP1 into the cytoplasm by sensing matrix stiffness on the 3D models.

overall_design: Comparions between pNSCs and simBOs or 2D differentiation and simBOs (3D)

first: Ji

last: Kang

first: Minhyung

last: Lee

first: Areum

last: Baek

first: Seongjun

last: Kim

first: Sun-Ku

last: Chung

first: Mi-Ok

first: Janghwan


title: RNA-Seq of U2OS cells with and without IFNα2 pretreatment

city: Utrecht

first: Sanne

last: Boersma

state: (None)

address: Uppsalalaan 8

institute: Hubrecht institute

summary: RNA viruses are among the most prevalent pathogens and represent a major burden on society. While RNA viruses have been studied extensively, little is known about the processes that occur during the first several hours of infection due to a lack of sensitive assays. Here, we develop a single-molecule imaging assay, virus infection real-time imaging (VIRIM), to study translation and replication of individual RNA viruses in live cells. VIRIM uncovered a striking heterogeneity in replication dynamics between cells and revealed extensive coordination between translation and replication of single viral RNAs. Furthermore, using VIRIM we identify the replication step of the incoming viral RNA as a major bottleneck of successful infection, and identify host genes that are responsible for inhibition of early virus replication. Single-molecule imaging of virus infection represents a powerful tool to study virus replication and virus-host interactions that may be broadly applicable to RNA viruses.

overall_design: identification of IFN-induced genes in U2OS cells

first: Marvin

last: Tanenbaum


title: KLF3 promotes the 8-cell-like transcriptional state in pluripotent stem cells

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

summary: This study identifies previously unrecognized heterogeneity due to KLF3 protein expression in mESCs.

overall_design: Examination of differential expressed genes between KLF3-GFP positive and KLF3-GFP negative / GFP and KLF3 over expressing mouse embryonic stem cells grown in normal ES culture media by Smart-seq2 and poly(A)+ RNA-Seq separately. Two biological replicates were completed for each groups.

first: Jing

last: Hao

first: Xi

last: Yang

first: Chao

last: Zhang

first: Xue-Tao

first: Ming

last: Shi

first: Shao-Hua

first: Li

last: Mi

first: Yu-Ting

last: Zhao

first: Huiqing

last: Cao


title: CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade (ATAC-Seq)

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

summary: Immune checkpoint blockade (ICB) has shown remarkable clinical efficacy across multiple cancer types. However, only a fraction of patients respond to ICB. Here, we performed pooled mutagenic screening with CRISPR-mediated genetically engineered mouse models (CRISPR-GEMMs) in ICB settings, and identified KMT2D as a major modulator of ICB response across multiple cancer types. Kmt2d encodes a histone H3K4 methyltransferase and is among the most frequently mutated genes in cancer patients. Kmt2d loss led to increased DNA damage and mutation burden, chromatin remodeling, intron retention, and activation of transposable elements. Additionally, Kmt2d-deficient cells exhibit increased protein turnover and IFN-γ-stimulated antigen presentation. In turn, Kmt2d-mutant tumors in both mouse and human are characterized by increased immune infiltration. These data demonstrate that KMT2D deficiency sensitizes tumors to ICB by augmenting tumor immunogenicity, highlighting the power of CRISPR-GEMMs for interrogating complex molecular landscapes in immunotherapeutic contexts that preserve the native tumor microenvironment.

overall_design: 3 ATAC-seq cellular replicates for each condition: Vector (-IFNG), Vector (+IFNG),sgKmt2d (-IFNG), and sgKmt2d (+IFNG)

first: Guangchuan

first: Sidi

last: Chen


title: CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade (RNA-Seq)

overall_design: PolyA RNA sequencing of mouse primary liver tumor cells (p53-/-, Myc overexpression), transduced in vitro with non-targeting vector or sgKmt2d. 3 cellular replicates for each condition.


title: Biliary-Atresia-associated Mannosidase-1-alpha-2 gene regulates biliary and ciliary morphogenesis and laterality

city: La Jolla

first: Shankar

last: Subramaniam

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

summary: RNA sequencing was performed to evaluate dysregulated genes in EGF, TGF, developmental hedgehog and ciliogenesis pathways in human Billiary Atresia (BA)

overall_design: Total RNA was extracted from four human BA recipient liver and three normal liver allografts and total RNA libraries were generated Illumina TruSeq Stranded total RNA kit.

first: Juhoon

last: So

first: Mylarappa

last: Ningappa

first: Joe

last: Glessner

first: Jun

last: Min

first: Brandon

middle: W

last: Higgs

first: Dong

last: Li

first: Qing

last: Sun

first: Lori

last: Schmitt

first: Amy

last: Biery

first: Steven

last: Dobrowolski

first: Christine

last: Trautz

first: Leah

last: Fuhrman

first: Molly

last: Schwartz

first: Nikolai

last: Klena

first: Joseph

last: Fusco

first: Krishna

last: Prasadan

first: Morayooluwa

last: Adenuga

first: Nada

last: Mohamed

first: Qi

last: Yan

first: Wei

first: William

last: Horne

first: Anil

last: Dhawan

first: Khalid

last: Sharif

first: Deirdre

last: Kelly

first: Robert

middle: H

last: Squires

first: George

middle: K

last: Gittes

first: Hakon

last: Hakonarson

first: Victor

last: Morell

first: Cecilia

last: Lo

first: Donghun

last: Shin

first: Rakesh

last: Sindhi


title: CRISPR-GEMM pooled mutagenic screening identifies KMT2D as a major modulator of immune checkpoint blockade

first: Ryan

last: Chow


title: Expression data from Human non-small cell lung cancer

first: Fuyun

last: Ji

summary: Chemoresistance induced by upregulated ZNF300 in A549/DDP, which was established with a low dosage of cisplatin treatment previously, was in clinical need of resolving.  Because ZNF300  was selected as a regulator in associated with drug resisance, we sought to find its modulating role in tumorogenesis or drug resistance.

overall_design: Lentivirus caring overexpressing and control vector of ZNF300  was utilized to tansfect the A549 cells for for RNA extraction and hybridization on Affymetrix microarrays with a view to evaluate the global gene expression profile regulated by ZNF300.

first: Shilong

last: Yu