title: Identification of open chromatin regions in mouse cardiopharyngeal mesoderm

summary: In the heart development, mesodermal progenitor cells in pharyngeal apparatus, termed cardiopharyngeal mesoderm, contribute to both atruim and right ventricle. Tbx1 gene, encoding a T-box transctiption factor and gene haploinsufficient in 22q11.2 deletion syndrome, is required for cardiac outflow tranct and branchiomeric muscle development. To understand how TBX1 affect open chromatin status in cardiopharyngeal mesoderm, we performed ATAC-seq in Tbx1-Cre lineage with/without Tbx1 expression.

overall_design: Tbx1 gene expressed in pharyngeal apparatus from E8.5 to E10.5 including mesoderm, endoderm and ectoderm.We collected GFP positive cell from Tbx1-Cre/+;GFPflox/+ embryos (control) and Tbx1-Cre/flox;GFPflox/+ embryos (conditional knockout) at E9.5 for ATAC-seq. To extract ATAC-seq peaks in mesodermal cells, we also perfomed ATAC-seq in sorted GFP positive cell from Mesp1-Cre/+;GFPflox/+ embryos at E9.5 then open chromatin regions found in both Tbx1-Cre lineage and Mesp1-Cre lineage were used for analysis.


title: Tbx1 regulates a cardiopharyngeal mesodermal niche in forming the heart and branchiomeric muscles [scRNA-Seq 2]

status: Public on Oct 10 2021

city: Bronx

first: Hiroko

last: Nomaru

state: NY

address: 1300 Morris Park ave

department: Genetics

country: USA

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: The heart and branchiomeric muscles are formed from the cardiopharyngeal mesoderm (CPM) during mammalian embryogenesis.  The molecular mechanisms for lineage progression in the CPM in mammals remain elusive.  Here, we have used single cell RNA-seq and lineage analysis and identified a cardiopharyngeal niche containing multilineage primed cells termed multilineage progenitors (MLPs), which is maintained throughout maturation of the pharyngeal apparatus.  We found that MLP function is dependent on Tbx1, encoding a T-box transcription factor and the gene for 22q11.2 deletion syndrome.  TBX1 positively regulates novel MLP enriched genes such as Aplnr and Nrg1, as well as known CPM genes related to both BrM and cardiac muscle cell development.  Further, loss of Tbx1 results in ectopic expression of neuronal and other non-mesodermal specification genes such as Bdnf and Pax8, respectively, indicating that normal developmental regulation is disrupted.  Integration of the multi-omic data generated a TBX1 gene regulatory network, including Isl1, Pitx2, Foxc2, Six1/2 and Tcf21, that regulates CPM lineage progression from MLPs. Our finding suggests that TBX1 is a one of the key regulators in MLP to maintain CPM property and promote differentiation toward both BrM and cardiac muscle cells.

overall_design: Mesp1 gene expresses in early cardiac mesodermal cells. To capture mesodermal cell lineages,  sorted GFP positive cell from Mesp1-Cre/+;GFPflox/+ embryos at E8.0 to E10.5 embryos were used for scRNA-seq analysis.

first: Bernice

middle: E

last: Morrow

first: Deyou

last: Zheng

first: Yang

last: Liu


title: In Vitro Transcription Recycling Assay Identifies PAF1 as a Driver of RNA Pol II Recycling

status: Public on Oct 07 2021

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: RNA Polymerase II transcriptional recycling is an underappreciated mechanism for which the required factors and contributions to overall gene expression levels are poorly understood. We describe an in vitro methodology facilitating unbiased identification of novel RNA Pol II transcriptional recycling factors and quantitative measurement of transcriptional output from recycled transcriptional components. Proof-of-principle experiments identified PAF1 complex components among recycling factors and detected defective transcriptional output from RNA Pol II recycling following PAF1 depletion. Dynamic ChIP-seq confirmed in vivo PAF1 complex cycling through gene bodies with RNA Pol II and recycling back to the transcription start sites, while PAF1 silencing triggered defective RNA Pol II recycling. Prostate tumors exhibited enhanced transcriptional recycling, which was attenuated by antibody-based PAF1 depletion. These findings identify RNA Pol II recycling as a potential target in cancer and demonstrate the assay’s applicability to characterize RNA Pol II recycling in cells and tissues from other disease states.

overall_design: We have performed time-resolved ChIP-seq of PAF1 and Pol II. PAF1 and Pol II ChIP-seq time course was generated during 0-, 10-, 20-, or 40-minute Flavopiridol treatment to block release of new Pol II into gene bodies and during 0-, 10-, 20- or 40-minute recovery time points after wash-out of Flavopiridol to release Pol II into the gene bodies in LNCaP-abl cells transfected with either non-targeting control siRNA or siPAF1.


title: Tbx1 regulates a cardiopharyngeal mesodermal niche in forming the heart and branchiomeric muscles

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

overall_design: Refer to individual Series


title: Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat

status: Public on Oct 01 2021

city: Gainesville

first: VIJAYENDRAN

last: CHANDRAN

state: FL

address: Assistant Professor, Department of Pediatrics,  University of Florida, School of Medicine, 1600 SW Archer Road, Box 100296

institute: University of Florida

summary:
Purpose: The goal of this study was to characterized the transcriptome profiles of whole-blood cells from 388 specimens obtained from 106 individuals before and after the meditation retreat at four-time points (T1–T4) by RNA sequencing (RNA-Seq). T1 samples were collected 5-8 weeks before the retreat, T2 samples were collected on the day of retreat before starting the meditation method, T3 samples were collected immediately after the retreat, and T4 samples were collected three months after the retreat.
Methods: The human blood samples were collected into PAXgene Blood RNA Tubes and stored at -80°C freezer. Before RNA extraction the samples were removed from -80°C and incubated overnight at room temperature. The samples were randomized before RNA extraction to eliminate any time point or age or sex or batch effect. Manufacturer’s protocol of manual purification of total RNA from human whole blood was followed (Qiagen, cat #762164). RNA was reverse transcribed to complementary DNA (Lexogen QuantSeq 3′ FWD), and sequenced on a HiSeq 4000 instrument (Illumina).
Results: We applied a comprehensive systems biology approach starting with whole blood gene expression profiling combined with multi-level bioinformatic analyses to characterize the co-expression, transcriptional, and protein-protein interaction networks to identify meditation-specific core network after an advanced eight-day Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were downregulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon (IFN) signaling were upregulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients.
Conclusions: The present proof-of-principle study demonstrates that the immune system can be voluntarily influenced by non-pharmaceutical interventions like yoga and meditation. This suggests that meditation as a behavioral intervention could have important implications for treating various conditions associated with excessive or persistent inflammation with a dampened immune system profile.

overall_design: RNA sequencing at four-time points (T1–T4) before and after the meditation retreat. (T1= 97, T2= 105, T3= 104, T4= 82; N= 388).

first: Vijayendran

last: Chandran


title: Impaired function of rDNA transcription initiation machinery leads to derepression of ribosomal genes with insertions of R2 retrotransposon

status: Public on Oct 09 2021

city: Moscow

first: Valentin

last: Poltorachenko

state: Moscow

address: Akademika Kurchatova square, 2

country: Russia

institute: Institute of Molecular Genetics of National Research Centre «Kurchatov Institute»

summary:
Eukaryotic genomes harbor hundreds of rRNA genes, many of which are transcriptionally silent.
However, little is known about selective regulation of individual rDNA units. In Drosophila melanogaster, some rDNA repeats contain insertions of the R2 retrotransposon, which is capable to be transcribed only as part of pre-rRNA molecules. rDNA units with R2 insertions are usually inactivated, although R2 expression may be beneficial in cells with decreased rDNA copy number. Here we found that R2-inserted rDNA units are enriched with HP1a and H3K9me3 repressive mark, whereas disruption of the heterochromatin components slightly affects their silencing in ovarian germ cells. Surprisingly, we observed a dramatic upregulation of R2-inserted rRNA genes in ovaries lacking Udd (Under-developed) or other subunits (TAF1b and ТAF1c-like) of the SL1-like complex, which is homologues to mammalian Selective factor 1 (SL1) involved in rDNA transcription initiation. Derepression of rRNA genes with R2 insertions was accompanied by a reduction of H3K9me3 and HP1a enrichment. We suggest that the impairment of the SL1-like complex affects a mechanism of selective activation of intact rDNA units which competes with heterochromatin formation. We also propose that R2 derepression may serve as an adaptive response to compromised rRNA synthesis.

overall_design: Udd ChIP libraries were sequenced on Illumina HiSeq 4000. rRNA-depleted RNA-seq in udd mutant ovaries.cDNA libraries were sequenced on MGISEQ-2000

middle: A

first: Mikhail

middle: S

last: Klenov


title: Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits (ATAC-Seq)

city: Philadelphia

first: Matthew

middle: C

last: Pahl

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

summary: To investigate the role of the hypothalamus in complex traits, we generated ATAC-seq, RNA-seq, and Promoter Focused Capture C to gain insight into the gene regulatory arcitecture contacting promoters in an embryonic stem cell dervived model of hypothalamic neuron differentiation

overall_design: We performed ATAC-seq, RNA-seq, and Promoter Focused Capture C on stages of ESC dervived hypothalamic like neuron differentiation (ESC: day 0; HP: day 12; HN: day 27).

first: Struan

last: . Grant


title: Cis-regulatory architecture of human ESC-derived hypothalamic neuron differentiation aids in variant-to-gene mapping of relevant common complex traits (Capture C)


title: Investigation of human peripheral T cells responsive to SARS-CoV-2 antigens

city: Suita

first: Daisuke

last: Motooka

address: Yamadaoka

country: Japan

institute: Osaka University

summary: To elucidate the T cell epitopes of SARS-CoV-2, we stimulated human PBMCs from healthy donors and convalescent COVID-19 patients with various SARS-CoV-2 antigens, sorted the activated T cells and performed sc-RNA and -TCR sequencing. We obtained thousands of T cell clonotypes that responded to SARS-CoV-2 antigens, and identified the epitopes and restricting HLAs of several clonotypes that were significantly expanded in the COVID-19 patients.

overall_design: Determination of the TCR and mRNA expression of human T cells stimulated with SARS-CoV-2 antigens.

first: Xiuyuan

last: Lu

first: Yuki

last: Hosono

first: Sho

last: Yamasaki


title: single cell transcriptomics and B-cell repertoire data from one vaccinated individual after Boostrix vaccination

status: Public on Oct 08 2021

city: Leiden

first: Indu

last: Khatri

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: LUMC

summary: The transcriptomics and BCR-rep data was meassured at the single-cell level from the longitudinal samples obtained from an individual following Boostrix vaccination. The donor had no known or suspected exposure to pertussis infection nor vaccination in the past 10 years. EDTA-blood samples for single-cell sequencing were collected at baseline and days 5 (d5), d7, d10 and d14 post-vaccination. At baseline, first 10,000 total CD19+ B cells were sorted, and after adjusting the sorting gate to exclusively sort PB/PCs, another 1,201 CD19+CD38++CD24+CD27+ PB/PCs were sorted. For subsequent visits, all available PB/PCs were sorted (11,051 cells). In total, we sorted 22,252 cells. Nearly 22,000 B cells enriched in PB/PCs from different time-points were processed into single cells in a Chromium Controller (10X Genomics). Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 3’ v3 protocol (10X Genomics) per manufacturer’s recommendations. After amplification of the cDNA, a 5 ́gene expression library and paired heavy and light chain library were generated from cDNA of the same cell using Chromium Single Cell VDJ reagent kit (scBCR-rep library; v1.1chemistry, 10X Genomics). After library preparation, quality control was performed using a bioanalyzer (Agilent 2100 Bioanalyzer; Agilent Technologies). The libraries were sequenced in the NovaSeq6000 sequencer (Illumina) using the v1.0 sequencing reagent kit (read length: 2 x 150bp).

overall_design: Longitudinal examination of five different time points at baseline and post vaccination (baseline, days 5, 7, 10 and 14 post vaccination)

first: Annieck

middle: M

last: Diks

first: Magdalena

last: Berkowska

first: Jacques

middle: J

last: van Dongen


title: Influence of Dnmt3a knockout on gene expression of preleukemia B cell and CLL cells

city: Boston

first: Catherine

last: Wu

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

summary: Although somatic mutations in the DNA methyltransferase 3A (DNMT3A) in chronic lymphocytic leukemia (CLL) are rare, DNMT3A transcript and protein expression is frequently reduced in CLL patients, and previous studies have associated low DNMT3A expression with more aggressive disease and poorer survival.

overall_design: Here we generate B cell-restricted conditional knockout of Dnmt3a in mice and used RNA-seq and to investigate its influence on gene expression in preleukemia B cells and CLL cells.

first: Shanye

last: Yin

first: Anat

last: Biran


title: Interplay between two peroxide stress regulators in the oxidative stress response and virulence of pathogenic Leptospira

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

summary: Pathogenic Leptospira spp. are the causative agents of the zoonotic disease leptospirosis. During infection, Leptospira are confronted with deadly reactive oxygen species (ROS). Withstanding ROS produced by the host innate immunity is an important strategy evolved by pathogenic Leptospira for persisting in and colonizing hosts. The peroxide stress regulator, PerRA, represses genes involved in ROS defenses in L. interrogans. We have identified an ORF encoding a putative second PerR in pathogenic Leptospira that we named PerRB. We have determined the transcriptomic profil of a single perRB and a double perRAperRB mutants. The concomitant inactivation of perRA and perRB has a pleiotropic effect on the transcriptomic profil of L. interrogans. The lack of both PerRA and PerRB regulators led to the differential expression of several virulence-associated genes and a loss of virulence. Our findings provide new insights into a new regulatory network that controls virulence and host colonization.

overall_design: RNA sequencing performed on L. interrogans WT, perRB, and perRAperRB mutant strains cultivated in EMJH medium at 30°C at hte exponential phase.

first: Crispin

last: Zavala-Alvarado

first: Odile

last: Sismeiro

first: Hugo

last: Varet

first: Giovanni

last: Bussotti

first: Céline

last: Lorioux

first: Anthony

last: Vincent

first: Jean-Yves

last: Coppée

first: Frédéric

last: Veyrier

first: Mathieu

last: Picardeau

first: Nadia

last: Benaroudj


title: Direct reprogramming of human Sertoli cells into male germline stem cells with the self-renewal and differentiation potentials via overexpressing DAZL/DAZ2/BOULE genes

status: Public on Sep 30 2021

city: shanghai

first: wenhui

last: zhang

address: jiuzun road 115

country: China

institute: shanghai jiaotong  University

summary:
In this study, we have demonstrated, for the first time, that overexpression of three genes of DAZ family members, namely DAZL, DAZ2, and BOULE, could directly reprogram human Sertoli cells to the cells with the biochemical phenotypes, the self-renewal and differentiation capacities of human SSCs. This study thus offers invaluable male gametes for treating the infertility of azoospermia patients.
We propose a new concept that human somatic cells can be converted to become male germline stem cells by the defined factors. Here we have demonstrated that the overexpression of DAZL, DAZ2, and BOULE could directly reprogram human Sertoli cells into the cells with the characteristics of human spermatogonial stem cells (SSCs), as evidenced by their similar transcriptomes and proteomics with human SSCs. Significantly, human SSCs derived from human Sertoli cells colonized and proliferated in vivo, and they could differentiate into spermatocyte and haploid spermatids in vitro. Human Sertoli cells-derived SSCs excluded Y chromosome microdeletions and assumed normal chromosomes. Collectively, human somatic cells could be converted directly to human SSCs with the self-renewal & differentiation potentials and high safety. This study is of unusual significance, because it provides an effective approach for reprogramming human somatic cells into male germ cells and offers invaluable male gametes for treating male infertility.

overall_design: Two samples are analyzed ;two replicates/sample

first: Wenhui

first: Liping

last: Wen


title: Genome-wide effect of carbon catabolic repressor 1 (Cre1) on genomic expression of Beauveria bassiana

status: Public on Oct 02 2021

city: HANGZHOU

first: REHAB

middle: ABDELMONEM

last: MOHAMED

address: YUHANGTANG ROAD NO.,886

institute: ZHEJIANG UNIVERSITY

summary:
Purpose: This transcriptomic analysis aims at unveiling all possible genes orchestrated by Cre1, which is evidently required for insect pathogenicity and virulence-related cellular events of Beauveria bassiana.
Methods: Total RNAs were extracted from three 3-day-old hyphal cultures (replicates) of cre1 deletion and wild-type strains grown under normal culture conditionsand and subjected to deep sequencing on Illumina NovaseqTM 6000 platform. The sequence reads that passed quality filters were mapped to the genome of Beauveria bassiana. All genes differentially expressed in the deletion mutant versus the wild-type strain were enriched to GO function classes and KEGG pathways.
Results: The resultant transcriptome comprises 10364 genes annotated or not annotated. Among those, 1881 genes (genomic 18.149%) were dysregulated in the absence of cre1, including 1117 down-regulated and 764 up-regulated.
Conclusions: Cre1 has profound impact on the genomic expression of Beauveria bassiana.

overall_design: RNA profiles from 3-day-old hyphal cultures of the cre1 deletion and wild-type strains.

first: Rehab

last: Mohamed

first: Ming-Guang

last: Feng


title: Sex-biased ZRSR2 mutations in myeloid malignancies impair plasmacytoid dendritic cell activation and apoptosis [patients]

first: Andrew

last: Lane

address: 450 Brookline Ave

summary: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is an aggressive leukemia of plasmacytoid dendritic cells (pDCs). BPDCN occurs at least three times more frequently in men than women, but the reasons for this sex bias are unknown. Here, studying genomics of primary BPDCN and modeling disease-associated mutations, we link acquired alterations in RNA splicing to abnormal pDC development and inflammatory response through Toll-like receptors. Loss-of-function mutations in ZRSR2, an X chromosome gene encoding a splicing factor, are enriched in BPDCN and nearly all mutations occur in males. ZRSR2 mutation impairs pDC activation and apoptosis after inflammatory stimuli, associated with intron retention and inability to upregulate the transcription factor IRF7. In vivo, BPDCN-associated mutations promote pDC expansion and signatures of decreased activation. These data support a model in which male-biased mutations in hematopoietic progenitors alter pDC function and confer protection from apoptosis, which may impair immunity and predispose to leukemic transformation.

overall_design: RNA sequencing of 11 BPDCNs and 4 normal pDC samples


title: Generation of functional ciliated cholangiocytes from human pluripotent stem

status: Public on Oct 03 2021

city: Toronto

first: Shinichiro

last: Ogawa

state: Ontario

address: 101 College Street

country: Canada

institute: McEwen Stem Cell Institute

summary: We report on the successful generation of functional ciliated cholangoocytes from hPSCs that will provide new opportunities to study and treat diseases of the liver. Both monolayer- and organoid-derived cells are adaptable for further bioengineering approcahes to produce more complex hPSC-deived liver tissue with biliary ductal structures. Additionally, the successful engraftment of differentiated cholangiocytes in the liver of immune-imcompetent mice provides the basis for developing novel therapeutic strategies to treat cholangiopathies.

overall_design: Examination of heterogeneity and global transcriptome between 2D and 3D cholangiocytes

first: Mina

first: Donghe

last: Yang


title: Recurrent rewiring of the adult hippocampal mossy fiber system by a single transcriptional regulator, Id2

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

summary: Circuit formation in the central nervous system has been historically studied during development, after which cell-autonomous and nonautonomous wiring factors inactivate. In principle, balanced reactivation of such factors could enable further wiring in adults, but their relative contributions may be circuit dependent and are largely unknown. Here, we investigated hippocampal mossy fiber sprouting to gain insight into wiring mechanisms in mature circuits. We found that sole ectopic expression of Id2 in granule cells is capable of driving mossy fiber sprouting in healthy adult mouse and rat. Mice with the new mossy fiber circuit solved spatial problems equally well as controls but appeared to rely on local rather than global spatial cues. Our results demonstrate reprogrammed connectivity in mature neurons by one defined factor and an assembly of a new synaptic circuit in adult brain.

overall_design:
To characterize single-cell transcriptome of GCs after chemical induction (70 nl 5 mM kainic acid, KA, microinjection into the hippocampus), patch-RNAseq was used to sample single dentate GCs for their transcriptomic content 1 and 14 days after KA microinjection. Partitioning of the data is as follows: (1) 1 day after KA: KA1_DG_ipsi, 63 cells; (2) 14 days after KA: Kainate_DG, 29 cells; (3) Control cells collected from non-injected mice: DG, 42 cells.
To characterize single-cell transcriptome of GCs after AAV-gene overexpression,  patch-RNAseq was used to sample single dentate GCs for their transcriptomic content 1 month after AAV injection. Partitioning of the data is as follows: (1) GFP overexpression as controls: GFP_Control, 70 cells; (2) Id2 overexpression: Id2_OE, 95 cells.

first: Wenshu

last: Luo

first: David

last: Lukacsovich

first: Lin

last: Que

first: Jochen

last: Winterer


title: Transposon-triggered innate immune response confers cancer resistance to the blind mole rat [array]

city: Rochester

first: Yang

last: Zhao

address: 60 Crittenden Blvd, Apt1240

department: Biology

institute: University of Rochester

type: Methylation profiling by genome tiling array

summary: Blind mole rats (BMRs) are small rodents, characterized by exceptionally long lifespan (> 21 years) and resistance to both spontaneous and induced tumorigenesis. Here we report that cancer resistance in the BMR is mediated by retrotransposable elements (RTEs). BMR cells and tissues express very low levels of DNA methyltransferase 1 (DNMT1). Upon cell hyperplasia, the BMR genome DNA loses methylation, resulting in activation of RTEs. Up-regulated RTEs form cytoplasmic RNA/DNA hybrids, which activate cGAS-STING pathway to induce cell death. Although this mechanism is enhanced in the BMR, we show that it functions in mice and human. We propose that RTEs were coopted to serve as tumor suppressors that monitor cell proliferation and are activated in premalignant cells to trigger cell death via activation of innate immune response. RTEs activation is a double-edged sword, serving as a tumor suppressor but in late life contributing to aging via induction of sterile inflammation.

sample_organism:
Mus musculus
Nannospalax ehrenbergi

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Using a custom Illumina chip HorvathMammalMethylChip40, we compared methylation of 37K conserved CpG sites between blind mole rat and mouse fibrolasts for both young and overproliferated cells. Five cell lines from each species were used for paired comparison.

first: Steve

last: Horvath

first: Vera

last: Gorbunova


title: DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response

status: Public on Oct 04 2021

city: Hong Kong

first: Danny

last: Leung

address: Clear Water Bay

country: Hong Kong

institute: Hong Kong University of Science and Technology

summary: Cytoplasmic DNA (cytoDNA) is a strong immune stimulus that evolved to protect the cell against invasion byDNA viruses. Curiously, cytoDNA is also found in the absence of viral infection in conditions such as cancer, neurodegeneration and immune system disorders. In mouse microglia, agents that enhance DNA damage lead to the accumulation of cytoDNA. In this report we demonstrate that cytoDNA resulting from reduced DNA repair comes from the cell nucleus and is actively exported to the cytoplasm by a CRM1-dependent mechanism. Once in the cytoplasm, it is degraded either by a cytosolic exonuclease, Trex1, or an autophagy pathway that ends with degradation in the lysosome. Blocking nuclear export, overexpression of Trex1 or induction ofautophagy are each able to block the accumulation of cytoDNA and prevent the emergence of aninflammatory reaction.Genomics analysis confirms that cytoDNA originates in the nuclear genome and not the mitochondria.Moreover, these fragments are enriched intranscriptionally inactive, intergenic regions, in particular repetitive elements and AT-rich sequences. These findings offer new insights into the cellular dynamics that create cytoDNA and thus offer new pathways to blunt its appearance and the downstream inflammatory responses

overall_design: Cytoplasmic DNA (cytoDNA) was isolated and sequenced to define cytoDNA regions

first: J

middle: T

last: Aw

first: D


title: HRD1-mediated METTL14 degradation regulates m6A mRNA modification to suppress ER proteotoxic liver disease

city: Chicago

first: Bryan

last: Harada

state: IL

address: 929 E 57th St

department: Chemistry

institute: University of Chicago

type: Methylation profiling by high throughput sequencing

summary: Accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) lumen triggers unfolded protein response (UPR) for stress adaptation, the failure of which induces cell apoptosis and tissue/organ damage. The molecular switches underlying how the UPR selects for stress adaptation over apoptosis remain unknown. Here we discovered that accumulation of unfolded/misfolded proteins selectively induces N6-adenosine-methyltransferase-14 (METTL14) expression. METTL14 promotes CHOP mRNA decay through its 3’UTR N6-adenosine methylation (m6A) to inhibit its downstream pro-apoptotic target genes expression.  UPR induces METTL14 expression through competing the HRD1-ERAD machinery to block METTL14 ubiquitination and degradation. Therefore, mice with liver-specific METTL14 deletion are highly susceptible to both acute pharmacological and alpha-1 antitrypsin (AAT) deficiency-induced ER proteotoxic stress and liver injury. Further hepatic CHOP deletion protects METTL14 knockout mice from ER stress-induced liver damage.  Our study reveals a crosstalk between ER stress and mRNA m6A pathways, the ERm6A pathway, for ER stress adaptation to proteotoxicity.

overall_design: To investigate the molecular mechanisms underlying how METTL14 protects mice from UPR-induced liver damage, we analyzed the mRNA expression profile in liver from Tm treated METTL14 LKO and WT mice by transcriptome-wide mRNA sequencing.

first: Juncheng

last: Wei

first: Chuan

last: He

first: Deyu

last: Fang


title: Expression data from thymic endothelial cells after damage (2)

city: Seattle

first: Kirsten

last: Cooper

state: WA

address: 1100 Fairview Ave. N, Rm S3-208

institute: Fred Hutchinson Cancer Research Center

summary: The thymus is extremely sensitive to damage but also has a remarkable ability to repair itself. However, the mechanisms underlying this endogenous regeneration remain poorly understood and this capacity diminishes considerably with age. To identify alternate regeneration pathways in the thymus, we performed an unbiased transcriptome analysis of the non-hematopoietic (CD45-) stromal cell compartment of the thymus, which is less sensitive to thymic damage compared to the CD45+ hematopoietic compartment.

overall_design:
We compared the gene expression of freshly isolated ECs from the mouse thymus at days 0 and 4 after a sublethal dose of total body irradiation (SL-TBI, 550cGy).
Thymic non-hematopoietic stromal cells were isolated using CD45 MACS cell depletion. Endothelial cells were then FACS purified (CD45- EpCAM- VE-Cad+). Microarray analysis was performed on an Affymetrix MOE 430 A 2.0 platform in triplicate for freshly isolated ECs from untreated mice, and in duplicate for day 4 SL-TBI mice.

first: Sinéad

last: Kinsella

first: Jarrod

last: Dudakov


title: RNA-seq analysis of A3250 inflammatory breast cancer (IBC) xenografts and cells in vitro

city: New York

first: Mihaela

last: Skobe

address: 1425 Madison Ave, Rm 15-20F

department: Oncological Sciences

institute: The Icahn School of Medicine at Mount Sinai

summary:
Purpose: Transcriptome profiling (RNA-seq) of a novel human Inflammatory Breast Cancer cell line A3250 and its xenograft tumors
Methods: A3250 tumor cells were maintained as adherent cultures in standard tissue culture dishes, in high-glucose DMEM supplemented with 4 mM L-glutamine, 10% FBS, and 1X antibiotics (100 U/ml penicillin, 100 U/ml streptomycin)
Tumor cells cultured in vitro were harvested for RNA-Seq analysis at 80% confluency. To generate tumors, A3250 tumor cells (1 x 10E6 cells in 100 µl PBS) were injected into the fourth mammary fat pads of eight to nine-week-old SCID mice. Tumors were harvested at 5-6 weeks post-injection, when they reached 4-5 mm in diameter.
Results: A3250 is a novel IBC cell line that recapitulates key features of human IBC in a mouse xenotransplant. RNA-Seq analysis identified expression profile characteristic for this cell line and its tumors.

overall_design: RNA-Seq analysis of A3250 Inflammatory Breast Cancer (IBC) xenografts (three biological replicates) and A3250 IBC tumor cells cultured in vitro (one sample).

first: Anita

last: Rogic

first: Aaron

last: Sun

first: Stuart

last: Aaronson


title: Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation [RNA-seq]

first: Grigorios

last: Georgolopoulos

address: 2211 Elliott Ave #400

institute: Altius Institute

summary: Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. We performed dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) along ex vivo human erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit the stem and progenitor stage. Collectively, these data provide novel insights into the global regulatory landscape during hematopoiesis.

overall_design: Total RNA-seq from bulk ex vivo erythroid differentiation cultures starting from GCSF-mobilized PBMC-derived CD34+ cells from 3 healthy adult donors.

first: Nikoleta

last: Psatha

first: Mineo

last: Iwata

first: Andrew

last: Nishida

first: Tannishtha

last: Som

first: Minas

last: Yiangou

first: John

last: Stamatoyannopoulos

first: Jeff

last: Vierstra


title: Transcriptomic analysis of A3250 inflammatory breast cancer (IBC) cells, SUM149 IBC and MDA-MB-231 non-IBC cells

summary:
Purpose: Transcriptome profiling (RNA-seq) of a novel human Inflammatory Breast Cancer cell line A3250 in comparison to SUM149 and MDA-MB-231
Inflammatory Breast Cancer (IBC) is the most aggressive form of breast cancer with distinct clinical and histopathological features, but understanding of the unique aspects of IBC biology lags far behind that of other breast cancers.
We describe a novel triple-negative IBC cell line, A3250, that recapitulates key features of human IBC in a mouse xenograft model.The purpose of this study was to compare differences in gene expression between A3250 IBC, MDA-MB-231 non-IBC and SUM149 IBC that does not present with typical clinical sympotms of IBC in a mouse model, with the goal of identifying unique molecular features for this unique type of breast cancer
Results: RNA-Seq analysis identified expression profile characteristic for the novel A3250 IBC cell line, compared to SUM149 IBC and MDA-MB-231 non-IBC.

overall_design: RNA-Seq analysis of A3250 IBC tumor cells (n=3), SUM149 IBC tumor cells (n=3) and MDA-MB-231 non-IBC tumor cells (n=3) cultured in vitro.

first: Ila

last: Pant


title: Nuclear-capture of endosomes drives depletion of nuclear G-actin to promote SRF/MRTF gene expression and cancer cell invasiveness

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Cancer Research UK Scotland Institute

summary: Signals are relayed from receptor tyrosine kinases (RTKs) at the cell surface to effector systems in the cytoplasm and nucleus, and coordination of this process is important for the execution of migratory phenotypes, such as cell scattering and invasion.  The endosomal system influences how RTK signalling is coded, but the ways in which it transmits these signals to the nucleus to influence gene expression are not yet clear. Here we show that an RTK, MET promotes Rab17- and clathrin-dependent endocytosis of EphA2, another RTK, followed by centripetal transport of EphA2-positive endosomes. EphA2 then mediates physical capture of endosomes on the outer surface of the nucleus; a process involving interaction between the nuclear import machinery and a nuclear localisation sequence in EphA2’s cytodomain. Nuclear capture of EphA2 promotes RhoG-dependent phosphorylation of the actin-binding protein, cofilin to oppose nuclear import of G-actin. The resulting depletion of nuclear G-actin drives transcription of Myocardin-related transcription factor (MRTF)/serum-response factor (SRF)-target genes to implement cell scattering and the invasive behaviour of cancer cells.

overall_design: mRNA profiles of the effect of EphA2 on cells treated with or without HGF

first: Sergi

last: Marco

first: Jim

last: Norman


title: Identification of pharmacologic inhibitors and activators of IL-4-induced macrophage polarization

city: Charlestown

first: Alexander

middle: G

last: Marneros

address: 13th Street

department: Department of Dermatology, Cutaneous Biology Research Center

institute: Massachusetts General Hospital, Harvard Medical School

summary: Macrophages polarize towards different subpopulations with distinct and partly antagonistic functions in various diseases. IFNγ/LPS-polarized M1-type macrophages can have antiangiogenic activity, whereas IL-4-induced M2-type macrophages can be proangiogenic and profibrotic. Therapeutic strategies to inhibit M2-type polarization while promoting M1-type polarization could serve to inhibit pathological angiogenesis and fibrosis. Here, by combining global quantitative time-course proteomics and phosphoproteomics with a small-molecule inhibitor screen we identify signaling events that promote specifically IL-4-induced and not IFNγ/LPS-induced macrophage polarization and found that the MEK inhibitor trametinib and the HDAC inhibitor panobinostat potently prevent M2-type macrophage polarization without inhibiting M1-type polarization. In contrast, selective B-Raf inhibition promotes M2-type polarization. Trametinib and panobinostat also blocked M2-type macrophage polarization and concomitantly angiogenesis and fibrosis in models of wound healing and neovascular age-related macular degeneration in vivo. Thus, these pharmacologic inhibitors could be utilized therapeutically to selectively block IL4-induced macrophage polarization and reduce pathologic angiogenesis and fibrosis.

overall_design: THP-1 cell M1-type and M2-type polarizations

first: Lizhi

last: He

first: Alaxander


title: Single-cell transcriptomics reveals a conserved metaplasia program in pancreatic injury

city: La Jolla

first: Zhibo

last: Ma

state: California

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: Acinar to ductal metaplasia (ADM) occurs in the pancreas in response to tissue injury and is a potential precursor for adenocarcinoma. We perfomed scRNAseq on lineage-traced cells resulting from acinar cells upon pancreas injury.

overall_design: Acinar cells were lineage-traced with enhanced yellow fluorescent protein (EYFP) to follow their fate upon injury. Mice were sacrificed after either 2 or 4 weeks of caerulein treatment and pancreata were collected. Two mice for each time point. Transcripts of over 13,000 EYFP+ cells were profiled. Single-cell trajectories were generated. Data were compared to gastric metaplasia and human pancreatitis.

first: Nikki

last: Lytle

first: Geoffrey

last: Wahl

first: Kathleen

last: DelGiorno


title: Novel ADNP syndrome mice reveal dramatic sex-specific peripheral gene expression with brain synaptic and Tau pathologies.

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

summary: Essential for brain formation and function, activity-dependent neuroprotective protein (ADNP) is a major autism gene. Here, a novel Tyr mouse carrying p.Tyr718* mutation (homologous to the most common ADNP syndrome p.Tyr719*) was generated using CRISPR-Cas9. Adnp p.Tyr718* inhibited early mouse development and showed sex-dependent gait deficits. Delayed speech acquisition was translated to sex-specific mouse syntax abnormalities. Mechanistically, dendritic spine densities/morphologies were significantly decreased in Tyr mice. All mentioned impediments were ameliorated by daily treatments with the ADNP fragment, drug candidate, NAP. Early onset tauopathy was male-specific (hippocampus and visual cortex) mimicking the human condition, paralleled by impaired visual evoked potentials and corrected by acute NAP treatment. RNA-sequencing of spleens revealed a comprehensive effect only on females, with 5 transcripts (SMOX, ARRB1, ADCY6, FOXO3, CPXM1), shared as deregulated by different human patient-derived ADNP mutated lymphoblastoid cell lines. With FOXO3 implicated in apoptosis and steroid synthesis, these changes, converging on AKT1, were further translated to sex-specific microbiota signatures. The Tyr mouse is thus a valid model for the ADNP syndrome, with a human-like pathology. NAP’s corrective effects attest to specificity, leading to future drug development with objective biomarkers, including rapidly responsive visual evoked potentials, blood proteomics and microbiota signatures.

overall_design: Samples include 14 week-mouse male and female spleens, wild-type or mutated ADNP (p.Tyr718*) and NAP treated or untreated, in triplicates.

first: Gidon

last: Karmon

first: Shlomo

last: Sragovich

first: Gal

last: Hacohen-Kleiman

first: Inbar

middle: B

last: Horin-Hazak

first: Petr

last: Kasparek

first: Björn

last: Schuster

first: Radislav

last: Sedlacek

first: Paschalis

last: Theotokis

first: Olga

last: Touloumi

first: Sofia

last: Zoidou

first: Linxuan

last: Huang

first: Pei

middle: Y

last: Wu

first: Roy

last: Shi

first: Oxana

last: Kapitansky

first: Alexandra

last: Lobyntseva

first: Eliezer

last: Giladi

first: Guy

last: Shapira

first: Noam

last: Shomron

first: Stefan

last: Bereswill

first: Markus

last: Heimesaat

first: Nikolaus

last: Grigoriadis

first: Anne

middle: R

last: McKunney

first: Moran

last: Rubinstein

first: Illana

last: Gozes


title: Minimizing the ex vivo confounds of cell-isolation techniques on transcriptomic profiles of purified microglia

city: Oklahoma City

first: Michael

last: Stout

state: OK

address: 825 N.E. 13th Street

department: Aging and Metabolism

institute: Oklahoma Medical Research Foundation

summary: Modern molecular neuroscience studies require analysis of specific cellular populations derived from brain tissue samples to disambiguate cell-type specific events. This is particularly true in glial cell types, such as microglia, which as minority cell populations in the brain, may be obscured in whole tissue analyses. Microglia have central functions in development, aging, and neurodegeneration and are a current focus of neuroscience research. A long-standing concern for glial biologists using in vivo models is whether cell isolation from CNS tissue could introduce ex vivo artifacts in microglia, which respond quickly to changes in the environment. Mouse microglia were purified by antibody-conjugated magnetic bead, and cytometer- and cartridge-based fluorescence-activated cell sorting approaches to compare and contrast performance. The Cx3cr1-NuTRAP (nuclear tagging and translating ribosome affinity purification) model was used to provide an endogenous fluorescent microglial marker and a microglial-specific translatome profile lacking cell isolation artifacts. All methods performed similarly for microgial purity with main differences being in cell yield and time of isolation. Ex vivo activation signatures occurred principally during the initial tissue dissociation and cell preparation and not the microglial cell sorting. Utilizing transcriptional and translational inhibitors during the cell preparation prevented the activational phenotype. These data demonstrate that a variety of microglial isolation approaches can be used, depending on experimental needs, and that inhibitor cocktails are effective at reducing cell preparation artifacts.

overall_design: Transcriptomic changes consistent with aspects of microglial activation occur during preparation of cell suspensions from brain tissue but no differences are observed between different types of microglial cell sorting.  Use of transcriptional and translational inhibitors during cell preparation can prevent many of these ex vivo changes. Magnetic bead, cytometer FACS, and cartridge FACS all perform to isolate microglia from brain tissue with choice of method dependent on experimental goals.  n=4/group. Control samples include tissue and cell input.

first: Sarah

last: Ocanas

first: Kevin

middle: D

last: Pham

first: Harris

last: Blankenship

first: Adeline

last: Machalinski

first: Ana

last: Chucair-Elliott

first: Willard

last: Freeman


title: Lithium treatment and human hippocampal neurogenesis

city: London

first: Timothy

last: Powell

address: 16 De Crespigny Park

department: Social, Genetic & Developmental Psychiatry

institute: King's College London

summary: Lithium is a first-line treatment for bipolar disorder, where it acts as a mood-stabilizing agent. Although its precise mechanism remains unclear, neuroimaging studies have shown that lithium accumulates in the hippocampus and that chronic use amongst bipolar disorder patients is associated with larger hippocampal volumes. Here, we tested the chronic effects of low (0.75 mM) and high (2.25 mM) doses of lithium on human hippocampal progenitor cells and used immunocytochemistry to investigate the effects of lithium on cell parameters implicated in neurogenesis. Corresponding RNA-sequencing and gene-set enrichment analyses were used to evaluate whether genes affected by lithium in our model overlap with those regulating the volume of specific layers of the dentate gyrus. We observed that high-dose lithium treatment in human hippocampal progenitors increased the generation of neuroblasts (P ≤ 0.01), neurons (P ≤ 0.01), and glia (P ≤ 0.001), alongside the expression of genes which regulate the volume of the molecular layer of the dentate gyrus. This study provides empirical support that adult hippocampal neurogenesis and gliogenesis are mechanisms that could contribute to the effects of lithium on human hippocampal volume.

overall_design: Transcriptomic profiling of human hippocampal progenitor cells exposed to low (0.75 mM) or high (2.25 mM) doses of lithium, and control cultures (no lithium).

first: Alish

last: Palmos

first: Rodrigo R

last: Duarte

first: Demelza

last: Smeeth

first: Erin

last: Hedges

first: Douglas

middle: F

last: Nixon

first: Sandrine

last: Thuret


title: Profiling of INO80-regulated transcription

city: Stanford

first: Ashby

last: Morrison

state: CA

address: 371 Serra Mall Gilbert Bldg, Room 326

institute: Stanford University

summary: We performed RNA-seq of primary human umbilical vein cells (HUVEC) before and after knockdown of Ino80 with siRNA

overall_design: mRNA profile of siINO80 and ctrl HUVEC cells using sequencing

first: Ka

last: Wong


title: Discrete regulatory modules instruct hematopoietic lineage commitment and differentiation [scRNA-seq]

first: Grigorios

last: Georgolopoulos

first: Nikoleta

last: Psatha

first: Mineo

last: Iwata

first: Andrew

last: Nishida

first: Tannishtha

last: Som

first: Minas

last: Yiangou

first: John

last: Stamatoyannopoulos

first: Jeff

last: Vierstra


title: LncRNA and mRNA expression in five paired lung tissues (lung cancer tissues versus nontumor tissues) from non-small cell lung cancer (NSCLC) patients

city: Nanjing

first: Chen

last: Wang

state: Jiangsu

address: 163 Xianlin Avenue

department: Life Sciences

institute: Nanjing University

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

summary: To determine the LncRNA and mRNA expression profile in lung cancer tissues and matched nontumor tissues, we used LncRNA microarray analysis from Arraystar to examine the expression of LncRNAs and mRNAs in lung cancer tissues and matched nontumor tissues.

overall_design: Paired lung tissues from five NSCLC patients surgery were distributed into two experimental groups: lung cancer tissue group and matched nontumor tissue group, then perform LncRNAs chips by Arraystar Human LncRNAs chip (Arraystar)

first: Tao


title: Epigenetic bases of grafting-induced vigour in eggplant [Bisulfite-Seq]

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

institute: University of Birmingham

summary: In horticulture, grafting is a popular technique used to combine positive features of two different plants, obtained by joining a scion (generally the part above the ground) onto a rootstock (constituted by the stem and roots). Despite its wide-use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype are not fully understood. Given that epigenetics is an important component of distance signalling in plants, we investigated the genome wide changes in the DNA methylation induced in eggplants grafted onto two interspecific rootstocks commercially used to induce scion vigour, compared to self-grafted plants. We found that vigour was associated to a specific change in scion gene expression and a genome wide hypo-methylation in CHH context. Interestingly, this hypomethylation correlated with downregulation of younger and potentially more active LTR retrotransposons. Our data indicate that graft-induced epigenetics modifications are associated to both physiological and molecular phenotypes in plants, and suggest that rootstocks can induce vigour by reducing DNA methylation in the scion genome, similarly to what observed in some heterotic hybrids.

overall_design: Examination of DNA methylation of 2 wild type Solanum melongena plants, and two replicates of S. melongena scions grafted on S. melongena (self graft), Solanum torvum and Solanum lycopersicum (var. Emperador).


title: CD20 positive CD8 T cells are a unique and transcriptionally-distinct subset of T cells with distinct transmigration properties

status: Public on Sep 29 2021

city: Groningen

first: Martijn

middle: Ruben

last: Vlaming

state: Groningen

address: Hanzeplein 1

institute: UMCG

summary: This study further delineates the properties CD20-positive T cells, which display a reduced transmigration and an enhanced adhesive profile combined with an enhanced activation status

overall_design: Identify the transcriptomic profile of CD20-positive T cells using RNA sequencing

first: Vrouyr

last: Bilemjian

first: Jimena

last: Freile

first: Harm

last: Lourens

first: Nienke

last: van Rooij

first: Gerwin

last: Huls

first: Tom

last: van Meerten

last: de Bruyn

first: Edwin

last: Bremer


title: Transcriptome (RNA-seq) of primary mouse hepatocytes (PMH) cells non-infected (NI) or infected (Inf.) with the pathogen Listeria monocytogenes (strain 10403S)

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Comparisons of gene expression profiles PMH infected or not by the bacterium Listeria monocytogenes (strain 10403S) for 72 hours and analysed by RNA-seq

overall_design: We used  RNA-seq to identify the repertoire of genes differentially expressed after 3 days of infection with Listeria monocytogenes 10403S strain in primary mouse hepatocytes.

first: Natalie

last: DESCOEUDRES

first: Luc

last: JOUNEAU

first: Kevin

last: GORRICHON

first: Hélène

last: BIERNE


title: Anthrax toxins regulate pain signaling and can deliver molecular cargoes to Antxr2+ DRG sensory neurons

city: Boston

first: Nicole

last: Yang

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: We found that intrathecal injection of anthrax edema toxin (ET), causes analgesia in adult B6J mice. In order to determine if DRG neuron transcriptional responses play a role in pain blockade, we performed a bulk RNA-seq experiment on dissected mouse DRG neurons. We report that anthrax edema toxin causes transcriptional responses in DRG neurons 2h after in vivo administration

overall_design: We injected 6 mice (intrathecally) with PBS (control) and 6 mice with ET. After waiting 2h and observing pain blockade in the ET injected animals, we dissected the lumber DRGs and proceeded to RNA-extraction

first: Dylan

last: Neel

first: Isaac

last: Chiu


title: Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGFβ signaling

city: Dallas

first: Robert

last: Tower

address: 5323 Harry Hines Blvd

institute: UTSW

summary: The patterning and ossification of the mammalian skeleton requires the coordinated actions of both intrinsic bone morphogens and extrinsic neurovascular signals, which function in a temporal and spatial fashion to control mesenchymal progenitor cell (MPC) fate. Here we show genetic inhibition of Tropomyosin receptor kinase A (TrkA) sensory nerve innervation of the developing cranium results in premature calvarial suture closure, associated with a decrease in suture MPC proliferation. In vitro, axons from peripheral afferent neurons derived from DRGs of wild type mice induce MPC proliferation in a spatially-restricted manner via a soluble factor when co-cultured in microfluidic chambers. Comparative spatial transcriptomic analysis of the cranial sutures in vivo confirmed a positive association between sensory axons and proliferative MPCs. SpatialTime analysis across the developing suture revealed regional-specific alterations in BMP and TGFβ signaling pathway transcripts in response to TrkA inhibition. RNA sequencing of DRG cell bodies following direct axonal co-culture with MPCs confirmed alterations in BMP/TGFβ signaling pathway transcripts. Among these, the BMP inhibitor FSTL1 (Follistatin-like 1) replicated key features of the neural-to-bone influence, including mitogenic and anti-osteogenic effects via inhibition of BMP/TGFβ signaling. Taken together, our results demonstrate that sensory nerve-derived signals, including FSTL1, function to coordinate cranial bone patterning by regulating MPC proliferation and differentiation in the suture mesenchyme.

overall_design: P0 calvaria were isolated from TrkAF592A homozygous (mutant) and heterozygous (control) mice in which mothers were treated with 1NMPP1 via their drinking water from the time of conception through birth. Sagittal sutures and flanking parietal bones were dissected out, stacked and fresh frozen in OCT. Frozen sections were applied to the 10X Visium spatial transcriptomics gene expression platform and processed according to manufacturers protocols. Following sequencing, alignment and image registration was conducted using SpaceRanger.

first: Thomas

middle: L

last: Clemens

first: Aaron

middle: W

last: James


title: Transcriptome of mouse leptomeningeal fibroblats

city: Leuven

first: Jan

last: Remsik

address: Campus Gasthuisberg, Herestraat 49

department: Center for Cancer Biology

country: Belgium

institute: VIB

summary: Meninges, or the membranous coverings of the brain and spinal cord, play host to dozens of morbid pathologies. In this study we provide a method to isolate the leptomeningeal cell layer, identify leptomeninges in histologic slides, and maintain leptomeningeal fibroblasts in in vitro culture. Using an array of transcriptomic, histological, and cytometric analyses, we identified ICAM1 and SLC38A2 as two novel markers of leptomeningeal cells in vivo and in vitro. Our results confirm the fibroblastoid nature of leptomeningeal cells and their ability to form a sheet-like layer that covers the brain and spine parenchyma. These findings will enable researchers in central nervous system barriers to describe leptomeningeal cell functions in health and disease.

overall_design: Mouse leptomeningeal cells were enriched using FACS and their transcriptome was assessed with bulk RNA-seq.

first: Fadi

last: Saadeh

first: Adrienne

last: Boire


title: A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models[RNA-seq]

city: Chapel Hill

first: Gang Greg

last: Wang

state: NORTH CAROLINA

address: 405 West Drive

department: UNC Lineberger Comprehensive Cancer Center; Department of Biochemistry and Biophysics

institute: University of North Carolina at chapel hill

summary: Biochemical interactions between WD40 repeat domain protein 5 (WDR5) and its various cellular partners such as Mixed Lineage Leukemia (MLL) and c-MYC are essential for sustaining oncogenesis in a range of human cancers. Thus, small molecules targeting WDR5 represent an attractive strategy for anti-cancer interventions.  However, currently available inhibitors designed to interfere with WDR5 binding to a specific partner (such as OICR-9429 that blocks WDR5-MLL interaction) show a promising but rather partial therapeutic effect, presumably due to incomplete blockade of WDR5 functionality and interactions with various partners. Here, we report the first-in-class, OICR-9429-based proteolysis targeting chimeras (PROTACs) of WDR5, including a prototypic compound MS33 and a further optimized MS67, that achieve specific and efficient depletion of WDR5 in cancer cells. Such an effect is not seen with OICR-9429 or MS33/67 analogs that are incapable of E3 ligand conjugation.  Medicinal chemistry, structural and cellular characterizations demonstrate that MS33 and MS67 bind both WDR5 and an E3 ligand VHL tightly, with MS67 showing a unique cooperative binding, an event that subsequently induces degradation of WDR5 through a VHL- and proteasome-dependent mechanism. Global proteomics profiling shows a highly specific effect of MS67 on WDR5. Genomics analysis further demonstrates that, relative to non-degrading inhibitors, MS67 is far more potent in suppressing overall transcription of WDR5-regulated genes crucially involved in oncogenesis and in reducing global H3K4 methylation, an enzymatic product of MLL/WDR5 complex. Importantly, using a panel of human MLL-rearranged acute myeloid leukemia (MLL-r AML) and pancreatic ductal adenocarcinoma (PDAC) cells, we found that, relative to non-degrading inhibitor controls, MS67 displays a superior anti-growth effect. MS67 also demonstrates optimal PK/PD properties in vivo and treatment with MS67 significantly suppressed tumorigenesis of MLL-r AML in tumor xenografted animal models.  Together, this study reports the first-in-class PROTACs of WDR5 and demonstrates its advantageous efficacies in the treatment of WDR5-dependent cancers.

overall_design: Examination of transcriptome profiles in the MV4;11 and MIA PaCA-2 cells post-treatment with either DMSO, OICR-9429 (a small molecule designed to interfere with WDR5 binding to MLL), MS67 (a WDR5-specific PROTAC/degrader) or MS67N (a MS67 analog control incapable of E3 ligand conjugation). Examination of transcriptome profiles in the MV4;11 and MIA PaCA-2 cells after induction of expression of the WDR5-targeted shRNA to induce WDR5 knockdown (KD), relative to empty vector mock (shEV).

first: Dongxu

last: Li

first: Greg


title: Lung transcriptome profile in healthy and OVA-sensitized/challenged mice fed a diet supplemented with or without Cap or ODNcap

city: Nagano

first: Takeshi

last: Shimosato

address: 8304, Minami-minowa, Kami-ina

department: Institute for Biomedical Sciences

institute: Shinshu University

summary: CpG-oligodeoxynucleotides (CpG-ODNs) constitute an attractive alternative for asthma treatment. We found that free feeding of an ODNcap (a CpG-ODN-embedded particle) -containing feed (ODNcap-F) prophylactically attenuates allergic airway inflammation, hyperresponsiveness, and goblet cell hyperplasia in an ovalbumin (OVA) -induced asthma model. To seek the suppressive mechanism of action of ODNcap-F in OVA-induced airway insults, we analyzed the lung transcriptome using DNA microarray analysis.

overall_design: Mice were fed standard feed (Ctrl-F, n = 2), control particle-containing feed (Cap-F, n = 2), or ODNcap-containing feed (ODNcap-F, n = 2) ad libitum for 70 days, and then were sensitized intraperitoneally and inhalation-challenged with ovalbumin (OVA). Mice in the healthy control group (NT, n = 2) were fed standard feed ad libitum for 70 days, and were not exposed to OVA. Lungs were isolated from each mouse, and were used for RNA isolation.

first: Suguru

last: Shigemori


title: A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models

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

overall_design: Refer to individual Series


title: RNaseT2 deficient mice reveal the interferon-driven brain phenotype of congenital CMV infection and type I interferonopathies

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

summary: Infantile-onset RNaseT2 deficient leukoencephalopathy is characterised by cystic brain lesions, multifocal white matter alterations, cerebral atrophy, and severe psychomotor impairment. The phenotype is indistinguishable from congenital cytomegalovirus brain infection and overlaps with typeI interferonopathies like Aicardi-Goutières syndrome, strongly suggesting a role for innate immunity in its pathophysiology. To date, pathophysiological studies have been hindered by the lack of mouse models recapitulating the neuroinflammatory encephalopathy found in patients. In this study, we generated Rnaset2-/- mice using CRISPR/Cas9-mediated genome editing. Strikingly, Rnaset2-/- mice revealed strong upregulation of interferon-stimulated genes and concurrent neuroinflammation, with infiltration of CD8+  effector memory T cells and inflammatory monocytes into the grey and white matter. Homeostatic dysfunctions in glia cells and neurons revealed by single nuclei RNA sequencing provides initial insights into the mechanism of hippocampal-accentuated brain atrophy and cognitive impairment. Thus, Rnaset2 -/- mice provide an important model, to develop therapies for inborn RNaseT2 deficiency, congenital viral brain infection and further type I interferonopathies.

overall_design: Single Cell Sequencing from hippocampus and putamen of RNaseT2 knockout mice and controls

first: Matthias

last: Kettwig

first: Katharina

last: Ternka

first: Kristin

last: Wendland

first: Dennis

last: Krüger

first: Silvia

last: Zampar

first: Charlotte

last: Schob

first: Anne

last: Winkler

first: Abhishek

last: Aich

first: Jonas

last: Franz

first: M

last: Sakib

first: Lalit

last: Kaurani

last: Epple

first: Hauke

last: Werner

first: Samy

last: Hakroush

first: Julia

last: Kitz

first: Marco

last: Prinz

first: Eva

last: Bartok

first: Gunther

last: Hartmann

first: Simone

last: Schröder

first: Peter

last: Rehling

last: Henneke

first: Susann

last: Boretius

first: A

last: Alia

first: Oliver

last: Wirths

first: Christine

last: Stadelmann

first: Stefan

last: Nessler

first: Jutta

last: Gärtner


title: A selective WDR5 degrader inhibits acute myeloid leukemia in patient-derived mouse models [ChIP-seq]

first: Gang Greg

last: Wang

overall_design: Examination of the genome-wide binding of H3K4me2 in MV4;11 and MIA PaCa-2 cells; a fraction of Drosophila chromatin was added to these human cells as spike-in controls for assessing relative levels of H3K4me2 across different samples after compound treatments.

first: Dongxu

last: Li

first: Greg


title: Signatures of GVHD and Relapse after Post-Transplant Cyclophosphamide Revealed by Immune Profiling and Machine Learning

status: Public on Sep 28 2021

city: Salt Lake City

first: Vedran

last: Radojcic

state: UT

address: 2000 Cir of Hope Dr

department: Huntsman Cancer Institute

institute: University of Utah


title: Specific and behaviorally consequential astrocyte G q GPCR signaling attenuation in vivo with iβARK

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: The Khakh laboratory used astrocyte selective AAVs expressing Rpl22-HA along with bARK for attenuating Gq pathway signaling in the dorsal striatum. In the control group, bARK(D110A), which is a mutated control of bARK was expressed instead of bARK. The mouse striatum expressing either bARK or bARK(D110A) was subjected to RNA-seq in order to compare striatal astrocyte transcriptomes with and without Gq-GPCR signaling attenuation.

overall_design: Whole striata were extracted from 4 adult (9 weeks old) C57BL/6J wild-type male mice with bARK or bARK(D110A) expression in astrocytes in vivo. After homogenization, RNA was purified from (i) cleared lysate as the input and control, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag.

first: Jun

last: Nagai

first: Arash

last: Bellafard

first: Qu

last: Zhe

first: Xinzhu

last: Yu

first: Blanca

last: Diaz-Castro

first: Giovanni

last: Coppola

first: Sarah

last: Schumacher-Bass

first: Peyman

last: Golshani

first: Viviana

last: Gradinaru

first: Baljit

last: Khakh


title: Signatures of GVHD and Relapse after Post-Transplant Cyclophosphamide Revealed by Immune Profiling and Machine Learning [17941R-18740R]

summary: Lymphocyte subsets (CD8, CD4 Tconv, NK cells) were sorted from patients' peripheral blood obtained on day 28 after haploidentical-donor allogeneic bone marrow transplantation followed by posttransplant cyclophosphamide (PTCy), tacrolimus, and MMF as GVHD prophylaxis (NCT00796562). Cohort of patients developed GVHD, or remained GVHD-free. Cohort of patients developed disease relapse, or remained relapse-free. RNA-sequencing was performed to analyze the transcriptional landscape of alloresponse in post-PTCy breakthrough GVHD and relapse.

overall_design: 11-14 unique patients were analyzed for each immune subset

first: Shannon

last: McCurdy

first: Hua-Ling

last: Tsai

first: Ante

last: Vulic

first: Elizabeth

last: Thompson

first: Sanja

last: Ivcevic

first: Christopher

last: Kanakry

first: Jonathan

last: Powell

first: Brian

last: Lohman

first: Djamilatou

last: Adom

first: Sophie

last: Paczesny

first: Kenneth

last: Cooke

first: Richard

last: Jones

first: Ravi

last: Vardahan

first: Heather

last: Symons

first: Leo

last: Luznik


title: TP53 loss initiates chromosomal instability in fallopian tube epithelial cells

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: High-grade serous ovarian cancer originates in the fallopian tube and is characterized by ubiquitous mutations in TP53. Here, we generated TP53 single-, TP53/BRCA1 and TP53/MYC double- and TP53/BRCA1/MYC triple-mutant subclones of the fallopian tube-derived cell line FNE1 using CRISPR/Cas9. These mutant subclones were subsequently subjected to RNA sequencing to determine the impact of these oncogenic mutations on signaling pathways.

overall_design: RNA sequencing of 27 fallopian tube-derived cell lines.

first: Daniel

last: Bronder

first: Anthony

last: Tighe

first: Darawalee

last: Wangsa

first: Dali

last: Zong

first: René

last: Wardenaar

first: Paul

last: Minshall

first: Daniela

last: Hirsch

first: Kerstin

last: Heselmeyer-Haddad

first: Louisa

last: Nelson

first: Diana

last: Spierings

first: Joanne

last: McGrail

first: Maggie

last: Cam

first: André

last: Nussenzweig

first: Floris

last: Foijer

last: Ried

first: Stephen

last: Taylor


title: CD137-CIS IO

city: Pamplona

first: Itziar

last: Otano

address: Avda Pio XII, 55

country: Spain

institute: CIMA-University of Navarra

summary:
CD137 cis-costimulation is superior to trans-costimulation at inducing transcriptomic differences in T-cell proliferation and DNA repair programs
We used microarrays to detail differentially expressed genes of cis- and trans CD137-costimulated CD8 T cells with respect to CD3-TCR stimulation

overall_design: Human CD8 T cells were purified from peripheral blood of 3 healthy donors. CD8 T cells were then activated with mAb coated microbeads for 32 hours.  mRNA was then extracted and mRNA expression profile was determine using Affymetrix human Clariom S assay

first: I

first: A

last: Azpilikueta

first: J

last: Glez-Vaz

first: P

last: Berraondo

last: Melero


title: Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation

city: Raleigh

first: Lisa

last: Van den Broeck

address: 112 Derieux Place

department: Plant and Microbial Biology

institute: North Carolina State University

summary: We performed a transcriptome analysis on the graft junction of tomato and pepper self grafts and heterografts.

sample_organism:
Capsicum annuum
Solanum lycopersicum

platform_organism:
Capsicum annuum
Solanum lycopersicum

overall_design: 50 Solanum lycopersicum (Var. M82) and 50 Capsicum anuum (var. Big Dipper) seedlings were wedge grafted. Graft junctions, consisting of 1 cm from the scion and 1 cm from the stock, were harvested at 1-day, 3-days, and 5-days post-grafting. Junctions were immediately flash frozen in liquid nitrogen, with 1 junction harvested per biological replicate and 4 biological replicates per time point. RNA was extracted using TRIzol reagent. The purified RNA was treated with DNAseI. RNA-seq libraries were constructed using 2.5 µg of total RNA per sample, isolated with the NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® using NEBNext® Multiplex Oligos for Illumina®. Six libraries were pooled per lane and run as a single-end sequencing run with 101 cycles on an Illumina HiSeq 2500 at the University of Delaware Sequencing and Genotyping Center.

first: Margaret

last: Frank

first: Ross

last: Sozzani

first: Ryan

last: Spurney

first: Hannah

last: Thomas


title: Interrogation of the microenvironmental landscape in spinal ependymomas reveals dual functions of tumor-associated macrophages

city: Beijing

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

institute: Institute of Biophysics

summary: Spinal ependymomas are the most common spinal cord tumors in adults, but their intratumoral cellular heterogeneity has been less studied, and how spinal microglia are involved in tumor progression is still unknown. Here, our single-cell RNA-sequencing analyses of three spinal ependymoma subtypes dissect the microenvironmental landscape of spinal ependymomas and reveal tumor-associated macrophage (TAM) subsets with distinct functional phenotypes. CCL2+ TAMs are related to the immune response and exhibit a high capacity for apoptosis, while CD44+ TAMs are associated with tumor angiogenesis. By combining these results with those of single-cell ATAC-sequencing data analysis, we reveal that TEAD1 and EGR3 play roles in regulating the functional diversity of TAMs. We further identify diverse characteristics of both malignant cells and TAMs that might underlie the different malignant degrees of each subtype. Finally, assessment of cell-cell interactions reveal that stromal cells act as extracellular factors that mediate TAM diversity. Overall, our results reveal dual functions of TAMs in tumor progression, providing valuable insights for TAM-targeting immunotherapy.

overall_design: single cell RNA-seq for ependymoma

first: Qianqian

last: Zhang

first: Sijin

last: Cheng

first: Xiaoqun

last: Wang

first: Qian

last: Wu


title: Alteration of genomic TERT-binding sites by BIBR1532  in primary neurons

city: Guangzhou

first: Chi Kwan

last: Tsang

address: Building #3, 613 Huangpu avenue west

department: Clinical Neuroscience Institute

institute: Jinan University

summary: The goal of this study is to understand how the specific TERT inhibitor BIBR1532 preconditioning regulates transcriptional reprogramming in mouse neuronal cells. We use CUT-Tag approach to comprehensively map the genomic binding sites of TERT in primary neurons and determine the alteration of is binding profile after BIBR1532 preconditioning. By obtaining over 10 million reads per sample, we generated genome-wide TERT chromatin-binding maps of mouse primary neurons. Under normal conditions, we show that more than 50% of the TERT binding sites were located at the promoter regions, many of them are previously unknown genomic loci. Intriguingly, BIBR1532 preconditioning significantly alters TERT-chromatin binding profile. Out of the total promoter binding sites by TERT, 30.4% (2,837 peaks) and 31.7% (2,954 peaks) are respectively upregulated and downregulated in TERT-binding after BIBR1532 preconditioning. Interestingly, we find that BIBR1532-preconditioned neurons show significant upregulation of promoter binding of TERT to the mitochondrial antioxidant genes. Together, these results identify the previously unknown TERT-binding sites in the mouse primary neurons and demonstrate that BIBR1532 preconditioning confers neuronal ischemic tolerance through TERT-mediated transcriptional reprogramming.

overall_design: Examination of TERT chrmatin binding sits  in mouse primary neuronal cells.

first: Chi

middle: K

first: Xuemin

last: Xie

first: Mingxi

last: Li

first: Mengyao

last: Zhou

first: Shing

last: Chow


title: Highly efficient SARS-CoV-2 infection of human cardiomyocytes: spike protein-mediated cell fusion and its inhibition

status: Public on Sep 27 2021

city: Rochester

first: Roberto

last: Cattaneo

state: MN

address: 222 3rd Ave SW

department: Molecular Medicine

institute: Mayo Clinic

summary: Severe cardiovascular complications can occur in coronavirus disease of 2019 (COVID-19) patients. Cardiac damage is attributed mostly to the aberrant host response to acute respiratory infection. However, direct infection of cardiac tissue by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also occurs. We examined here the cardiac tropism of SARS-CoV-2 in spontaneously beating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs).These cardiomyocytes express the angiotensin-converting enzyme 2 (ACE2) receptor but not the transmembrane protease serine 2 (TMPRSS2) that mediates spike protein cleavage in the lungs. Nevertheless, SARS-CoV-2 infection of hiPSC-CMs was prolific: viral transcripts accounted for about 88% of total mRNA. In the cytoplasm of infected hiPSC33 CMs, smooth walled exocytic vesicles contained numerous 65-90 nm particles with canonical ribonucleocapsid structures, and virus-like particles with knob-like spikes covered the cell surface. To better understand how SARS-CoV-2 spreads in hiPSC-CMs we engineered an expression vector coding for the spike protein with a monomeric emerald-green fluorescent protein fused to its cytoplasmic tail (S-mEm). Proteolytic processing of S-mEm and the parental spike were equivalent. Live cell imaging tracked spread of S-mEm cell-to-cell and documented formation of syncytia. A cell-permeable, peptide-based molecule that blocks the catalytic site of furin and furin-like proteases abolished cell fusion. A spike mutant with the single amino acid change R682S that disrupts the multibasic furin cleavage motif was fusion inactive. Thus, SARS42 CoV-2 replicates efficiently in hiPSC-CMs and furin and/or furin-like-protease activation of its spike protein is required for fusion-based cytopathology. This hiPSC-CM platform enables target-based drug discovery in cardiac COVID-19.

overall_design: The hiPSC CMs were infected with mock or SARS-CoV-2/UW001/Human/2020/Wisconsin (UW-001) at MOI of 0.01 for 48hrs. Cells were lysed in Trizol and were kept at -80 ºC. Total RNA of the lysate was extracted using Direct-zol RNA Miniprep kit (R2050). Library preparation and sequencing was performed at Mayo Clinic Genome Analysis Core (GAC).

first: Chanakha

last: Navaratnarajah

first: David

last: Pease

first: Peter

last: Halfmann

first: Biruhalem

last: Taye

first: Alison

last: Barkhymer

first: Kyle

last: Howell

first: Jon

middle: E

last: Charlesworth

first: Trace

middle: A

last: Christensen

first: Yoshihiro

last: Kawaoka

first: Jay

last: Schneider


title: Epigenetic bases of grafting-induced vigour in eggplant [RNA-Seq]

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

institute: University of Birmingham

summary: In horticulture, grafting is a popular technique used to combine positive features of two different plants, obtained by joining a scion (generally the part above the ground) onto a rootstock (constituted by the stem and roots). Despite its wide-use, the biological mechanisms driving rootstock-induced alterations of the scion phenotype are not fully understood. Given that epigenetics is an important component of distance signalling in plants, we investigated the genome wide changes in the DNA methylation induced in eggplants grafted onto two interspecific rootstocks commercially used to induce scion vigour, compared to self-grafted plants. We found that vigour was associated to a specific change in scion gene expression and a genome wide hypo-methylation in CHH context. Interestingly, this hypomethylation correlated with downregulation of younger and potentially more active LTR retrotransposons. Our data indicate that graft-induced epigenetics modifications are associated to both physiological and molecular phenotypes in plants, and suggest that rootstocks can induce vigour by reducing DNA methylation in the scion genome, similarly to what observed in some heterotic hybrids.

overall_design: Transcriptional profile of 2 wild type Solanum melongena plants, and two replicates of S. melongena scions grafted on S. melongena (self graft), Solanum torvum and Solanum lycopersicum (var. Emperador).


title: Signatures of GVHD and Relapse after Post-Transplant Cyclophosphamide Revealed by Immune Profiling and Machine Learning [15065R]

first: Vedran

last: Radojcic

summary: Lymphocyte subsets (CD8, CD4 Tconv, CD4 Treg) were sorted from patients' peripheral blood obtained on day 28 after matched-donor allogeneic bone marrow transplantation followed by posttransplant cyclophosphamide (PTCy) as a single agent GVHD prophylaxis (NCT00809276). Cohort of patients developed GVHD, or remained GVHD-free. RNA-sequencing was performed to analyze the transcriptional landscape of alloresponse in post-PTCy breakthrough GVHD.

overall_design: 5-7 samples per cohort (GVHD vs no GVHD) were analyzed for each immune subset

first: Shannon

last: McCurdy

first: Hua-Ling

last: Tsai

first: Ante

last: Vulic

first: Elizabeth

last: Thompson

first: Sanja

last: Ivcevic

first: Christopher

last: Kanakry

first: Jonathan

last: Powell

first: Brian

last: Lohman

first: Djamilatou

last: Adom

first: Sophie

last: Paczesny

first: Kenneth

last: Cooke

first: Richard

middle: J

last: Jones

first: Ravi

last: Vardahan

first: Heather

last: Symons

first: Leo

last: Luznik


title: Butyrate protects pancreatic beta cells from cytokine induced dysfunction

city: Copenhagen

first: Nils

last: Billestrup

address: Blegdamsvej

country: Denmark

institute: University of Copenhagen

summary: Beta cell dysfunction, caused by metabolic and inflammatory stress, contributes to the development of type 2 diabetes. Butyrate, produced by the gut microbiota, has shown beneficial effects on glucose metabolism and may directly affect beta cell function, but the mechanisms are poorly described. The aim of this study was to investigate the effect of butyrate on IL-1β-induced β cell dysfunction. We showed that long-term exposure of mouse islets to non-cytotoxic concentrations of IL-1β impaired insulin secretion and content and reduced proliferation. This dysfunction was prevented when the islets were exposed to butyrate and butyrate alone also boosted insulin secretion. In contrast, butyrate further downregulated the proliferation. To get a better indication of mechanisms of actions we investigated the global mRNA expression profiles using RNA sequencing. Our results indicated that the protective effects of butyrate are associated with upregulation of secretion/transport-related genes and downregulation of inflammatory genes induced by IL-1β. In addition, several cell cycle related genes were strongly inhibited by butyrate. In conclusion, butyrate plays an essential role in supporting beta cell function under inflammatory conditions, suggesting a potential for therapeutic use in treatment and prevention of T2D.

overall_design: RNA sequencing was performed on RNA extracted from mouse islets exposed to IL-1β (50 pg/ml), butyrate (0.2 mM), the combination or left unexposed for 10 days. The islets were isolated from 12-week-old C57BL/6JRj male mice (Janivier). In total, four independent experiments were performed.

first: Michala

last: Prause

first: Signe

middle: S

last: Pedersen


title: Effect of Cited2 knockout on gene expression in haematopoietic stem cells

city: London

first: Kamil

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

summary: The pleiotropic transcriptional regulator CITED2 is essential for lifelong maintenance of haematopoiesis.  To understand the molecular roles of CITED2 in normal haematopoiesis, we performed RNA-sequencing on CD48−CD150+ haematopoietic stem cells (HSCs) derived from young mice.

overall_design: One sample per mouse was taken from 5 WT vs 5 KO mice.

first: Louie

middle: N

last: van de Lagemaat

first: Amelie

middle: V

last: Guitart


title: Liver transcriptome regulated by CtBP2

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

institute: University of Tsukuba

summary: adenovirus mediated overexpression of wild-type CtBP2 and Rossmann fold mutant CtBP2 along with control GUS in dietary induced obese mice

overall_design: CtBP2 mutant overexpression


title: Transcriptome (RNA-seq) of Huh7 cells non-infected (NI) or infected (Inf.) with the pathogen Listeria monocytogenes (strain EGD-e)

status: Public on Sep 26 2021

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Comparisons of gene expression profiles of human hepatocytes (Huh7) infected or not by the bacterium Listeria monocytogenes (strain EGD-e) for 72 hours and analysed by RNA-seq

overall_design: We used  RNA-seq to identify the repertoire of genes differentially expressed after 3 days of infection of Huh7 cells with Listeria monocytogenes EGDe strain.

first: Natalie

last: DESCOEUDRES

first: Luc

last: JOUNEAU

first: Kevin

last: GORRICHON

first: Hélène

last: BIERNE


title: A subpopulation of deep cerebellar nuclei glutamatergic neurons contributes to cerebellar control of satiation

city: Singapore

first: Jessica

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

summary: We profiled micro-dissected deep cerebellar nuclei (DCN) from 2-3 month old mice for single-nucleus RNAseq to study the cellular populations present in the region and in particular, to define the molecular subtype identity of glutamatergic neurons. From our data, we isolated vGluT2-expressing transcriptomes and identified a graded and anti-correlated expression of two sets of genes associated with the first principal component (PC1) in our dataset, defining separate cell populations. Multiplexed in situ hybridization analysis confirmed the nonoverlapping expression patterns and revealed their topography within the DCN. We then probed the function of these neurons in further experiments and found that one of the two populations was associated with food intake. Our broader study defines a conserved satiation centre and neural mechanism that may represent a novel therapeutic target for the management of excessive eating.

overall_design: Single-nuclei RNA sequencing of mouse deep cerebellar nuclei

first: Aloysius

last: Low

first: Alaric

last: Yip

first: Albert

middle: I

last: Chen

first: Norliyana

last: Zainolabidin

first: Toh

middle: H

last: Ch'ng

first: J.

last: Betley

first: October

middle: M

last: Sessions


title: FlowCT for the analysis of large immunophenotypic datasets and biomarker discovery in cancer immunology

city: New York

first: Juan-Jose

last: Garces

state: New York

address: 321 E 61st St

institute: Memorial Sloan Kettering Cancer Center

summary: Large-scale immune monitoring is becoming routinely used in clinical trials to identify determinants of treatment responsiveness, particularly to immunotherapies. Flow cytometry remains one of the most versatile and high throughput approaches for single-cell analysis; however, manual interpretation of multidimensional data poses a challenge to capture full cellular diversity and provide reproducible results. We present FlowCT, a semi-automated workspace empowered to analyze large datasets that includes pre-processing, normalization, multiple dimensionality reduction techniques, automated clustering and predictive modeling tools. As a proof of concept, we used FlowCT to compare the T cell compartment in bone marrow (BM) vs peripheral blood (PB) of patients with smoldering multiple myeloma (MM); identify minimally-invasive immune biomarkers of progression from smoldering to active MM; define prognostic T cell subsets in the BM of patients with active MM after treatment intensification; and assess the longitudinal effect of maintenance therapy in BM T cells. A total of 354 samples were analyzed and immune signatures predictive of malignant transformation in 150 smoldering MM patients (hazard ratio [HR]: 1.7; P <.001), and of progression-free (HR: 4.09; P <.0001) and overall survival (HR: 3.12; P =.047) in 100 active MM patients, were identified. New data also emerged about stem cell memory T cells, the concordance between immune profiles in BM vs PB and the immunomodulatory effect of maintenance therapy. FlowCT is a new open-source computational approach that can be readily implemented by research laboratories to perform quality-control, analyze high-dimensional data, unveil cellular diversity and objectively identify biomarkers in large immune monitoring studies.

overall_design: Ten T cell populations FACS sorted from 3 healthy donors

first: Cirino

last: Botta

first: Catarina

last: Maia

first: Juan-José

last: Garcés

first: Rosalinda

last: Termini

first: Cristina

last: Pérez

first: Irene

last: Manrique

first: Leire

last: Burgos

first: Aintzane

last: Zabaleta

first: Diego

last: Alignani

first: Sarai

last: Sarvide

first: Juana

last: Merino

first: Noemi

last: Puig

first: Maria-Teresa

last: Cedena

first: Marco

last: Rossi

first: Pierfrancesco

last: Tassone

first: Massimo

last: Gentile

first: Pierpaolo

last: Correale

first: Ivan

last: Borrello

first: Evangelos

last: Terpos

first: Tomas

last: Jelinek

first: Artur

last: Paiva

first: Aldo

last: Roccaro

first: Hartmut

last: Goldschmidt

first: Hervé

last: Avet-Loiseau

first: Laura

last: Rosiñol

first: Maria-Victoria

last: Mateos

first: Joaquin

last: Martinez-Lopez

last: Lahuerta

first: Joan

last: Bladé

first: Jesus

last: San-Miguel

first: Bruno


title: CtBP2 ChIP-seq normal mouse liver

first: Motohiro

last: Sekiya

summary: CtBP2 recruitment on genome in normal mouse liver

overall_design: genomic distribution of CtBP2 in normal mouse liver using pooled livers from 4 mice


title: Human hepatocellular carcinoma RNAseq data

status: Public on Sep 25 2021

city: Shinjuku-ku

first: Yutaka

last: Kurebayashi

state: Tokyo

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: This is a series of RNAseq data obtained from the predominant region of 29 treatment-naïve, surgically-resected human HCCs.

overall_design: mRNA was purified from fresh frozen human hepatocellular carcinoma tissue and RNAseq was performed.

first: Kosuke

last: Matsuda

first: Akihisa

last: Ueno

first: Hanako

last: Tsujikawa

first: Ken

last: Yamazaki

first: Yohei

last: Masugi

first: Kathryn

last: Effendi

first: Hidenori

last: Ojima

first: Michiie

last: Sakamoto


title: Signatures of GVHD and Relapse after Post-Transplant Cyclophosphamide Revealed by Immune Profiling and Machine Learning [17618R]

first: Vedran

last: Radojcic

summary: Lymphocyte subsets (CD8, CD4 Tconv, CD4 Treg) were sorted from patients' peripheral blood obtained 180 days after matched-donor allogeneic bone marrow transplantation followed by posttransplant cyclophosphamide (PTCy) as a single agent GVHD prophylaxis (NCT00809276). Cohort of patients developed GVHD, or remained GVHD-free. RNA-sequencing was performed to analyze the transcriptional landscape of alloresponse in post-PTCy breakthrough GVHD.

overall_design: 8-10 samples per cohort (GVHD vs no GVHD) were analyzed for each immune subset

first: Shannon

middle: R

last: McCurdy

first: Hua-Ling

last: Tsai

first: Ante

last: Vulic

first: Elizabeth

last: Thompson

first: Sanja

last: Ivcevic

first: Christopher

middle: G

last: Kanakry

first: Jonathan

middle: D

last: Powell

first: Brian

last: Lohman

first: Djamilatou

last: Adom

first: Sophie

last: Paczesny

first: Kenneth

last: Cooke

first: Richard

last: Jones

first: Ravi

last: Vardahan

first: Heather

last: Symons

first: Leo

last: Luznik


title: Spatial gene expression maps of the intestinal lymphoid follicle and associated epithelium identify zonated expression programs

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

institute: Weizmann Institute

summary: We combined RNA sequencing of laser capture microdissected-tissues with single molecule transcript imaging to obtain a spatial gene expression map of the ILF and its associated FAE in the mouse small intestine.

overall_design: LCM samples extracted from mouse jejunum were sequenced in an Illumina NextSeq.

first: Noam

last: Cohen

first: Hassan

last: Massalha

first: Shani

last: Ben-Moshe

first: Adi

last: Egozi

first: Milena

last: Rozenberg

last: Bahar Halpern

first: Shalev

last: Itzkovitz


title: BET Inhibition Enhances TNF Mediated Anti-Tumor Immunity

status: Public on Sep 24 2021

city: South San Francisco

first: Simon

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

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

overall_design: Refer to individual Series


title: Targeting EYA2 tyrosine phosphatase activity in glioblastoma stem cells induces mitotic catastrophe

city: San Diego

first: Jeremy

last: Rich

address: 9500 Gilman Drive #0695

institute: University of California, San Diego

summary: Glioblastoma ranks among the most lethal of primary brain malignancies, with glioblastoma stem cells (GSCs) at the apex of tumor cellular hierarchies. Here, to discover novel therapeutic GSC targets, we interrogated gene expression profiles from GSCs, differentiated glioblastoma cells (DGCs), and neural stem cells (NSCs), revealing EYA2 as preferentially expressed by GSCs. Targeting EYA2 impaired GSC maintenance and induced cell cycle arrest, apoptosis, and loss of self-renewal. EYA2 displayed novel localization to centrosomes in GSCs, and EYA2 tyrosine (Tyr) phosphatase activity was essential for proper mitotic spindle assembly and survival of GSCs. Inhibition of the EYA2 Tyr phosphatase activity, via genetic or pharmacological means, mimicked EYA2 loss in GSCs in vitro and extended the survival of tumor-bearing mice. Supporting the clinical relevance of these findings, EYA2 portends poor patient prognosis in glioblastoma. Collectively, our data indicate that EYA2 phosphatase function plays selective critical roles in the growth and survival of GSCs, potentially offering a high therapeutic index for EYA2 inhibitors.

overall_design: Two glioma stem cell models were treated with a non-targeting shRNA or one of two shRNAs targeting EYA2 and profiled by RNA-sequencing. One replicate was used for analysis

first: Guoxin

last: Zhang


title: Total RNA sequencing data for transcriptome analysis of testicular aging in mice

city: Gwangju

first: Gwidong

last: Han

address: GIST

country: South Korea

institute: Gwangju Institute of Science and Technology

summary: Expression profiles were analyzed of mouse testis in four age groups (3, 6, 12, 18 postnatal month) by total RNA sequencing.

overall_design: Expression profiles were analyzed of mouse testis in four age groups by total RNA sequencing. Each of groups have 3 biological replicates.

first: Chunghee

last: Cho


title: Whole genome DNA methylation analysis with reduced representation bisulfite sequencing (RRBS) to identify Myod1 promoter methylation in brown adipose tissues of D1KO and their respective wild type control mice

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

country: USA

institute: Georgia State University

summary: Our RRBS profiling indicated that the methylation rate at the proximate promoter and 5’-region of Myod1 gene was significantly decreased in brown adipose tissues of D1KO mice compared to their respective wild type control mice

overall_design: RRBS profiling of DNA methylation level at the proximate promoter and 5’-region of Myod1 gene in brown adipose tissues of D1KO and their respective wild type control mice

first: Hang

last: Shi


title: Human resident memory T cells exit the skin and mediate systemic Th2-driven inflammation.

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

country: Austria

institute: Medical University of Vienna

summary: To investigate the transcriptional profile of human circulating T cells with skin tissue-resident memory phenotype (cTRM) in GVHD we performed bulk RNA sequencing from SMART-seq2 of sorted human cTRM (CD3+ CD4+ CLA+ CD103+) and conventional T cells (CD3+ CD4+ CD103-), and single cell RNA sequencing from 10X Genomics of sorted human CD45+, both from isolated blood PBMCs of patients with active acute GVHD.

overall_design:
Frozen PBMC isolated of whole blood from patients with active acute GVHD were thawed, stained for FACS-sorting and sorted for live CD45+ cells, which were submitted for 10X Genomics single-cell RNA sequencing (n=2, two replicates for donor 2), or sorted for live cTRM (live CD45+ CD3+ CD4+ CLA+ CD103) and Tconv (live CD45+ CD3+ CD4+ CD103-), wich were submitted for SMART-seq2 bulk RNA sequencing (n=3).

*** Submitter Comment: Due to security issue we are not submitting the raw data ***

first: J

last: Strobl

first: L

last: Gail

first: R

last: Dingelmaier-Hovorka

first: T

last: Krausgruber

last: Pandey

first: G


title: ATAC-seq analysis of chromatin accessibility across the entire genome in brown adipose tissues from UTXKO and their respective control mice fed high fat diet

summary: We performed ATAC-seq assay on nuclei isolated from control and UTXKO mouse brown fat to delineate the role of UTX in setting chromatin accessibility. We analyzed the effects of UTX deficiency on a set of brown fat specific genes and observed reduced accessibility at ATAC-seq peaks and mRNA expression for many of these genes, including PRDM16 and PGC1a.

overall_design: ATAC-seq profiles of the accessible chromatin region in brown adipose tissues of WT and UTXKO mice fed high fat diet


title: RNA-seq Facilitates Quantitative Analysis of brown adipose tissues (iBATs) from UTXKO and their respective WT control mice fed high fat diet (HFD) for 12 wks, D1KO and their respective WT control mice fed chow diet (CD) as well as WT mice fed CD and HFD.

summary: Our RNA-seq analysis revealed a dramatic up-regulation of myogenic markers in the iBATs of UTXKO mice, D1KO mice and high fat diet-fed mice, suggesting a myocyte-like remodeling in brown fat.

overall_design:
Brown adipose tissue mRNA profiles of WT and UTXKO mice fed high fat diet, WT and D1KO mice fed chow diet as well as WT fed chow or high fat diet

***Please note that the raw data files for GSM5342433-GSM5342436 are either lost or corrupted, and thus are not provided***