title: The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis [ATAC-seq]


title: An amyloid protein and the lipopeptide fengycin are involved in the communication and beneficial interaction of B. subtilis with seeds

status: Public on Apr 20 2022

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

type: Expression profiling by high throughput sequencing

summary: We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of cucumis melo seeds and leaves to the treatment with B. subtilis cells or the secondary metabolite fengycin

overall_design: Transcriptomic comparison of cucumis melo seeds and leaves untreated and treated with with B. subtilis cells or the secondary metabolite fengycin

first: M

middle: V

last: Berlanga-Clavero

first: C

last: Molina-Santiago

first: D

last: Romero


title: Amniogenesis occurs in two independent waves in primate embryos

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

summary: In primates the amnion emerges through cavitation of the epiblast during implantation, whereas in other species by folding of the ectoderm later around gastrulation. How the mechanisms of amniogenesis diversified in evolution remains unknown. Here we employed the naïve-to-primed transition of human pluripotent stem cells (hPSC) to model peri-implantation epiblast development. We discovered that during this transition hPSC transiently gain the ability to differentiate into cavitating epithelium that transcriptionally matches the early amnion of human embryos. In contrast, primed hPSC produce cells resembling late amnion, uncovering an independent differentiation route. Unexpectedly, single-cell analysis of primate embryos revealed two transcriptionally distinct amniogenesis waves. The early wave occurs through a trophectoderm-like route and encompasses cavitation, whereas the late wave follows an ectoderm-like pathway during gastrulation. The discovery of two independent waves of amniogenesis both of which can be modelled in hPSC explains how amniogenesis through cavitation emerged during the evolution of primates.

overall_design: (1) Partially primed and primed hPSC were treated with MAPK and NODAL inhibitors for 5 days, then the cells were collected for 10X single-cell RNAseq. (2) Partially primed hPSC were treated with MAPK and NODAL inhibitors for 5 days, the cells were collected on day 0, 1, 3, 5 for bulk RNAseq. Experiment was done in biological duplicates.

first: Maria

last: Rostovskaya

first: Simon

last: Andrews

first: Wolf

last: Reik

first: Peter

last: Rugg-Gunn


title: Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA [ChIRP-Seq]

city: San Diego

first: Yajing

last: Hao

state: CA

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

country: USA

institute: University of California, San Diego

summary: To investigate the exact locations of CCTT-chromatin interaction on a genome-wide scale, we modified previously reported ChIRP-seq (chromatin isolation by RNA purification followed by deep-sequencing) with a crosslinker 4’- aminomethyltrioxalen (AMT, a psoralen derivative), which allows fixation of nucleic acid interaction by ultraviolet light without crosslinking proteins. We designed 8 complementary DNA oligonucleotides that tiled the Alu-depleted part of CCTT. Affinity-purified CCTT-binding DNAs were sequenced and mapped to the HuRef genome hg38, which contains human α-satellite sequence models in each centromeric region. In contrast with 5.38% of input reads mapping to α-satellite sequence, 16.89% of CCTT-binding reads were enriched at α-satellites. Peaks bound by lnc-CCTT were identified by MACS2 algorithm, which compared the reads in CCTT-captured samples with that in input ones. CCTT-binding peaks mapped across the centromeric regions of all 23 reference centromeres. Next, we validated the enrichment of centromeric peaks located at all chromosomes via ChIRP-qPCR. To validate our ChIRP-seq results, we selected representatives of three major subpopulations: multimapping peaks in one specific chromosome and several chromosomes, as well as single-copy peaks. We performed ChIRP-qPCR and found abundant CCTT-binding centromeric peaks throughout all 23 chromosomes. Importantly, CCTT ChIRP-seq profile was highly correlated with the previously reported ChIP-seq profiles of CENP-C (Pearson correlation R = 0.82), both of which showed very strong, extensive signals across entire centromeric regions in HeLa cells.

overall_design: Identification and characterization of DNA regions bound by lnc-CCTT in Hela cells

first: Dongpeng

last: Wang

first: Chong

last: Zhang

first: Yan

last: Teng

first: Xiao

last: Yang

first: Runsheng

last: Chen


title: RNA-seq for Cold-treated bamboo

status: Public on Apr 22 2022

city: 福州市

first: Qiang

last: Zhu

state: 福建省

address: 福建农林大学海峡联合研究院

country: China

institute: 福建农林大学

summary: Identification of the Cold-responsive gene

overall_design: Bamboo seedlings were treated with Cold and the materials were havested at different time point for RNA sequencing

first: Yuan

middle: Y

last: Liu


title: Study of the role of c-Maf in type 2 innate lymphoid cells

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

summary: Group 2 innate lymphoid cells (ILC2s) are involved in type 2 inflammatory diseases such as allergy. In response to repeated allergen inhalations, lung epithelial cells secrete innate cytokines that activate ILC2s to release interleukin-5 (IL-5) and interleukin-13 (IL-13) resulting in eosinophil infiltration, mucus hyper-production, and airway hyperreactivity. Beside GATA3, very little is known about the role of specific transcription factors in the regulation of ILC2’s function. Here we identify c-Maf as a crucial regulator of ILC2 function and identity. c-Maf deficient ILC2s are impaired in IL-5 and IL-13 production and eosinophil recruitment. Transcriptomic analysis underlined a reduced expression of genes associated with Th2/ILC2 identity and memory development that we confirmed both in mice and human, either in ILC2s engineered to express less c-Maf or in naturally c-Maflow ILC2s from cord blood. Our results indicate that c-Maf is a core node that connects immature to primed/trained ILC2s.

overall_design: Study of WT and c-Maf-KO ILC2 after papain induced lung inflammation. ILC2 were sorted from lungs of mouse, either WT or c-Maf KO, 5 replicates were included for each genotype.

first: Sara

last: Trabanelli

first: Grégory

last: Verdeil

first: Camilla

last: Jandus


title: eIF4A2 targets developmental potency and histone H3.3 transcripts for translational control of embryonic and cancer stemness [eCLIP-seq]

city: New York

first: Jianlong

state: NY

department: Department of Medicine

institute: Columbia University Irving Medical Center

summary: Stemness is a defining feature in embryonic and cancer stem cells. How stemness is regulated at the mRNA translational initiation remains undefined. We carried out an RNAi screen for key translation initiation factors that maintain the stemness in mouse embryonic stem cells (ESCs). We identified eIF4A2 and defined its mechanistic action through Rps26-depleted and -containing ribosomes in translational initiation activation of mRNAs encoding pluripotency factors and H3.3 for embryonic and extraembryonic lineage repression, respectively. eIF4A2 also mediates translation initiation activation of Ddx6, which acts together with eIF4A2 to restrict the totipotent 2-cell (2C) transcription program in ESCs through Zscan4 mRNA degradation and translation repression. Knockdown of eIF4A2 disrupts ESC proteome causing the loss of stemness in ESCs as well as in human glioblastomas where eIF4A2 is highly enriched. Collectively, our study establishes an eIF4A2-mediated translation initiation control of stemness and provides insight into cancer therapeutics targeting the translation initiation machinery.

overall_design: eIF4A2 binding profiling was investigated via eCLIP-seq analysis in mouse embryonic stem cells.

first: Dan

last: Li

first: Jihong


title: Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA [irCLIP-Seq]

summary: To fine-map the position of lnc-CCTT that directly interact with CENP-C, we performed irCLIP-seq (infrared crosslingking and immunoprecipitation followed by high throughput RNA sequencing), which utilize ultraviolet (UV) light to induce zero-length covalent bonds between RNA and the directly attached protein and an infrared-dye-conjugated and biotinylated ligation adaptor to isolate RNA fragments. irCLIP-seq identified a possible CENP-C binding region of lnc-CCTT ranging from nucleotides 127-177nt.


title: Mouse paternal RNAs initiate a pattern of metabolic disorders in a strain-dependent manner

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

country: France

institute: Nice Sophia Antipolis

type: Non-coding RNA profiling by high throughput sequencing

summary: A wide range of animal diseases result from environmental effects, and the level of many native transcripts altered. In particular, the contribution of the noncoding RNAs (ncRNAs) is becoming widely recognized. However, the composition and degree of heritability of the signals remain unclear. Here, we performed functional assays with mouse founders with different genotypes who were raised under the same conditions and diet to follow the transfer of their phenotype of obesity/diabetes to the next generation. From the results of RNA-based microinjection assays using sperm from male mice fed a high-fat diet (HFD) injected into fertilized eggs, previous reports indicated a modulation in the expression of endogenous functional alleles, leading to an obesity/diabetes phenotype in the newly generated mice. Here, two lines (F1 B6/D2 hybrid and Dnmt2-/-) demonstrate resistance to a HFD. However, the sperm RNAs from both lines administrated in a sensitive line raised on a normal diet (ND) induce obesity and diabetes. A reversal of the obesity phenotype was a centerpiece in an obese line administered with sperm RNAs from animals raised on a ND. Our results suggest that disease changes in endogenous transcripts level due to diet variation can be reversed by RNAs. Finally, we discuss the possibility that global RNA/DNA hybrid structures within a genome can act as molecular markers for directing induced epigenetic modifications.

overall_design: Paternal non-coding RNAs in obesity and diabetes.

first: Guzide

last: Satir-Basaran

first: Leila

last: Kianmehr

first: Ecmel

last: Mehmetbeyoğlu

first: Kezban

middle: K

last: Bayram

first: Esra

last: Tufan

first: Mehmet

last: Memis

first: Serpil

last: Taheri

first: Fahrettin

last: Keleştimur


title: The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis [RNA-seq]

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

summary: The purpose of this study was to decipher the molecular function of ARID3A. We leveraged gene expression (RNA-Seq) and chromatin profiling (ATAC-Seq and CUT&RUN) to evaluate gene expression changes upon restoring Arid3a expression in the context of the Gata1s mutation and miR-125b overexpression

overall_design: We induced Arid3a-FLAG protein using doxycyline in Gata1s-FLCs lentivirally expressing miR-125b

first: Oriol

last: Alejo-Valle


title: Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA [RIP-Seq]

first: Yajing

last: Hao

summary: To identify potential lncRNAs that associate with CENP-C, RNA immunoprecipitation (RIP) using the CENP-C and control IgG antibody was performed in the whole-cell lysates of HeLa cells, followed by Illumina short-read sequencing (RIP-seq). We found three CENP-C-binding lncRNAs that meet the enrichment criteria (fold change > 2, p < 0.01), including AGAP2-AS1, GS1-124K5.4, and AC124789.1 (lnc-CCTT) . Consistent with the results of RIP-seq, RIP-qPCR assay in whole-cell lysates showed that all three lncRNAs could bind to CENP-C, while lnc-CCTT showing the most robust association of CENP-C. ). It is well-established that the localization of lncRNAs within the cell is the primary determinant of their molecular functions. RT-qPCR (quantitative PCR with reverse transcription) assay of subcellular fractionation and RNA fluorescence in situ hybridization (RNA-FISH) revealed that AGAP2-AS1 and GS1-124K5.4 dominantly distributed in the cytoplasm, whereas lnc-CCTT, specifically and almost exclusively, localized to the nucleus. Thus, lnc-CCTT appears to be a prime interacting RNA of CENP-C at centromere.

overall_design: Identification and characterization of non-coding RNAs associated with CENPC in Hela cells

first: Dongpeng

last: Wang

first: Chong

last: Zhang

first: Yan

last: Teng

first: Xiao

last: Yang

first: Runsheng

last: Chen


title: Genome-wide binding sites of COUP-TFII in the E14.5 mesonephroi

city: Durham

first: Humphrey

middle: Hung-Chang

last: Yao

state: NC

address: 111 TW Alexander Drive

institute: NIEHS/NIH

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In an XX embryo, the Wolffian duct regresses under the control of the mesenchymal transcription factor COUP-TFII. To understand cellular and molecular actions underlying Wolffian duct regression, we preformed transcriptomic analyses of XX mesonephroi with or without Coup-tfII and genome-wide analysis of COUP-TFII chromatin occupancy in XX mesonephroi.  The integrative analysis of COUP-TFII genome-wide binding and transcriptomic analysis revealed the suppression of muscle differentiation and extracellular matrix genes by COUP-TFII and identified a group of COUP-TFII’s potential transcriptional partners in the mesenchyme that potentially facilitate Wolffian duct regression. These findings provide insights into the molecular action of COUP-TFII in the Wolffian duct mesenchyme and identify a list of biologically relevant candidate genes and pathways for future functional analyses in sexual differentiation of reproductive tracts.

overall_design: ChIP-seq for COUP-TFII and input on chromatin from pools of mouse CD1 fetal mesonephroi (E14.5).

first: Fei

last: Zhao

middle: H


title: Gene expression profile of germinal center B cells lacking Miz1 interaction with Myc

city: London

first: Dinis

middle: Pedro

last: Calado

address: Midland Road

institute: The Francis Crick Institute

summary:
Splenic germinal center B cells (B220pos, CD19pos, CD38 low, FAS high) were isolated from animals 10 days sheep red blood cell immunised animals using flow cytometry cell sorter.
Animals carry a combination of alleles that allows germinal center B cell deletion of endogenous Myc allele and simultaneous conditional overexpression of human MYC in its wild-type for or mutant form in which a valine in residue 394 has been substituted by an aspartic acid.

overall_design: The mouse WG-6 v2.0 expression beadchip array (Illumina) was used to determine gene expression of germinal center B cells

first: Martin

last: Janz

first: Probir

last: Chakravarty


title: Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA

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

overall_design: Refer to individual Series


title: Phosphorylated MED1 Links Transcription Recycling and Cancer Growth

first: Zhong

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

summary: Mammalian RNA polymerase II (Pol II) initiation, elongation, termination and reinitiation are well studied, but how Pol II dynamically recycles after the transcription cycle remains unclear. By establishing in vitro and in vivo transcription recycling systems, we find that human Mediator 1 (MED1), when phosphorylated at the mammal-specific threonine 1032 by cyclin-dependent kinase 9, dynamically travels with Pol II throughout the transcribed genes to drive Pol II recycling. Mechanistically, MED1 phosphorylation leads to an increase of recycled Pol II via the molecular bridge of MED31, enhancing mRNA output during the transcription recycling process. Importantly, MED1 phosphorylation increases during prostate cancer progression to the lethal phase, and pharmacological inhibition of CDK9 decreases prostate tumor growth through decreasing MED1 phosphorylation and Pol II recycling. Our findings reveal essential mechanisms underlying Pol II recycling and suggest a neglected, yet fundamental Pol II transcription process for therapeutic intervention.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
We have performed time-resolved ChIP-seq of pMED1, Pol2 and histone marks.

We have performed RNA-seq and analyzed transcriptome changes in LNCaP-abl cells treated with vehicle or a CDK9 inhibitor (Atuveciclib).

first: Zhenqing

last: Ye


title: Long noncoding RNA CCTT recruits CENP-C to centromeres by directly binding to centromeric DNA [SHAPE-Map]

summary: To refine the authentic CENP-C binding sites of lnc-CCTT and globally map lnc-CCTT secondary structure, we also performed SHAPE-MaP (selective 2’-hydroxyl acylation analyzes by primer extension and mutational profiling), which uses hydroxyl-selective electrophiles to modify the 2’-hydroxyl groups of unbound single-stranded nucleotides, in HeLa cells both ex vivo and in vivo. Lnc-CCTT secondary structure was modeled by combination SHAPE data from cell-free ex vivo with pairing probabilities. As expected, nucleotides 43-79 nt, a determinant for RNA-DNA triplex formation, exhibited a continuous single-strandedness, which may be prone to binding DNA. More importantly, only nucleotides 118-177 nt, which was folded into a stem-loop structure in the secondary structure, showed a significant reduced SHAPE reactivities in cell when comparing to cell-free state, suggesting this region could be attributed to interaction with protein components.

overall_design: Predict the lnc-CCTT secondary structure and CENP-C bound regions in Hela cells


title: Comparative transcriptome analysis reveals mechanisms of folate accumulation in maize grains

status: Public on Apr 19 2022

city: Beijing

first: Tong

last: Lian

address: Zhongguancun South Street

department: Biotechnology Research Institute

institute: CAAS

summary: Two maize inbred lines, DAN3130 and JI63, with different patterns of folate accumulation and different total folate contents in mature kernels were used to investigate the transcriptional regulation of folate metabolism during late stages of kernel formation by comparative transcriptome analysis; The fresh kernel samples of each inbred line were collected on DAP 24, DAP 35 days, respectively. Mature kernel samples were harvested after all the plants turned yellow. Three biological replicates of each sample were collected, and total RNA with high quality was pooled and sent for sequencing. Total RNA of high quality was pooled for transcriptome analysis, and raw RNA-seq data of DAP 24, DAP35 and mature kernels for both two inbred lines were obtained. The folate accumulation during DAP 24 to mature kernels could be controlled by circumjacent pathways of folate biosynthesis, such as pyruvate metabolism, glutamate metabolism and serine/glycine metabolism. In addition, the folate variation between these two inbred lines was related to those genes among folate metabolism, such as genes in the pteridine branch, ρ-ABA branch, serine/THF/5-M-THF cycle and the conversion of tetrahydrofolate monoglutamate to tetrahydrofolate polyglutamate; The findings provided insight into folate accumulation mechanisms during maize kernel formation to promote folate biofortification.

overall_design: Examination of 2 different maize inbred lines of kernel on DAP 24, DAP 35 and mature kernel. Each sample has three replicates.

first: Xuxia

first: Huan

first: Ling

last: Jiang


title: Znhit1-deficiency caused sarcoplasmic reticulum originated vacuolar cardiomyopathy

city: Nanjing

first: Yingchao

last: Shi

state: Jiangsu

address: 22 Hankou Road

institute: Nanjing University


title: The megakaryocytic transcription factor ARID3A suppresses leukemia pathogenesis.

first: Jan-Henning

last: Klusmann


title: RNA-Seq for control and Znhit1-deficient heart tissues from postnatal day 17 and 25 mice

summary: To investigate the function of Znhit1 in mouse hearts, we deleted Znhit1 using conditional Znhit1-knockout mice (Znhit1 flox/flox; Myh6-Cre; Znhit1 cKO). Through RNA-Seq, we tested the genome-wide transcriptional changes at postnatal day 17 and 25.

overall_design: Heart mRNA profiles of control (Znhit1 flox/flox) and Znhit1 cKO mice (Znhit1 flox/flox; Myh6-Cre) at postnatal day 17 (P17) and postnatal day 25 (P25).

first: Zhongzhou


title: BTS Is a Negative Regulator for the Cellular Energy Level and the Expression of Energy Metabolism-Related Genes Encoded by Two Organellar Genomes in Leaf Tissues

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

summary: E3 ligase BRUTUS (BTS), a putative iron sensor, is expressed in both root and shoot tissues in seedlings of Arabidopsis thaliana. The role of BTS in root tissues has been well established. However, its role in shoot tissues has been scarcely studied. Comparative transcriptome analysis with shoot and root tissues revealed that BTS is involved in regulating energy metabolism by modulating expression of mitochondrial and chloroplast genes in shoot tissues. Moreover, in shoot tissues of bts-1 plants, levels of ADP and ATP and the ratio of ADP/ATP were greatly increased with a concomitant decrease in levels of soluble sugar and starch. The decreased starch level inbts-1 shoot tissues was restored to the level of shoot tissues of wild-type plants upon vanadate treatment. Through this study, we expand the role of BTS to regulation of energy metabolism in the shoot in addition to its role of iron deficiency response in roots.

overall_design: Total RNA expression profiles of wild-type (Col-0) and bts-1 mutant (bts-1) were examined by Illumina HiSeq 2500

first: Inhwan

last: Hwang

first: Daehee


title: Evolutionary divergence of Firre localization and expression

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: CU Boulder

summary: Long non-coding RNAs (lncRNAs) are rapidly evolving and thus typically poorly conserved in their sequences. The extent to which these sequence differences affect the characteristics and potential functions of lncRNAs with shared synteny remains unclear. Here we show that the syntenically conserved lncRNA Firre displays distinct expression and localization patterns in human and mouse. Single molecule RNA FISH reveals that in a range of cell lines, mouse Firre (mFirre) is predominantly nuclear, while human FIRRE (hFIRRE) is distributed between the cytoplasm and nucleus. This localization pattern is maintained in human/mouse hybrid cells expressing both human and mouse Firre, implying that the localization of the lncRNA is species autonomous. We find that the majority of hFIRRE transcripts in the cytoplasm are comprised of isoforms that are enriched in RRD repeats. We furthermore determine that in various tissues, mFirre is more highly expressed than its human counterpart. Our data illustrate that the rapid evolution of syntenic lncRNAs can lead to variations in lncRNA localization and abundance, which in turn may result in disparate lncRNA functions even in closely related species.

overall_design: To assess whether abundance and localization differences between human and mouse Firre are sequence intrinsic, RNA-seq was performed on the wild type mouse/human hybrid cell line AHA 11a (Coriell, GM10324) which retains the human X chromosome. Three biological replicates for rRNA-depleted (total) and poly-A selected RNA were sequenced using 75-bp paired-end sequencing and mapped to mm39 with human chrX from hg38 appended. Reads were aligned and quantified with nf-core/rnaseq v1.4.2 using the Salmon v0.14.1 pseudo-aligner.

first: Gabrijela

last: Dumbović

first: Christian

last: Much

first: Michael

middle: J

last: Smallegan

middle: L


title: Macrophages govern antiviral responses in human lung tissues protected from SARS-CoV-2 infection

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

summary: The majority of SARS-CoV-2 infections among healthy individuals result in asymptomatic to mild disease. However, the immunological mechanisms defining effective lung tissue protection from SARS-CoV-2 infection remain elusive. Unlike mice solely engrafted with human fetal lung xenograft (fLX), mice co-engrafted with fLX and a myeloid-enhanced human immune system (HNFL mice) are resistant to SARS-CoV-2 infection, severe inflammation, and histopathology. Effective control of viral infection in HNFL mice associated with significant macrophage infiltration, and the induction of a potent macrophage-mediated interferon response. The strong upregulation of the USP18-ISG15 axis, a negative regulator of IFN responses, by macrophages was unique to HNFL mice and represented a prominent correlate of reduced inflammation and histopathology. Altogether, our work shed lights on unique cellular and molecular correlate of lung tissue protection during SARS-CoV-2 infection, and underscores macrophage IFN responses as prime targets for developing immunotherapies against coronavirus respiratory diseases.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design: 12 human fetal lung xenografts implanted in mice: 4- Naïve (non-inoculated in non-infected mice) human fetal lung xenografts from NRG-L mice. 3-human fetal lung xenografts from NRG-Flk2-/- mice co-engrafted with a human immune system at 2-days and 7-days post infection using 1x10^6 PFU SARS-CoV-2 WA-Isolate. 3 Naïve (non-infected graft in non-infected mice) human fetal lung xenografts from NRG-Flk2-/- mice co-engrafted with a human system were sequenced as a control.

first: Florian

last: Douam

first: Devin

last: Kenney

first: Aoife

last: O'Connell

first: Jacquelyn

last: Turcinovic

first: Paige

last: Montanaro

first: Ryan

last: Hekman

first: Tomokazu

last: Tamura

last: Connor

first: Andrew

last: Emili

first: Nicholas

last: Crossland

first: Alexander

last: Ploss


title: Effect of DNA damage on ligand stimulated EGFR signaling pathways

city: Jerusalem

first: Jacob

last: Rachmilewitz

department: Goldyne Savad Institute of Gene Therapy

country: Israel

institute: Hadassah-Hebrew University Medical Center

summary: We examined the cellular response of primary normal cells to EGFR stimulation under normal and DNA damage conditions.

overall_design: Examining changes in the response to EGFR triggering in cells suffering form DNA damage

first: Yael

last: Volman

first: Ruth

last: Hefetz


title: RANKL regulates testicular cancer growth and Denosumab has tumor suppressive effects in GCNIS and advanced seminoma

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Testicular germ cells tumors (TGCTs) have a high sensitivity to cisplatin-based chemotherapy and a high cure rate, although with possible serious adverse effects. In the search for tumor suppressive drugs, the RANKL inhibitor Denosumab, used to treat osteoporosis came up as a candidate since RANKL signaling was recently identified in the testis. RANKL signals through the receptor RANK and this signaling is antagonized by the decoy receptor OPG. Here, we demonstrate expression of RANKL, RANK, and OPG in germ cell neoplasia in situ (GCNIS), TGCTs, and TGCT-derived cell lines. RANKL inhibition reduced proliferation of seminoma-derived TCam-2 cells but had no effect on embryonal carcinoma-derived NTera2 cells in vitro. Denosumab did not potentiate the effect of cisplatin treatment in vitro but inhibition of RANKL in vivo resulted in reduced tumor growth in a TCam-2 but not a NTera2 xenograft model. Moreover, Denosumab treatment decreased proliferation in human testicular GCNIS tissue culture in vitro. In TGCT patients, serum RANKL was not linked with tumor burden, relapse, or other prognostic markers. In conclusion, this study shows that the RANKL signaling system is expressed in GCNIS and seminoma where RANKL inhibition suppress tumor growth in vitro and in vivo. Future studies are needed to determine whether RANKL is important for the malignant transformation and the transition from GCNIS to invasive tumors.

overall_design: Testing the effects of RANKL and RANKL inhibitors on two human derived pluripotent germ cell cancer cell lines

first: Christine

last: Andreassen

first: Mette

last: Lorenzen

first: John

middle: E

last: Nielsen

first: Sam

last: Yahyavi

first: Birgitte

middle: G

last: Toft

middle: R

first: Christoffer

last: Clemmensen

first: Lene

last: Rasmussen

first: Carsten

last: Bokemeyer

first: Anders

last: Juul

first: Anne

last: Jørgensen

first: Martin

middle: B

last: Jensen


title: m6A mRNA modification is a rheostat to maintain colonic epithelial cell homeostasis [scRNA-seq]

city: Shanghai

first: Bing

middle: Hua

last: Li

address: 280 Chongqing South Rd, Building #5, Room 602, Shanghai

institute: Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine

summary: The function of m6A modification in colonic epithelial cells has been validated in our study that depletion of METTL14 in colonic epithelial cells triggers cell death. To further explore the biological effects of m6A deficiency in colonic epithelial cell heterogeneity, we performed single cell RNA-seq of colonic epithelial cells form 2-week-old Mettl14-KO and WT control mice

overall_design: Single Cell Profiles of  Mettl14 WT and Mettl14 KO colonic epithelial cells of two weeks

first: Ting

last: Zhang

first: Huabing


title: Microarray expression profile analysis of lncRNAs in human Pancreatic Ductal Adenocarcinoma

city: Xi'an

first: Shibin

last: Qu

state: Shaanxi

address: 127 West Changle Road

department: Department of Hepatobiliary Surgery

institute: Xijing Hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: To explore the potential involvement of lncRNAs in pancreatic ductal adenocarcinoma (PDAC) oncogenesis, we conducted lncRNA profiling in six pairs of human PDAC and adjacent normal tissue  by microarray. Our results showed that clusters of lncRNAs were aberrantly expressed in PDAC compared with normal samples, and provided potential targets for future treatment of PDAC and novel insights into PDAC biology.

overall_design: analyze lncRNA expression in pancreatic ductal adenocarcinoma (PDAC) by microarray platform

first: Haimin

first: Zhengcai

last: Liu


title: Microarray-based Gene Expression Analysis of WA09 human cerebral organoids with CRISPR-KO of NGLY1

city: Ft Worth

first: Victor

last: Lin

address: 3500 Camp Bowie Blvd

institute: UNTHSC

summary: Analysis of human cerebral organoids developed from both WA09 human embryonic stem cells with CRISPR-KO of NGLY1. The hypothesis tested was that NGLY1 is key to normal human brain development and when knocked out would alter cerebral development of organoids through the differential expression of various key genes.

overall_design: Total RNA obtained  from human cerebral organoids developed using WNT & TGFbeta inhibition (3uM IWR-1e & 10uM SB431542). Organoid samples were collected along the development timeline from the pluripotent stem cell stage to day 80 of cerebral maturation

first: Yu-chieh

last: Wang


title: Multi-omic rejuvenation of human cells by maturation phase transient reprogramming [Transient array]

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

type: Methylation profiling by genome tiling array

summary: Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.

overall_design: methylation of fibroblasts undergoing maturation phase transient reprogramming.

first: Diljeet

last: Gill

first: Aled

last: Parry

first: Fátima

last: Santos

first: Irene

last: Hernando-Herraez

first: Thomas

middle: M

last: Stubbs

first: Inês

last: Milagre

first: Wolf

last: Reik


title: Transgenerational whole genome bisulphite sequencing data from adult zebrafish exposed to low level TCDD

city: Gainesville

first: Tracie

last: Baker

state: FL

institute: University of Florida

type: Methylation profiling by high throughput sequencing

summary: Exposure to TCDD early in development produces reproductive abnormalities and decreased reproductive capacity in males in subsequent generations. We used WGBS to investigate differential methylation in testicular tissue and identified distinct multigenerational and transgenerational methylation changes due to legacy TCDD exposure in males.

overall_design: Zebrafish were exposed to sublethal TCDD or vehicle (DMSO) during early development, males in the next two generations were analyzed for phenotypic, gene expression, and methylation changes as adults. 4 TCDD and 4 Control males for the F0, F1, and F2 generations.


title: Self-renewal of Differentiated Microglia Involves Two Distinct Mechanisms II

city: San Francisco

first: Wulin

last: Tan

state: California

address: Room 345, Rock Hall, 1550 4th St

department: Anesthesia

institute: UCSF

summary: single cell gene expression profiling of microglia after peripheral nerve injury in Cx3cr1-yfp-creER/+ animals and Cx3cr1-yfp-creER/+; Tnfaip3 fl/fl animals

overall_design: microglia (YFP+) were FACS sorted from lumbar part in the naïve animals or animals after peripheral nerve injury and single cell sequencing was performed.

first: Po-Yi

middle: P

last: Su

first: Jacqueline

last: Leff

first: Xiang

last: Gao

first: Jiao

last: Chen

first: Gokul

last: Kalyanasundaram

first: Zhonghui

last: Guan


title: DPP-4 inhibitor sitagliptin improves vascular endothelial function by modulating lncRNA and mRNA expression profiles in obese mouse aortae.

city: BeiJing

first: Yi

last: Zong

address: No. 38 Xue Yuan Road

institute: Peking University Health Science Center

summary: To investigated the therapeutic mechanism underlying the sitagliptin improves vascular endothelial function in obesity, we performed bioinformatics analyses on the expression profiles of long noncoding RNAs (lncRNAs) and message RNAs (mRNAs) in the aortae from obese mice with or without sitagliptin treatment.

overall_design: The animals were divided to the following three groups (3 mice per group): (i) C57BL/6J as Vehicle group; (ii) C57BL/6J were fed with high-fat diet for four months without oral sitagliptin treatment (DIO); (iii) Oral SItagliptin treatment (3 mg/kg/d) of high-fat diet-fed C57BL/6J.


title: Multi-omic rejuvenation of human cells by maturation phase transient reprogramming [Sendai_RNAseq]

first: Felix

last: Krueger

overall_design: RNA-seq of fibroblasts undergoing Sendai virus iPSC reprogramming.


title: Expanded CUG repeat RNA alters gene expression profiles in myotonic dystrophy model cells

city: Suita

first: Masayuki

last: Nakamori

state: Osaka

address: 2-2, D-4, Yamadaoka

department: Neurology

country: Japan

institute: Osaka University Graduate School of Medicine

summary: Myotonic dystrophy type 1 (DM1) is a dominantly inherited disorder due to a toxic gain of function of RNA transcripts containing expanded CUG repeats (CUGexp). Patients with DM1 present with multisystemic symptoms, such as muscle wasting, cognitive impairment, cataract, frontal baldness, and endocrine defects, which resemble accelerated aging. Although the involvement of cellular senescence, a critical component of aging, was suggested in studies of DM1 patient-derived cells, the detailed mechanism of cellular senescence caused by CUGexp RNA remains unelucidated. Here, we developed a DM1 cell model that conditionally expressed CUGexp RNA in human primary cells so that we could perform a detailed assessment that eliminated the variability in primary cells from different origins. To identify the pathway that induced cellular senescence, we conducted comprehensive gene expression analysis using RNA sequencing (RNA-Seq) in CUGexp+ and CUGexp− cells.

overall_design: We analyzed of mRNA expression in CUGexp+ and CUGexp− cells.

first: Yuhei

last: Hasuike


title: Next generation sequencing quantitatively analyzes transcriptomes of primary CLL cells tranfected with non-specific control (NSC) or ZAP-70 siRNA (-anti-IgM dataset)

first: Irina

last: Mohorianu

address: Puddicombe Way

department: Wellcome-MRC Cambridge Stem Cell Institute

institute: University of Cambridge

summary: RNA seq profiles of primary CLL cells transfected with non-specific control (NSC) or ZAP-70 siRNA ± anti-IgM. This submission is -anti-IgM.

overall_design: mRNA profiles of primary CLL cells tranfected with non-specific control (NSC) or ZAP-70 siRNA (± anti-IgM) were generated by deep sequencing, in two patients, each in triplicate.

first: Jingyu

first: Vijitha

last: Sathiaseelan

first: Arash

last: Shahsavari

first: Ingo

last: Ringshausen


title: Next generation sequencing quantitatively analyzes transcriptomes of primary CLL cells tranfected with non-specific control (NSC) or ZAP-70 siRNA (+anti-IgM dataset)

summary: RNA seq profiles of primary CLL cells transfected with non-specific control (NSC) or ZAP-70 siRNA ± anti-IgM. This submission is +anti-IgM.


title: PGE2-EP3 axis controls brown adipose tissue development

status: Public on Apr 18 2022

city: Tianjin

first: Yujun

last: Shen

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

summary: PGE2/EP3 signaling and m6A modification is required for brown adipocyte differentiation and BAT development, but the underlying mechanisms involved remain to be elucidated. The Arraystar mousen M6a-MRNA&lncRNA Epitranscriptomic microarray analysis was performed on mouse brown preadipocytes with or without EP3 deletion.

overall_design: Mouse brown preadipocytes were divided into 2 groups: EP3F/F and Myf5CreEP3F/F, each containing 1 sample pooled from approximately 30 mice.

first: Xixi

last: Tao


title: Adenosine Alleviates Necrotizing Enterocolitis by Enhancing the Immunosuppressive Function of MDSCs in Newborns

first: Jie

last: Zhou

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

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

overall_design: Refer to individual Series


first: John

last: Connor

state: MA

address: 620 Albany St.

department: National Emerging Infectious Diseases Laboratories

institute: Boston University

overall_design: 20 human fetal lung xenografts implanted in mice. Four are uninfected, one is mock-infected with PBS, and 12 are infected with 1E+6 PFU of SARS-CoV-2. An additional 3 are uninfected xenografts contralateral to infected xenografts. 4 infected xenografts were harvested and sequenced at 2 DPI along with the 3 contralateral grafts. The remaining 8 infected xenografts were harvested at 7 DPI.

first: Douam

last: Florian

first: Kenney

last: Devin

first: O'Connell

last: Aoife

first: Turcinovic

last: Jacquelyn

first: Montanaro

last: Paige

first: Hekman

last: Ryan

first: Tamura

last: Tomokazu

first: Connor

last: John

first: Emili

last: Andrew

first: Crossland

last: Nicholas

first: Ploss

last: Alexander


title: Next generation sequencing quantitatively analyzes transcriptomes of primary CLL cells tranfected with non-specific control (NSC) or ZAP-70 siRNA

first: Irina

last: Mohorianu


title: rBC2LCN-positive subpopulation of PC-3 cells exhibits cancer stem-like properties

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

institute: National Institute of Advanced Industrial Science and Technology (AIST)

summary: We found that PC-3 cells consisted of rBC2LCN-positive and -negative subpopulations. To examine a global gene expression comparison between the rBC2LCN-positive and -negative subpopulations, DNA microarray was performed.

overall_design: Human prostate cancer cell line, PC-3 cells, was maintained in F-12K medium (ATCC, 30-2004) supplemented with 10 % FBS (GIBCO, 12483-020) and 1 % Penstrep (SIGMA, I0516-5ML) at 37 °C and 5 % CO2. PC-3 cells were separated into rBC2LCN-positive and -negative subpopulations by live cell sorting using HiLyte Fluor 647-conjugated rBC2LCN. The total mRNAs were extracted from rBC2LCN-positive and -negative subpopulations using ISOGEN (NIPPON GENE). DNA microarray was performed by a SurePrint G3 Human GE Microarray Kit, 8 x 60 K Ver. 1 (Agilent, G4851A).

first: Shuuji

last: Mawaribuchi


title: Multi-omic rejuvenation of human cells by maturation phase transient reprogramming

first: Felix

last: Krueger

department: Bioinformatics


title: Tumor promoting effect of long non-coding RNA RP11-556E13.1 and its clinical significance as a prognostic factor in hepatocellular carcinoma.

city: Hangzhou

first: Jie

last: Li

address: 866 Yuhangtang Road, Hangzhou, Zhejiang Province, China

institute: Zhejiang University School of Medicine

summary:
Objective: The aim of this study was to reveal the function of the long non-coding RNA (lncRNA) RP11-556E13.1 (RP11) and its clinical significance in hepatocellular carcinoma.
Methods: LncRNA and mRNA expression profiling was performed using lncRNA and mRNA microarrays in 5 pairs of HCC and adjacent tissues. 112 paired HCC and adjacent tissue samples were analyzed by semiquantitative real-time polymerase chain reaction (sqRT-PCR) to evaluate the expression of RP11 and its possible associated clinical significance. Smart silencer RNA (siRNA) was used to knockdown the expression of RP11 in HCC cells. After knockdown, the function of RP11 was determined in vitro using some kinds of cell functional experiments in HCC cells including cell proliferation assay, cell apoptosis assay and cell cycle assay. Western blotting (WB) was performed to detect proteins that were presumably associated with these functional changes. An Affymetrix Human HTA2.0 microarray was used to detect differentially expressed genes in HCC cells after RP11 knockdown. GO enrichment and KEGG pathway enrichment analysis were then performed to elucidate the biological roles of these differentially expressed mRNAs.

overall_design: Total RNA was extracted from Huh7 and Hep3B cells transfected with siRNA or negative control after 48 hours. 3 sample pairs of Huh7 and Hep3B cells were used for the following experiment. 3BRP: Hep3B cells transfected with siRNA; 3BNC: Hep3B cells transfected with negative control RNA.Hu7RP: Huh7 cells transfected with siRNA; Hu7NC: Huh7 cells transfected with negative control RNA;

first: Zhikun

last: Liu

first: Jianguo

last: Wang

first: Xuyong

last: Wei

first: Qiang

first: Shusen

last: Zheng

first: Xiao

last: Xu


title: Multi-omic rejuvenation of human cells by maturation phase transient reprogramming [Sendai array]

overall_design: methylation of fibroblasts undergoing Sendai virus iPSC reprogramming.

first: Diljeet

last: Gill

first: Aled

last: Parry

first: Fátima

last: Santos

first: Irene

last: Hernando-Herraez

first: Thomas

last: Stubbs

first: Inês

last: Milagre

first: Wolf

last: Reik


title: Strigolactone action in mitochondria triggers retrograde signaling for root growth modulation

city: Klosterneuburg

first: Michelle

last: Gallei

address: Am Campus 1

country: Austria

institute: IST Austria

summary: Strigolactones (SL) are a new class of plant hormones with a broad range of roles in symbiosis, germination and developmental regulation. The well-characterized signaling pathway for SL involves the canonical signaling component MAX2. Here we identified a novel, MAX2-independent SL signaling mechanism, which initiates in mitochondria, signals to the nucleus and regulates root development. By a forward genetic approach, we identified the SL-insensitive pig1 mutant, which altered the kinetic properties of the mitochondrial pyruvate dehydrogenase complex. SL has an unknown target in mitochondria, where it uncouples respiration. This leads to metabolic aberrations, mitochondria-to-nucleus retrograde signaling upregulating transcription of mitochondrial dysfunction genes and downregulating auxin-regulated genes. SL-triggered mitochondrial uncoupling is communicated to the nucleus via cleavage and translocation of the ER-localized transcription factor ANAC017. These observations establish a novel mechanism for SL signaling emanating from mitochondria and regulating development.

overall_design: total RNA from 7-day old whole Arabidopsis thaliana seedlings, 3 biological replicates, rep1 of Col-0 Acetone and GR24 samples is the control for pig1 and PIN1-GFP samples, rep1 of Col-0 Acetone and GR24 samples is the control for anac017 samples

first: Chun-Pong

last: Lee

first: Pawel

last: Baster

first: Aleš

last: Pěnčík

first: Robin

last: Pottie

first: Gergely

last: Molnar

first: Petr

last: Valosek

first: Frank

last: van Breusegem

first: Ondřej

last: Novák

first: A

last: Millar

first: Philip

last: Brewer

first: Jiří

last: Friml


title: Candida parapsilosis Mdr1B and Cdr1B are drivers of Mrr1-mediated clinical fluconazole resistance

city: Memphis

first: David

last: Rogers

state: TN

address: 262 Danny Thomas Place, Mail Stop 313, Room I5200

department: Pharmacy and Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

summary: Previous work has demonstrated that non-synonymous mutations in the gene encoding the putative transcription factor CpMrr1 can influence fluconazole susceptibility; however, the direct contribution of these mutations and how they influence fluconazole resistance in clinical isolates is poorly understood. We identified ten non-synonymous CpMRR1 mutations in a collection of 35 fluconazole resistant clinical isolates. The mutations leading to the A854V, R479K, and I283R substitutions were further examined and found to be activating mutations leading to increased fluconazole resistance. In addition to CpMDR1, we identified  another major facilitator superfamily (MFS) transporter gene (CpMDR1B, CPAR2_603010) and an ATP-binding Cassette (ABC) transporter gene (CpCDR1B, CPAR2_304370), as being up-regulated in isolates carrying CpMRR1 activating mutations.

overall_design: Comparing the gene expression of Candida parapsilosis azole-susceptible and -resistant isolates to corresponding strains containing SNPs in MRR1 or MRR1 gene corrected to wild-type sequence

first: Laura

middle: A

last: Doorley

first: Jeffrey

last: Rybak

first: Elizabeth

last: Berkow

first: Qing

last: Zhang

first: Joachim

last: Morschhäuser

first: P

middle: D


title: Temporal perturbation of histone deacetylase activity reveals a requirement for HDACs 1-3 in mes-endoderm cell differentiation

city: Brisbane

first: Nathan

middle: J.

last: Palpant

state: QLD

address: 306 Carmody Rd

country: Australia

institute: University of Queensland

summary:
We investigate the genome-wide chromatin landscape during mes-endoderm and cardiac progenitor specification to reveal dynamic changes to chromatin accessibility upon HDAC1-3 inhibition.
To evaluate the changes to chromatin accessibility upon inhibition of HDACs 1-3 during cardiac lineage specification, we performed ATAC-seq using the Omni-ATAC protocol (Corces et al., 2017) on Day 5 differentiated hiPSCs treated for 48 hours using small molecule HDAC inhibitors with isozyme selectivity

overall_design: ATAC-seq analysis of cells at Day 5 of cardiac-directed hiPSC differentiation treated for 48 hours with HDAC inhibitors (1 µM MS275 and 1 µM BRD4884)  (3 biological replicates per condition)

first: Enakshi

last: Sinniah

first: Marina

last: Naval-Sabchez

first: Xiaoli

last: Chen

first: Christian

last: Nefzger


title: Transcriptional analysis of murine CXCR3+ vs. CXCR3- peritoneal cavity B cells 8 days following infection with Ehrlichia muris.

city: Syracuse

first: Krista

last: Newell

address: 766 Irving Ave.

department: Microbiology & Immunology

institute: SUNY Upstate Medical University

summary: We performed bulk RNA sequencing on murine CXCR3+ and CXCR3-negative live singlet IgM+ IgD-neg CD19+ CD138-neg (B1 B cell-like) peritoneal cavity B cells to compare the transcriptomes of the two populations following i.p. infection with the intracellular bacterium Ehrlichia muris. Total RNA was extracted and sequenced, followed by pseudoalignment, quality assessment, normalization, and analysis of differential gene expression. The CXCR3+ B1 B cell-like population was highly enriched for genes involved in proliferation, metabolism, and cell division, whereas the CXCR3- B1 B cell-like population transcriptionally resembled canonical B1 B cells and did not appear to be proliferative. These results suggest local proliferation of CXCR3+ B cells occurs in the peritoneal cavity during acute infection with an intracellular bacterium.

overall_design: Comparison of bulk gene expression between CXCR3+ and CXCR3-negative live singlet IgM+ IgD-neg CD19+ CD138-neg peritoneal cavity B cells from 3 biological replicates

first: Gary

last: Winslow


title: m6A mRNA modification is a rheostat to maintain colonic epithelial cell homeostasis

first: Bing

last: Li

address: 280 Chongqing South Rd, Building #5, Room 602, Shanghai

institute: Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine


title: m6A mRNA modification is a rheostat to maintain colonic epithelial cell homeostasis [bulkRNA-seq]

summary: The function of m6A modification in colonic epithelial cells has been validated in our study that depletion of METTL14 in colonic epithelial cells triggers cell death. To further explore the biological effects of m6A deficiency in colonic epithelial cells, we performed RNA sequencing analysis of colonic epithelial cells form 2-week-old Mettl14-KO and WT control mice.The bioinformatic analysis revealed that METTL14 depletion increased the mRNA expression of NF-kB inhibitor Nfkbia, which favored TNF-induced cell death.

overall_design: RNA samples from Mettl14-KO and WT control colonic epithelial cells were collected, and then RNA purification, reverse transcription, library construction and sequencing were performed according to the manufacturer's instructions (Illumina).

first: Ting

first: Huabing


title: Grape Berry Ripening Signature Gene Expression Analysis

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

department: Plant Science

institute: South Dakota State University

summary: Study of Frontenac and Marquette Grape berry ripening profile using Transcriptomics

overall_design: Gene expression in Frontenac and Marquette grape berry skin and pulp during ripening

first: Padmapriya

last: Swaminathan

first: Patricia

last: Salas

first: Yuxin

last: Yao


title: Adenosine Alleviates Necrotizing Enterocolitis by Enhancing the Immunosuppressive Function of MDSCs in Newborns [cell]

first: Jie

last: Zhou

summary: Adenosine-induced MDSCs represent an essential immune axis for intestinal homeostasis in newborns.

overall_design: Newborn mice spleen PMN-MDSC were treated with NECA 5 days for RNA-sequencing.

first: Dongmei


title: Benchmark Dose Modeling Approaches for Volatile Organic Chemicals using a Novel Air-Liquid Interface In Vitro Exposure System

status: Public on Apr 17 2022

city: RTP

first: Logan

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

summary: Inhalation is the most relevant route of volatile organic chemical (VOC) exposure; however, due to unique challenges posed by their chemical properties and poor solubility in aqueous solutions, in vitro chemical safety testing is predominantly performed using direct application dosing/submerged exposures. To address the difficulties in screening toxic effects of VOCs, our cell culture exposure system permits cells to be exposed to multiple concentrations at air-liquid interface (ALI) in a 24-well format. ALI exposure methods permit direct chemical-to-cell interaction with the test article at physiological conditions. In the present study, BEAS-2B and primary normal human bronchial epithelial cells (pHBEC) are used to assess gene expression, cytotoxicity, and cell viability responses to a variety of volatile chemicals including acrolein, formaldehyde, 1,3-butadiene, acetaldehyde, 1-bromopropane, carbon tetrachloride, dichloromethane, and trichloroethylene. BEAS-2B cells were exposed to all the test agents, while pHBECs were only exposed to the latter four listed above. The VOC concentrations tested elicited only slight cell viability changes in both cell types. Gene expression changes were analyzed using benchmark dose (BMD) modeling. The BMD for the most sensitive gene set was within one order of magnitude of the threshold-limit value reported by the American Conference of Governmental Industrial Hygienists, and the most sensitive gene sets impacted by exposure correlate to known adverse health effects recorded in epidemiologic and in vivo exposure studies. Overall, our study outlines a novel in vitro approach for evaluating molecular-based points-of-departure in human airway epithelial cell exposure to volatile chemicals.

overall_design: We developed a cell culture exposure system (CCES) that permits cells to be exposed to multiple concentrations of test agent at air-liquid interface (ALI) in a 24-well format. ALI exposure methods permit direct chemical-to-cell interaction at physiological conditions, providing a more environmentally realistic airway exposure condition, as compared to submerged cultures. We tested eight widespread volatile organic chemicals (VOCs) in BEAS-2B cells with four of those test agents repeated in primary human bronchial epithelial cells (pHBECs). To stay within relevant concentrations and below overt cytotoxicity, the highest concentration tested was targeted as 10-fold higher than the threshold for human occupational exposure limits as determined by the American Conference of Governmental Industrial Hygienists (ACGIH) threshold limit value (TLV) documentation. The primary endpoint focused on using TempO-Seq to identify changes in gene expression at both the gene and aggregate gene set level to determine the biological pathway altering concentration (BPAC) of a particular test agent.

first: Adam

last: Speen

first: Jessica

last: Murray

first: Q

middle: T

last: Krantz

first: David

last: Davies

first: Paul

last: Evansky

first: Joshua

last: Harrill

first: Joseph

last: Bundy

first: Lisa

last: Dailey

first: Jazzlyn

last: Hill

first: Wyatt

last: Zander

first: Elise

last: Carlsten

first: Michael

last: Monsees

first: Jose

last: Zavala

first: Mark

last: Higuchi


title: Integrated Omic Analyses Identify Pathways and Regulators Associated with Chemical Alterations of in vitro Neural Network Formation

first: Susan

last: Hester

address: 109 TW Alexander Dr

institute: US EPA

summary: Development of in vitro new approach methodologies (NAMs) has been driven by the need for developmental neurotoxicity (DNT) hazard data on thousands of chemicals. The network formation assay (NFA) characterizes DNT hazard based on changes in network formation but provides no mechanistic information. This study investigated nervous system signaling pathways and upstream physiological regulators underlying chemically-induced neural network dysfunction. Rat primary cortical neural networks grown on microelectrode arrays were exposed (0.1 -10 µM) for 12 days in vitro (DIV) to cytosine arabinoside (CA), 5 fluorouracil (5FU), domoic acid (DA), cypermethrin (CM), deltamethrin (DM), and haloperidol; these exposures targeted specific concentrations that altered network activity in previous studies. RNA-seq from cells and GC/MS of media extracts collected on DIV 12 provided gene expression and metabolomic identification, respectively. The integration of differentially expressed genes and metabolites for each neurotoxicant were analyzed using Ingenuity Pathway Analysis (IPA). All six compounds altered gene expression that linked to developmental disorders and neurological diseases. Other enriched canonical pathways overlapped among compounds of the same class; for example, genes altered by both CA and 5FU exposures are enriched in axonal guidance pathways. Analysis of upstream regulators was heterogeneous across compounds, but identified regulators included CREB1, BDNF, TGFβ1, NTRK2, and PRODH. These results demonstrate that transcriptomic and metabolomic changes following chemical exposure can be determined in the NFA and that different classes of compounds produce differing responses. This approach can enhance information obtained from NAMs and contribute to the identification and development of AOPs associated with DNT.

first: Carmen

last: Marabel

first: Christopher

last: Frank

first: Roland

middle: F

last: Seim

first: W

last: Henderson

first: Brian

last: Chorley

first: Timothy

last: Shafer


title: Multi-omic rejuvenation of human cells by maturation phase transient reprogramming [Transient_RNAseq]

first: Felix

last: Krueger

address: Granta Park

institute: Altos Labs

summary: Ageing is the gradual decline in organismal fitness that occurs over time leading to tissue dysfunction and disease. At the cellular level, ageing is associated with reduced function, altered gene expression and a perturbed epigenome. Somatic cell reprogramming, the process of converting somatic cells to induced pluripotent stem cells (iPSCs), can reverse these age-associated changes. However, during iPSC reprogramming somatic cell identity is lost, and can be difficult to reacquire as re-differentiated iPSCs often resemble foetal rather than mature adult cells. Recent work has demonstrated that the epigenome is already rejuvenated by the maturation phase of reprogramming, which suggests full iPSC reprogramming is not required to reverse ageing of somatic cells. Here we have developed the first “maturation phase transient reprogramming” (MPTR) method, where reprogramming factors are expressed until this rejuvenation point followed by withdrawal of their induction. Using dermal fibroblasts from middle age donors, we found that cells reacquire their fibroblast identity following MPTR, possibly as a result of persisting epigenetic memory at enhancers. Excitingly, our method substantially rejuvenated multiple cellular attributes including the transcriptome, which was rejuvenated by around 30 years as measured by a novel transcriptome clock. The epigenome, including H3K9me3 histone methylation levels and the DNA methylation ageing clock, was rejuvenated to a similar extent. MPTR fibroblasts produced youthful levels of collagen proteins, suggesting functional rejuvenation. Overall, our work demonstrates that it is possible to separate rejuvenation from pluripotency reprogramming, which should facilitate the discovery of novel anti-ageing genes and therapies.

overall_design: RNA-seq of fibroblasts undergoing maturation phase transient reprogramming.

first: Diljeet

last: Gill

first: Aled

last: Parry

first: Fátima

last: Santos

first: Irene

last: Hernando-Herraez

first: Thomas

last: Stubbs

first: Inês

last: Milagre

first: Wolf

last: Reik


title: CUT&Tag for H2A.Z using mouse heart tissues from control and Znhit1-deficient mice

city: Nanjing

first: Yingchao

last: Shi

address: 22 Hankou Road

institute: Nanjing University

summary: Znhit1 is an important subunit of the SRCAP complex, which regulates gene transcription by replacing histone H2A with a variant H2A.Z at gene promoter regions. Deletion of Znhit1 has also been reported to impact the incorporation of H2A.Z in genome. To explore the function of Znhit1 in heart tissues, we performed CUT&Tag assays for H2A.Z to examine the distribution changes of H2A.Z on the genome.

overall_design: CUT&Tag assays for H2A.Z using mouse heart tissues from control (Znhit1 flox/flox) and Znhit1 cKO (Znhit1 flox/flox; Myh6-Cre) mice at postnatal day 17 (P17) and postnatal day 25 (P25).

first: Zhongzhou

last: Yang


title: Adenosine Alleviates Necrotizing Enterocolitis by Enhancing the Immunosuppressive Function of MDSCs in Newborns [tissue]

first: Jie

last: Zhou

overall_design: Newborn mice intestine were treated with NECA 5 days for RNA-sequencing.

first: Dongmei


title: Next generation sequencing revealed disease-specific microglia classes relying on distinct transcriptomes

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Microglia in the spinal dorsal horn have been implicated in the pathogenesis of neuropathic pain following peripheral nerve injury. We have revently found that CD11c-expressing spinal microglia appear after the development of behavioral pain hypersensitivity following nerve injury and are essential for recovery from neuropathic pain. In order to better understand the gene expression profiles of CD11c-expressing microglia, we performed quantitative bulk RNA sequencing of microglia isolated from mice expressing Venus fluorescent protein under the control of CD11c promoter. We found that CD11c-expressing microglia show distinct gene expression profile compared to CD11c-negative microglia following nerve injury.

overall_design: Transcriptome profiles of microglia from spinal dorsal horn of CD11c-venus mice before and after peripheral nerve injury were generated by deep sequencing.

first: Makoto

last: Tsuda

first: Takahiro

last: Masuda

first: Keita

last: Kohno

first: Kaori

last: Tanaka


title: Arabidopsis Apoplastic Fluid Contains sRNA- and Circular RNA-Protein Complexes that Are Located Outside Extracellular Vesicles

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

institute: University of California - Davis

summary: The extracellular space within plant leaves is called the apoplast, and functions as a key battlefield between plants and pathogens. Previously, we have shown that apoplastic wash fluid purified from Arabidopsis leaves contains small RNAs (sRNAs). To investigate whether these RNAs are encapsulated inside extracellular vesicles (EVs), we treated EVs isolated from Arabidopsis leaves with the protease trypsin and RNase A, which should degrade RNAs located outside of EVs, but not those located inside. These analyses revealed that apoplastic RNAs are mostly located outside of EVs and are associated with proteins. Additional analyses of these extracellular RNAs (exRNAs) revealed that they are made up both sRNAs and long non-coding RNAs (lncRNAs), including circular RNAs (circRNAs). We also found that exRNAs are highly enriched in the post-transcriptional modification N6-methyladenine (m6A). Consistent with this, we identified a putative m6A-binding protein in apoplastic wash fluids, GLYCINE-RICH RNA BINDING PROTEIN 7 (GRP7), as wells as the small RNA-binding protein ARGONAUTE2 (AGO2).  These two proteins co-immunoprecipitated with each other, and with lncRNAs, including circRNAs. Mutation of GRP7 or AGO2 caused changes in both the sRNA and lncRNA content of apoplastic wash fluid, suggesting that these proteins contribute to the secretion and/or stabilization of exRNAs.

overall_design: circular RNA profiling of extracellular RNA treated in ago2 and grp7 mutants.

last: Baldrich

first: Hana

last: Zand Karimi

first: Brian

last: Rutter

first: Kamil

middle: K

last: Zajt

first: Blake

middle: C

last: Meyers

first: Roger

middle: W

last: Innes


title: Expression data of osimertinib tolerant H1975 cells

status: Public on Apr 16 2022

city: Hiroshima

first: Kentaro

last: Tokumo

state: Hiroshima

address: 1-2-3 Kasumi, Minami-ku

department: Molecular and Internal Medicine

institute: Hiroshima University

summary:
Even after osimertinib is administered to lung adenocarcinomas with EGFR mutations, there are a few cells which survive, and these tolerant cells are considered to be the source of later recurrence.
We used microarray analysis to explore the mechanism behind the tolerance to osimertinib in lung adenocarcinoma cells with EGFR mutations.

overall_design: H1975 cells surviving 1 week after treatment with 0.5 µM osimertinib (OR) and naive H1975 cells cultured without treatment (C) were collected and RNA was extracted and hybridized on Affymetrix microarrays.

first: K


title: NanoString nCounter NF1-mutant melanoma gene expression

city: New York

first: Department of Pathology

last: NYU Langone Health

state: NY

address: 240 East 38th Street

department: Department of Pathology

institute: NYU Langone Health Ambulatory Care Center

summary:
Purpose: Digital spatial profiling was used to elucidate the interplay between the tumor cells and the surrounding microenvironment FFPE tissues.
Methods: Two tissue microarrays (TMA) were generated from each FFPE block using the ISNET Galileo CK4500 computer-driven tissue microarray. Images of H&E-stained cores were demarcated by a pathologist and were utilized alongside NanoString immunofluorescent staining for morphology markers S100, CD45, CD3, and DAPI to draw region of interest.

overall_design: Multiplex gene expression analysis covers 73 endogenous genes from 24 different immune cell types and 48 gene-derived signatures measuring biological variables crucial to the tumor-immune interaction.

first: George

last: Jour


title: Nuclear Vav3 is required for canonical PRC1 activity in B-cell lymphoblastic leukemogenesis

city: cincinnati

first: Ramesh

last: Nayak

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's

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

overall_design: Refer to individual Series


title: Expression data of osimertinib tolerant PC-9 cells

overall_design: PC-9 cells surviving 1 week after treatment with 0.5 µM osimertinib (OR) and naive PC-9 cells cultured without treatment (C) were collected and RNA was extracted and hybridized on Affymetrix microarrays.


title: Mesenchymal Stem Cell-Derived Extracellular Vesicles Protect Retina in a Mouse Model of Retinitis Pigmentosa by Anti-inflammation Through miR-146a-Nr4a3 Axis

city: Qingyuan

first: le

last: li

address: B24 Yinquan South Road, Qingyuan 511518, Guang Dong, China

institute: the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital

summary: Retinitis pigmentosa (RP) is a rod-cone degenerative disease that induces irreversible vision loss. Stem cell-derived extracellular vehicles (EVs) have been reported to prevent retinal neurons from apoptosis and inflammation, but the molecular mechanisms remained unclear. Here we probed the ability of mesenchymal stem cell-derived EVs (MSC-EVs) to protect the retinas of RP model mice rd10 and explored the underlying mechanisms. Treatment with MSC-EVs increased the survival of photoreceptors and preserved their structure and visual function. Mechanistically, MSC-EVs suppressed the activation of microglial, Müller glial, macrophages and the NF-κB pathway. MSC-EVs upregulated anti-inflammatory cytokines and downregulated pro-inflammatory cytokines. MSC-EVs application in vitro decreased the number of TUNEL-positive photoreceptor cell line 661W co-cultured with LPS-stimulated glial cell BV2, with similar impact on the cytokine expression as in vivo study. MiR-146a, one of the major miRNAs in MSC-EVs was upregulated in co-cultured cells after MSC-EVs treatment. Upregulation of miR-146a decreased the expression of the transcription factor Nr4a3, and its inhibition promoted Nr4a3 expression in both cells. Nr4a3 was further identified as the target gene of miR-146a. Therefore, MSC-EVs delays retinal degeneration in rd10 mice mainly by its anti-inflammatory effect via the miR-146a-Nr4a3 axis, indicating a strong potential of applying MSC-EVs to treat neurodegenerative diseases.

overall_design: MSC-EVs (MSC-Exo) were injected into the vitreous of rd10 mice at postnatal day 14 (P14) and P21; retinal morphology, function and RNA-seq were examined at P28.

first: Jia

last: Zhang

first: Ling

last: Qi


title: Arabidopsis Apoplastic Fluids Contain sRNA- and Circular RNA-Protein Complexes That Are Located Outside of Extracellular Vesicles

overall_design: extracellular RNA profiling of RNA treated with trypsin and RNase

middle: Z

last: Karimi


title: Microarray profiles from tubulointerstitial compartment of kidney biopsies from adults screened for enrollment in the NEPTUNE cohort

status: Public on Apr 15 2022

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

summary: Tubulointerstitial Transcriptome from kidney biopsies of patients screened for enrollment into NEPTUNE

overall_design: Kidney biopsies were microdissected into glomerular and tubulointerstitial comparments; RNA was extracted, labeled and hybridized. Arrays were annotated using a custom CDF platform (Brainarray v19) and processed using RMA.

first: Viji

last: Nair

first: Laura

last: Mariani

first: Felix

last: Eichinger

first: Brad

last: Godfrey

first: Matthias

last: Kretzler


title: Nuclear Vav3 is required for canonical PRC1 activity in B-cell lymphoblastic leukemogenesis (RNA-Seq)

summary: Acute B-cell lymphoblastic leukemia (B-ALL) represents a multiclonal evolution of B-cell progenitors endowed with both tumor-initiating and propagating properties. We have previously shown that the concurrent overexpression and activation of both the Rac guanine nucleotide exchange factor (RacGEF) Vav3 and Rac GTPases is required for BCR-ABL-mediated leukemogenesis. Here, we show that upon BCR-ABL expression, Vav3 expression becomes predominantly nuclear. In this location, Vav2 interacts with BCR-ABL, Rac, and the canonical polycomb repression complex proteins Bmi1, Ring1b and Ezh2. The GEF activity of Vav3 is required for B-cell proliferation and Bmi1-dependent B-cell progenitor self-renewal, nuclear Rac activation, protein interaction with Bmi1, H2A(K119) mono-ubiquitination (H2AK119Ub), and repression of downstream target loci. Vav3 deficiency results in de-repression and repression of loci encoding negative regulators of cell proliferation and oncogenic transcriptional factors, respectively. Mechanistically, we show that Vav3 prevents the Phlpp2-sensitive and Akt (S473)-dependent phosphorylation of Bmi1 on the regulatory residue S314 that, in turn, promotes the transcriptional factor reprogramming of leukemic B-cell progenitors. These results highlight the importance of non-canonical nuclear Rho GTPase signaling in leukemogenesis.

overall_design: Here, we performed  bulk RNAseq experiment. p190 BCR-ABL+ B-cell progenitors from the bone marrow of WT and Vav3-/- transplanted leukemic chimeric mice were sorted and total RNA was extracted using RNAeasy minikit (QIAGEN, Catalog.74104).  Then, RNA samples (10ng) were used for library preparation followed by next generation paired end sequencing. The Wild type samples were used as control/ reference sample

first: Kyung

middle: H

last: Chang

first: Abhishek

last: Singh

first: Michael

last: Kotliar

first: Megha

last: Desai

first: Ashley

last: Wellendorf

first: Mark

last: Wunderlich

first: James

last: Bartram

first: Benzamin

last: Mizukawa

first: M

last: Cuadrado

first: P

last: Dexheimer

first: Artem

last: Barski

first: Xose

last: Bustelo

first: Nicolas

middle: N

last: Nassar

first: José

last: Cancelas


title: Diurnal oscillations in murine brown adipose tissue analyzed by ChIP-seq

city: Leiden

first: Robin

last: van Eenige

address: Albinusdreef 2

department: Division of Endocrinology, Department of Medicine

country: Netherlands

institute: Leiden University Medical Center

summary: Brown adipose tissue (BAT) burns fatty acids to produce heat, and shows diurnal oscillation with peak activity in glucose and triglyceride-derived fatty acid uptake at wakening. To gain further insight in the diurnal regulation of metabolic BAT activity, we performed chromatin immunoprecipitation sequencing (ChIP-seq) on pooled interscapular (i)BAT samples collected from chow-fed male C57BL/6J mice (10 weeks old) exposed to mild cold (22°C) at 3-hour intervals throughout a 24-hour period (n=8 mice per time point). All mice were entrained to a 12h:12h light:dark cycle, and therefore time is denoted as Zeitgeber Time (ZT) in which ZT0 indicates the onset of the light (active) phase.

overall_design: We applied ChIP-seq on murine iBAT obtained at 3 hour-intervals throughout a 24-hour period (8 time points in total; 1 replicate per time point).

first: Wietse

last: In het Panhuis

first: Patrick

last: Rensen

first: Sander

last: Kooijman


title: Pod development transcriptomes of four Phaseolus vulgaris accesions

city: Irapuato

first: Alfredo

middle: Heriberto

last: Herrera

state: Guanajuato

address: Libr.  Norte Carr. Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

summary:
The goal of this study was to detemine the genes responsible of the pod indehiscence in Phaseolus vulgaris by comparing 4 accesions with total, middle and null dehiscence
transcriptomes of three stages of pod develoment of Phaseolus vulgaris

overall_design:
Three stages of pod development were collected and sequenced with the Illumina HiSeq 500 1x75 platform
Mapped reads renders expression to 36996 transcripts. Differential expression genes by pairwise comparison was done between stages

last: Estrella


title: The microRNA profiles of ovarian clear cell carcinoma

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

summary: To investigate the microRNA profiles of ovarian clear cell carcinoma (OCCC), microRNA sequencing was performed using formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen clinical samples. Moreover, patient-derived xenograft (PDX) tumors and cell lines were also investigated.

overall_design: Comprehensive microRNA sequencing was performed using FFPE samples of 20 primary, five recurrent ovarian clear cell carcinoma, and ten contralateral normal ovary samples. Moreover, we included two patients with metastatic OCCC, and their fresh-frozen samples were used. Furthermore, the miRNA profiles of three paired PDX and primary tumors and cell lines were also investigated.

first: Akira

last: Yokoi

first: Hiroaki

last: Kajiyama


title: Microarray profiles from glomerular compartment of kidney biopsies from adults screened for enrollment in the NEPTUNE cohort

first: Sean

last: Eddy

summary: Glomerular Transcriptome from kidney biopsies of adult patients screened for enrollment into NEPTUNE

first: Viji

last: Nair

first: Laura

last: Mariani

first: Felix

last: Eichinger

first: Brad

last: Godfrey

first: Matthias

last: Kretzler


title: The   FUS-DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma

city: Boston

first: Cigall

last: Kadoch

address: 44 Binney St

institute: Dana-Farber Cancer Institute

summary: Mammalian SWI/SNF (mSWI/SNF or BAF) ATP-dependent chromatin remodeling complexes play critical roles in governing genomic architecture and gene expression and are frequently perturbed in human cancers. Transcription factors (TFs), including fusion oncoproteins, can bind to BAF complex surfaces to direct chromatin targeting and accessibility, often activating oncogenic gene loci. Here, we demonstrate that the FUS-DDIT3 fusion oncoprotein hallmark to myxoid liposarcoma (MLPS) inhibits BAF complex-mediated remodeling of adipogenic enhancer sites via sequestration of the adipogenic TF, CEBPB, from the genome. In mesenchymal stem cells, small molecule inhibition of BAF complex ATPase activity attenuates adipogenesis via failure of BAF-mediated DNA accessibility and gene activation at CEBPB target sites genome-wide. BAF chromatin targeting and gene expression profiles of FUS-DDIT3-expressing cell lines and primary tumors exhibit similarity to SMARCB1-deficient BAF loss-of-function tumor types. These data present a novel mechanism by which fusion oncoproteins generate BAF complex loss-of-function phenotypes, independent of deleterious subunit mutations.

overall_design: ChIP-seq, Cut & Run, RNA-seq, and ATAC-seq in MLPS-1765-92 (FUS-DDIT3 fusion), MLPS-402-91 (FUS-DDIT3 fusion), 1BD5 (MLPS-1765-92 SMARCB1-null), 3AA3 (MLPS-1765-92 SMARCB1-null), hTERT-MSC, AD-MSC, and MLPS primary tumors to investigate the role of the FUS-DDIT3 fusion oncoprotein on BAF complex targeting and activity, especially in the context of Myxoid Liposarcoma and adipogenesis

first: Hayley

last: Zullow

first: Akshay

last: Sankar


title: Diurnal oscillations in murine brown adipose tissue analyzed by RNA-seq

first: Robin

last: van Eenige

summary: Brown adipose tissue (BAT) burns fatty acids to produce heat, and shows diurnal oscillation with peak activity in glucose and triglyceride-derived fatty acid uptake at wakening. To gain further insight in the diurnal regulation of metabolic BAT activity, we performed RNA-sequencing (RNA-seq) on interscapular (i)BAT samples collected from chow-fed male C57BL/6J mice (10 weeks old) exposed to mild cold (22°C) at 3-hour intervals throughout a 24-hour period (n=4 mice per time point). All mice were entrained to a 12h:12h light:dark cycle, and therefore time is denoted as Zeitgeber Time (ZT) in which ZT0 indicates the onset of the light (active) phase.

overall_design: We applied RNA-seq on total RNA isolated from murine iBAT obtained at 3 hour-intervals throughout a 24-hour period (8 time points in total; 4 replicates per time point).

last: In het Panhuis


title: Single cell RNA sequencing of sorted bone marrow stromal cells from Osx-Cre, Ai9 mice

city: Saint Louis

first: Christopher

last: Miller

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St Louis

summary: We used single cell RNA sequencing to confirm that Ai9 reporter accurately labeled the cell of interest in an Osc-Cre tartgeted mouse model.

overall_design: Lineage- Pdgfrb+ stromal cells sorted from bone marrow of one male and one female Osx-Cre, Ai9 mice were combined for 10x Genomics single cell RNA-seq

first: Juo-Chin

last: Yao

first: Daniel

last: Link

first: Karolyn

last: Oetjen


title: Regulation of human trophoblast gene expression by endogenous retroviruses [ChIP-seq]

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

summary: The placenta is a fast-evolving organ that displays large morphological and histological differences across eutherians, but the genetic changes driving placental evolution have not been fully elucidated. Transposable elements, through their capacity to quickly generate genetic variation and affect host gene regulation, may have helped to define species-specific trophoblast gene expression programmes. Here were assessed the contribution of transposable elements to human trophoblast gene expression by acting as enhancers or promoters. Using epigenomic data from primary trophoblast and human stem cell lines, we identified multiple endogenous retrovirus families with regulatory potential that lie close to genes with preferential trophoblast expression. These largely primate-specific elements are associated with inter-species gene expression differences, and are bound by transcription factors with key roles in placental development. Using genetic editing we demonstrated that several elements act as expression enhancers of important placental genes, such as CSF1R and PSG5. We also identified an LTR10A element that regulates ENG expression, affecting trophoblast migration and secretion of soluble ENG, with potential implications for preeclampsia. Our data show that transposons have made important contributions to human trophoblast gene regulation, and suggest that their activity may affect pregnancy outcomes.

overall_design: ChIP-seq for histone modifications in human trophoblast stem cells.

first: Jennifer

last: Frost

first: Samuele

last: Amante

last: Okae

first: Eleri

last: Jones

first: Brogan

last: Ashley

first: Rohan

last: Lewis

first: Jane

last: Cleal

first: Matthew

last: Caley

first: Takahiro

last: Arima

first: Tania

last: Maffucci


title: Transcriptomic differences between fibrotic and non-fibrotic testicular tissue reveal possible key players in Klinefelter syndrome-related testicular fibrosis

city: Jette

first: Margo

last: Willems

state: Brussels

address: Laarbeeklaan 103

department: Reproduction, genetics and regenerative medicine

country: Belgium

institute: Vrije Universiteit Brussel

summary: In this study, two gene expression analyses were performed. The first analysis, comparing the DEGs between fibrotic and non-fibrotic tissue, revealed genes which may play a role in testicular fibrosis, including VCAM1. In addition, this analysis revealed a pertinent role for genes involved in the TGF-β1 pathway. Secondly, a differential gene expression analysis between KS and TA samples was performed. GO analysis revealed genes involved in the chronic inflammatory responses. When comparing the X-linked genes of the first analysis (fibrotic versus non-fibrotic) with those of the second analysis (KS versus TA), X-linked fibrotic genes involved in KS revealed, i.e. MXRA5, DCX and VCX3B. Their potential role in KS-related testicular fibrosis needs further study.

overall_design: Transcriptome analysis on extracted RNA from testicular biopsies from patients with and without testicular fibrosis

first: Catharina

last: Olsen


title: Improved Atrial Differentiation of Human Pluripotent Stem Cells by Activation of Retinoic Acid Receptor Alpha (RARα)

city: Enschede

first: Carla

last: Cofiño Fabrés

address: Drienerlolaan 5

institute: University of Twente

summary: Induction of the specific retinoic acid receptor alpha (RARα) increased the efficiency of atrial differentiation to 72% compared with 45% after odulating the retinoic acid (RA) pathway with all-trans RA (atRA). For further purification of the AMs, we describe a metabolic selection procedure that enhanced the AM percentage to more than 90% without compromising the AM yield (15,542 per EB, equal to 3.11 per hPSC) or functionality of the AMs as evaluated by RNAseq, immunostaining, and optical action potential measurement.

overall_design: At day 28 of spin-EB RARa-induced atrial differentiation, total RNA of three hESC-derived AM replicates was sequenced.

first: Verena

last: Schwach

last: Cofiño-Fabrés

first: Rebecca

last: Snabel

first: Gert

middle: J

last: Veenstra

first: Robert

last: Passier


title: Amphoterin-Induced Gene and Open Reading Frame 2 (AMIGO2) Interacts with CAPN2 and Promotes the Proliferation and Migration of Hypopharyngeal Cancer Cell

city: Beijing

first: Wei

last: Gu

address: Shuaifuyuan No.1

department: Otolaryngology Head and Neck Surgery

institute: Peking Union Medical College Hospital

summary: Background: Amphoterin-induced gene and open reading frame 2 (AMIGO2) has been reported to play a detrimental role in multiple cancer types. However, the precise role of AMIGO2 in hypopharyngeal squamous cell carcinoma (HPSCC) remains elusive.   Methods: Bioinformatic analysis was employed to identify the differential expression and prognostic value of AMIGO2 in the head and neck cancer. Proliferation, apoptosis, and migration assays were then conducted after short hairpin RNA-mediated knockdown of AMIGO2 in FaDu cell line and in xenograft mouse model. Co-immunoprecipitation and mass spectrometry analysis were performed to determine the protein interaction between AMIGO2 and CAPN2. Rescue experiments with respect to the overexpression of CAPN2 were also performed. RNA sequencing after AMIGO2 knockdown with and without CAPN2 overexpression were conducted, followed by pathway enrichment analysis.  Results: AMIGO2 expression was up-regulated in head and neck cancer and correlated with a poor prognosis. Functionally, HPSCC cell proliferation and migration were significantly inhibited in vivo and in vitro upon AMIGO2 knockdown. AMIGO2 binds to CAPN2 in cell context, and overexpression of CAPN2 could effectively reverse the inhibition from AMIGO2 knockdown. Bioinformatics analysis based on RNA sequencing indicated that the interaction between AMIGO2 and CAPN2 might be involved in multiple signaling pathways.  Conclusions: Our work suggests that AMIGO2 promotes the proliferation and migration of HPSCC by interacting with CAPN2, implying that AMIGO2 can be therapeutically targeted to treat HPSCC.

overall_design: RNA-seq analysis was performed on three groups of FaDu cells, i.e., AMIGO2 knockdown (KD_NC), AMIGO2 knockdown combined with CAPN2-overexpression (KD_OE), and normal controls (NC_NC).

first: Jian

last: Wang


title: Regulation of human trophoblast gene expression by endogenous retroviruses [RNA-seq]

first: Miguel

last: Branco

overall_design: RNA-seq on human trophoblast stem cells treated with either a JNK inhibitor (SP600125) or DMSO control.

first: Jennifer

last: Frost

first: Samuele

last: Amante

first: Hiroaki

last: Okae

last: Jones


title: Multiple modes of regulation control dynamic transcription patterns during the mitosis-G1 transition

city: Storrs

first: Luke

last: Wojenski

state: CT

address: 181 Auditorium Drive unit 3197  ESB, Room 306B

department: Molecular & Cell Biology

institute: University of Connecticut

summary: Following cell division, genomes must reactivate gene expression patterns that reflect the identity of the cell.  Here, we use PRO-seq to examine the mechanisms that reestablish transcription patterns after mitosis. We uncover regulation of the transcription cycle at multiple steps including initiation, promoter-proximal pause positioning and escape, poly-A site cleavage and termination during the mitotic-G1 transition.  During mitosis, RNA polymerase activity is retained at initiation sites, albeit shifted in position relative to non-mitotic cells. This activity is strongly linked to maintenance of local chromatin architecture during mitosis and is more predictive of rapid gene reactivation than histone modifications previously associated with bookmarking. These molecular bookmarks, combined with sequence-specific transcription factors, direct expression of select cell growth and cell specific genes during mitosis followed by reactivation of functional gene groups with distinct kinetics after mitosis. This study details how dynamic regulation of transcription at multiple steps contributes to gene expression during the cell cycle.

overall_design: Profiling of nascent transcription (PRO-seq) and chromatin accessibility (ATAC-seq) during and after release from mitosis in HeLa-S3 and HEK293T cells.

first: Leighton

last: Core


title: Claspin is required for growth recovery from serum starvation through regulating the PI3K-PDK1-mTOR pathway

city: Tokyo

first: Chi-Chun

last: Yang

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

summary: Growth recovery from serum starvation requires the activation of PI3 kinase (PI3K)- PDK1-Akt-mTOR pathways. Claspin plays multiple important roles in regulation of DNA replication as a mediator for the cellular response to replication stress, an integral replication fork factor that facilitates replication fork progression and a factor that promotes initiation by recruiting Cdc7 kinase. Here, we report a novel role of Claspin in growth recovery from serum starvation. In the absence of Claspin, cells do not proceed into S phase and eventually die. Claspin interacts with PI3K and mTOR, and is required for activation of PI3K-PDK1-mTOR and for that of mTOR downstream factors, p70S6K and 4E-BP1, but not for p38 MAPK cascade during the recovery from serum starvation. PDK1 interacts with Claspin, notably with CKBD, in a manner dependent on phosphorylation of the latter protein, and is required for interaction of mTOR with Claspin. p53 and ROS (Reactive Oxygen Species) inhibitors increased survival of Claspin-deficient cells released from serum starvation. Thus, Claspin plays a novel role as a mediator/protein platform for nutrition-induced proliferation/survival signaling by activating the mTOR pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MEF claspin(f/-) cells and MEF claspin(f/-) cells in serum stravation and release from serum starvation.


title: Mucosal viral infection induces a regulatory T cell activation phenotype distinct from tissue residency in mouse and human tissues [single-cell RNA-seq]

city: Seattle

first: Brianna

last: Traxinger

state: Washington

address: 1100 Eastlake Ave E

department: Vaccine and Infectious Disease Division

institute: Fred Hutch

summary: Vaginal tissue Tregs acquire a inflammatory cytokine-dependent, infection-specific phenotype after local infection with HSV-2

overall_design: CD4+ FoxP3+ Tregs were isolated from the draining lymph nodes and vaginal tissue of FoxP3GFP mice +/- HSV-2 infection. These cells were then processed for  transcriptional profiling using  5' whole transcriptomic approaches (10x)

first: Martin

last: Prlic


title: Mucosal viral infection induces a regulatory T cell activation phenotype distinct from tissue residency in mouse and human tissues

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

overall_design: Refer to individual Series


title: Disruption of DNA Repair and Survival Pathways through Heat Shock Protein inhibition by Onalespib to Sensitize Malignant Gliomas to Chemoradiation therapy

city: Columbus

first: Maciej

last: Pietrzak

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: Purpose: Proficient DNA repair by homologous recombination (HR) facilitates resistance to chemo-radiation in glioma stem cells (GSCs). We evaluated whether compromising HR by targeting HSP90, a molecular chaperone required for the function of key HR proteins, using onalespib, a long-acting, brain-penetrant HSP90 inhibitor, would sensitize high-grade gliomas to chemo-radiation in vitro and in vivoExperimental Design: The ability of onalespib to deplete HR client proteins, impair HR repair capacity, and sensitize GBM to chemo-radiation was evaluated in vitro in GSCs, and in vivo using zebrafish and mouse intracranial glioma xenograft models. The effects of HSP90 inhibition on the transcriptome and cytoplasmic proteins was assessed in GSCs and in ex vivo organotypic human glioma slice cultures.Results: Treatment with onalespib depleted CHK1 and RAD51, two key proteins of the HR pathway, and attenuated HR repair, sensitizing GSCs to the combination of radiation and temozolomide (TMZ). HSP90 inhibition reprogrammed the transcriptome of GSCs and broadly altered expression of cytoplasmic proteins including known and novel client proteins relevant to GSCs. The combination of onalespib with radiation and TMZ extended survival in a zebra fish and a mouse xenograft model of GBM compared to the standard of care (radiation and TMZ) or onalespib with radiation.Conclusions: The results of this study demonstrate that targeting HR by HSP90 inhibition sensitizes GSCs to radiation and chemotherapy and extends survival in zebrafish and mouse intracranial models of GBM. These results provide a preclinical rationale for assessment of HSP90 inhibitors in combination with chemoradiation in GBM patients.

overall_design: GSC lines (811 and 262) or primary GBM tissue (149) were exposed to onalespib for 24 hr, RNA extracted and libraries were prepared for RNA Seq.

first: Vinay

last: Puduvalli

first: Deepa

last: Sampath


title: REST transcription factor holds the balance between the invasion and cell differentiation in IDH-mutant and IDH-wild type gliomas

city: Warsaw

first: Adria-Jaume

last: Roura

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

summary: Glioblastoma is the deadliest brain tumor with median survival of 15 months due to diffusive growth and lack of efficient therapy. Recurrent mutations in genes coding for isocitrate dehydrogenases (IDH) 1 or 2 cause to a change in function of the enzymes, resulting in production of 2-hydroxyglutarate, which leads to DNA hypermethylation phenotype, affecting transcription activators/repressors binding to DNA and gene expression. REST is a canonical repressor of neuronal genes in non-neuronal cells, whose levels differ between IDH wt and mut gliomas and whose expression levels correlate with the patients’ survival probability.

overall_design: IDH1 mutant-U-87 Isogenic Cell Line and malignant glioma U-87 MG were used in the experiments. For each cell line, REST-chromatin immunoprecipitation was performed twice, followed by sequencing and position weight matrix (PWM) analysis. Total RNA was extracted from U-87 MG and IDH1 mutant-U-87 isogenic cell lines that had not been treated, had control siRNA transfected, and had REST-targeting siRNA transfected. Following the construction and sequencing of mRNA sequencing libraries, differential analysis between REST knockdown and control samples was performed.

first: Malgorzata

last: Perycz

first: Marta

last: Jardanowska

first: Adria

first: Karolina

last: Stepniak

first: Bartlomiej

last: Gielniewski

first: Michal

last: Dabrowski

first: Bozena

last: Kaminska

first: Bartosz

last: Wojtas


title: Nuclear Vav3 is required for canonical PRC1 activity in B-cell lymphoblastic leukemogenesis (CUT&RUN)

city: cincinnati

first: Ramesh

last: Nayak

address: 3333 Burnet Ave

institute: Cincinnati Children's

summary: Acute B-cell lymphoblastic leukemia (B-ALL) represents a multiclonal evolution of B-cell progenitors endowed with both tumor-initiating and propagating properties. We have previously shown that the concurrent overexpression and activation of both the Rac guanine nucleotide exchange factor (RacGEF) Vav3 and Rac GTPases is required for BCR-ABL-mediated leukemogenesis. Here, we show that upon BCR-ABL expression, Vav3 expression becomes predominantly nuclear. In this location, Vav2 interacts with BCR-ABL, Rac, and the canonical polycomb repression complex proteins Bmi1, Ring1b and Ezh2. The GEF activity of Vav3 is required for B-cell proliferation and Bmi1-dependent B-cell progenitor self-renewal, nuclear Rac activation, protein interaction with Bmi1, H2A(K119) mono-ubiquitination (H2AK119Ub), and repression of downstream target loci. Vav3 deficiency results in de-repression and repression of loci encoding negative regulators of cell proliferation and oncogenic transcriptional factors, respectively. Mechanistically, we show that Vav3 prevents the Phlpp2-sensitive and Akt (S473)-dependent phosphorylation of Bmi1 on the regulatory residue S314 that, in turn, promotes the transcriptional factor reprogramming of leukemic B-cell progenitors. These results highlight the importance of non-canonical nuclear Rho GTPase signaling in leukemogenesis.

overall_design: Here, we performed cleavege under target and release using nuclease for Bmi1, Ring1b and H2AK119Ub followed by library preparation and subsequent next generation sequecing (CUT&RUNseq) for global mapping of Bmi1, Ring1b and H2ak119Ub binding  in WT and Vav3-/- leuekmic B-cell progenitors derived from bone maarow of WT and Vav3-/- leukmeic chimeric mice.  Leukemic B-cell progenitors (FSChiB220+IgM-CD43+CD19+) were sorted, bound to Concanavalin A (Con-A) magnetic bead, permeabilized using digitonin. The Con-A bound and digitonin permeabilized cells were treated with antibodies against Bmi1, Ring1b and H2aK119Ub followed by protein A-MNase (pA-MNase) binding and targeted digestion in presence of CaCl2. The CUT&RUN released DNA fragments were extracted using QIAGEN MinElute Reaction Cleanup kits, and were used for library preparation prepared using NEBNext Ultra II DNA library preparation kit for Illumina and NEBNext multiplex Oligoes for Illumina. Libraries followed next generation paired end sequencing.

first: Kyung

last: Chang

first: Abhishek

last: Singh

first: Michael

last: Kotliar

first: Megha

last: Desai

first: Ashley

last: Wellendorf

first: Mark

last: Wunderlich

first: James

last: Bartram

first: Benzamin

last: Mizukawa

first: M

last: Cuadrado

first: P

last: Dexheimer

first: Artem

last: Barski

first: Xose

last: Bustelo

first: Nicolas

last: Nassar

first: José

last: Cancelas