title: N-Glycome regulation limits the transdifferentiation of endothelial cells into hematopoietic stem cells

city: New Haven

first: Stefania

last: Nicoli

state: CT

address: 300 George street

department: Internal Medicine

institute: Yale University

summary: Hematopoietic stem and progenitor cells (HSPCs) are required to establish and maintain the adult blood system in vertebrates. During development, HPSCs are generated from hemogenic endothelial cells that undergo an endothelial-to-hematopoietic transition (EHT). Growth factors and epigenetic changes can promote EHT, but these mechanisms do not explain its tight spatiotemporal regulation during development. Here, we show that microRNA (miR) miR-223-mediated regulation of N-glycan biosynthesis intrinsically restrains EHT, representing a new pathway that prevents excessive HSPC production. We find that miR-223 is uniquely expressed in hemogenic endothelial cells undergoing EHT and in nascent HSPCs. Loss of miR-223 promotes the expansion of these cells in the zebrafish and mouse aorta-gonad-mesonephros (AGM), where EHT occurs. miR-223 targets alg2 (alpha 1,3/ 1,6 mannosyltransferase) in the AGM endothelium to restrict hemogenic and HSPC specification. This enzyme is involved in the attachment of the N-glycans,  a common co-translational modification9-12 that influences several pathophysiological processes, but has not yet been implicated in EHT. Using an N-glycosensor, we demonstrate that abundant protein N-glycan attachment occurs in vascular cells during EHT, and this process is required for HSPC production. High-throughput glycome analysis upon loss of miR-223 revealed that terminal alpha 1,3/6 mannose modifications are increased at the expense of alpha 2,3/6 sialic acid sugars. Importantly, pharmacological manipulation targeting these N-glycan types in wild-type embryos phenocopies the loss of miR-223 and enhances EHT as well as HSPC production. Thus, the N-glycome plays a previously unappreciated role as an intrinsic regulator of EHT, with specific mannose and sialic acid modifications serving as key endothelial determinants to restrict the hematopoietic fate.

overall_design: Single cell RNA sequencing for zebrafish Tg(kdrl:hras-mCherry)s896 endothelial cells at 27 hpf for wildtype and miR-223(ya303) backgrounds

first: Dionna

last: Kasper

first: Yinyu

last: Wu

first: Hanna

middle: K

last: Mandl

first: Kevin

last: Salinas

first: Joey

last: Ghersi

first: Jared

last: Hintzen

first: William

last: Armero

first: Zhiheng

last: He

first: Daniel

last: Heindel

first: Eon

last: Park

middle: C

last: Sessa

first: Lara

last: Mahal

first: Karen

last: Hirschi


title: Hepatocyte-specific YAP is crucial for CAR-driven hepatocyte proliferation, but not for induction of drug metabolism genes in mice

status: Public on Sep 09 2021

city: Pittsburgh

first: George

middle: K.

last: Michalopoulos

state: Pennsylvania

address: 200 Lothrop Street

country: USA

institute: University of Pittsburgh

summary:
Constitutive androstane receptor (CAR) agonists, such as TCPOBOP, are known to cause robust hepatocyte proliferation and hepatomegaly in mice along with induction of drug metabolism genes, without any associated liver injury. Yes-associated protein (YAP) is a key transcription regulator that tightly controls organ size including that of liver. Ours and other previous studies suggested increased nuclear localization and activation of YAP after TCPOBOP treatment in mice and potential role of YAP in CAR-driven proliferative response. Here, we investigated a direct role of YAP in CAR-driven hepatomegaly and hepatocyte proliferation using hepatocyte-specific YAP-KO mice. AAV8-TBG-CRE vector was injected to YAP-floxed mice for achieving hepatocyte-specific YAP deletion followed by TCPOBOP treatment. YAP deletion did not alter protein expression of CAR or CAR-driven induction of drug metabolism genes (including Cyp2b10, Cyp2c55 and UGT1a1). However, YAP deletion substantially reduced TCPOBOP-induced hepatocyte proliferation. TCPOBOP-driven cell cycle activation was disrupted in YAP-KO mice due to delayed (and decreased) induction of cyclin D1 and higher expression of p21, resulting in decreased phosphorylation of retinoblastoma (Rb) protein. Further, induction of other cyclins, which are sequentially involved in progression through cell cycle (including cyclin E1, A2 and B1) and important mitotic regulators (such as aurora B kinase and polo-like kinase 1) was remarkably reduced in YAP-KO mice. Microarray analysis revealed that 26% of TCPOBOP‐responsive genes mainly related to proliferation, but not to drug metabolism, were altered by YAP deletion. YAP regulated these proliferation genes via alerting expression of cMyc and FOXM1, two critical transcriptional regulators of CAR-mediated hepatocyte proliferation. Conclusion: Our study revealed an important role of YAP signaling in CAR-driven hepatocyte proliferation; however, CAR-driven induction of drug metabolism genes was independent of YAP.
We used microarrays to detail the global programme of gene expression in livers of hepatocyte-specific YAP KO mice following TCPOBOP treatment

overall_design: Hepatocyte-specific deletion of YAP  was carried out by administering AAV8.TBG.PI.Cre.rBG to YAP-floxed mice. AAV8.TBG.PI.eGFP.WPRE.bGH8 administered to YAP-floxed mice served as wild-type (WT) control. TCPOBOP was administered by oral gavage 10 days after AAV8 injection. Liver tissue were harvested from WT and YAP KO mice at Day 0, 1 and 2 after TCPOBOP administration for gene arrays.

first: Bharat

last: Bhushan


title: Repression of bZIP11 expression in Seedlings

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

country: Sweden

institute: Umeå Plant Science Centre

type: Expression profiling by high throughput sequencing

summary: Inducible amiRNA expression in seedlings leads to repression of amiRNA target bZIP11 and thereby changed of bZIP11 target gene expression.

overall_design: Transgenic and wt plant were treated with inducer (estradiol) or mock treatment. Total RNA was harvested from treated seedlings and used for library construction.

first: Matthew

middle: J

last: Prior

first: Jebasingh

last: Selvanayagam

first: Jung-Gun

last: Kim

first: Monika

last: Tomar

first: Martin

last: Jonikas

first: Mary

middle: B

last: Mudgett

first: Sjef

last: Smeekens

first: Wolf

last: Frommer


title: Effects of reduced expression of Arabidopsis bZIP11 during starvation

summary: Artificial bZIP11 miRNAS harboring plants and wt grown with and without sucrose in medium

overall_design: 10 day old seedling growth phenotypes were monitored on half strength MS medium with 50 μM estradiol ± 30 mM sucrose (16-h light, 120 µE m-2 s-1).

first: Jeba

last: Singh


title: Inactivation of RNase P in Escherichia coli significantly changes post-transcriptional RNA metabolism

city: Athens

first: Bijoy

last: Mohanty

state: GA

address: 120 E. Green Street

department: Genetics

institute: University of georgia

summary:
Ribonuclease P (RNase P) is the only ribonuclease responsible for 5'-end maturation of tRNAs in all kingdoms of life.  In Escherichia coli, it is also essential for separation of pre-tRNAs from multiple polycistronic transcripts.  Using RNA sequencing (RNA-seq), we show here that RNase P affects the abundance
of ~44% of the expressed mRNAs demonstrating a much more widespread role in mRNA decay than previously thought.  Furthermore, our data also demonstrate for the first time that the polyadenylation of transcripts by PAP I modulates RNase P-mediated mRNA decay as well as tRNA processing.

overall_design:
RNA-seq experiments were conducted on RNAs isolated from wild type, DpcnB, rnpA49 and DpcnB rnpA49 strains of E. coli.  For each library (12 libraries comprising three biological replicates for each strain), ~42 million cDNAs were sequenced out of which the number of reads that mapped uniquely to MG1655 genome was between 76-86%.
Furthermore, ERCC (External RNA Control Consortium) RNAs were spiked into the RNA-seq libraries in known amounts and then aligned to ERCC references.  These alignments were then used to calculate a Pearson correlation coefficient for each sample.
The ERCC control correlation coefficients were 0.98, 0.95 and 0.95 for three replicates of the wild type strain; 0.97, 0.95, 0.94 for three replicates of the DpcnB mutant; 0.98, 0.98, 0.98 for the three replicates of the rnpA49 mutant and 0.98, 0.97, 0,97 for the three replicates of the rnpA49 DpcnB double mutant (data not shown).
Based on the nearly identical correlation coefficients of the three replicates for each strain, the RNA-seq reads from the three replicates of each strain were merged.

first: Sidney

middle: R

last: Kushner


title: SPOP mutation reshapes chromatin landscape and transcriptional response to androgens.

city: New York

first: Ivana

last: Grbesa

address: 413 E 69th St

department: Urology

institute: Weill Cornell Medicine

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Transcriptional effect of RZ-2994 vs. DMSO on T-cell acute lymphoblastic leukemia cell line

city: Cambridge

first: Gabriela

last: Alexe

state: MA

address: 415 Main St.

department: Computational Biology and Bioinformatics

institute: Broad Institute

summary:
Purpose: Identify new therapeutic pathways for T-cell acute lymphoblastic leukemia (T-ALL) therapy.
Methods: KOPTK1 cells were grown in the presence of 2µM RZ-2994 vs DMSO, and cells collected at 24 and 72 hours of treatment. Three samples were collected per treatment condition per time point.  RNA was extracted from cells with an RNeasy Kit (Qiagen).
Results: RZ-2994 treatment of T-ALL cell lines resulted in changes pathways affecting cell cycle control, amino acid metabolism and gene sets associated with  MYC changes.
Conclusions: Our study supports the therapeutic targeting of SHMT1 and SHMT2 in T-ALL.

overall_design: KOPTK1 Tcell ALL cell lines treated with RZ-2994 and DMSO, in triplicate, for one day and for three days

first: Kimberly

last: Stegmaier

first: Yana

last: Pikman


title: An MRG-mediated chromatin switch operates at the SOC1 gene to modulate abiotic stress responses during the onset of flowering

city: Pozuelo de Alarcón

first: Manuel

last: Pineiro

state: Madrid

address: Autopista M-40, Km 38

country: Spain

institute: Centro de Biotecnologia y Genomica de Plantas (CBGP)

summary: The mechanisms underlying the precise integration of environmental and developmental signals necessary for plant adaptation to suboptimal environments remain obscure. Here we show that a chromatin switch, mediated by MRG proteins, acts on the floral activator SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) to coordinate flowering initiation with plant responsiveness to adverse conditions. SOC1 constitutes a central hub in a mechanism that tunes down stress responses likely to optimize plant reproductive success and fitness

overall_design: Transcriptomic profiling through RNAseq of Arabidopsis plants grown on soil under long day photoperiod (16h light / 8h dark). Plants were grown at 22°C for 12 days on soil, taking samples at Zeitgeber time (ZT) ZT8. Three libraries were generated using RNA from three independent experiments.

first: Javier

last: Barrero-Gil

first: Alfonso

last: Mouriz

first: Raquel

last: Piqueras

first: Julio

last: Salinas

first: José

middle: A

last: Jarillo

last: Piñeiro


title: RNA-sequencing in two MYCN amplified/high-risk and one non-MYCN amplified/low-risk neuroblastoma cell lines

city: Parkville

first: Jack

middle: Aatto Laasonen

last: Cooper

state: Victoria

address: 49 College Crescent

country: Australia

institute: University of Melbourne

summary: RNA-sequencing has been used to obtain and observe transcriptome-wide differences that occur in two parasspeckle-deficient, MYCN-amplified/model high-risk and one paraspeckle-abundant, non-MYCN-amplified/low-risk cell lines, to decipher the role of paraspeckles in this cancer type.

overall_design: Methods: Cell lines were grown without any treatment for 48 hours, after which cells were lysed. RNA-seq was conducted to show transcriptome wide differences occurring between low and high risk neuroblastoma cell lines. Our study has shown differential NEAT1_1 and NEAT1_2 expression levels in low versus high risk neuroblastoma cell lines.

first: Alina

last: Naveed

first: Ruohan

last: Li

first: Alysia

last: Hubbard

first: Tao

last: Liu

first: Steve

last: Wilton

first: Sue

last: Fletcher

first: Archa

last: Fox


title: Genome-wide transcriptomic and translatomic profiling in halofuginone and vehicle treated mouse fibroblasts

city: Rochester

first: Peng

last: Yao

state: NY

address: 601 Elmwood Avenue

department: Medicine

institute: Aab Cardiovascular Research Institute

summary:
Purpose: In mammals, glutamyl-prolyl-tRNA synthetase (EPRS) catalyzes the attachment of two amino acids, glutamic acid (E) and proline (P), to their cognate tRNAs for protein synthesis. We aim to study the mechanism of EPRS in translational regulation of cardiac fibrosis and establish EPRS or its downstream target genes as potential anti-fibrosis therapeutic targets. The goals of this study are to use next generation sequencing (NGS)-derived fibroblast transcriptome profiling (RNA-seq) and translatome profiling (polysome-seq) followed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods to identify the downstream effector genes that are preferentially regulated by EPRS at the transcriptional and translational levels.
Results: Using a well established data analysis workflow from the Genomic Research Center from University of Rochester Medical Center,  we analyzed RNA-seq and polysome-seq data. We have identified novel Pro-rich (PRR) gene pathways that are preferentially regulated by EPRS via enhanced translation elongation at Pro-rich codons and antagonized by Halofuginone. Considering the translation active state in both light and heavy polysome fractions, we redefined the 4 groups by overlapping genes from heavy and light polysome associated transcripts compared to their total RNA expression change (p value <0.05 for differential expressed genes). 1371 genes were downregulated at translation (indicated by polysome-seq) and steady-state mRNA (indicated by RNA-seq) levels, and 775 genes were upregulated at both levels. There are a small number of genes whose gene regulation was changed in the opposite direction at the mRNA and translation levels. These observations indicate a coordinated regulatory effect between steady-state mRNA level and translation efficiency under the EPRS inhibitory condition. KEGG analysis of the genes that are reduced at RNA and translation levels revealed multiple pro-fibrotic pathways, including ECM-receptor interaction and proteoglycans. In contrast, the genes that are induced at RNA and translation levels are enriched in general translation factors, including ribosome and aminoacyl-tRNA biosynthesis, which suggests a compensatory amino acid starvation response upon EPRS inhibition. Altered expression of typical Pro-rich collagen and other genes was confirmed with qRT-PCR.
Conclusions: Our study represents the first detailed analysis of fibroblast translatome in comparison with transcriptome under EPRS inhibitory condition (halofuginone treatment), with biological triplicates, generated by RNA-seq and polysome-seq technology. Our results show that the next generation sequencing offers a comprehensive qualitative and quantitative evaluation of mRNA content and its translation state within cells treated with translation inhibitory drug halofuginone (EPRS inhibitor). Based on our results, we conclude that Pro-rich motif bearing genes are preferential targets of EPRS, and mild inhibition of EPRS leads to inefficient translation of these PRR genes.

overall_design: We treated NIH/3T3 mouse fibroblasts with halofuginone (EPRS-specific inhibitor; 100 nM) or vehicle (PBS) in biological triplicates. For polysome-Seq, all the fractions were pooled into 3 samples, polysome free (free mRNP, 40S, 60S subunit), light polysomes (monosome, disome, trisome, etc.), and heavy polysomes (>5 ribosomes). Total RNA was extracted from the same volume of 3 samples and subjected to next generation RNA deep sequencing for translatome profiling as polysome-seq. For transcriptome profiling, total RNA extracted from the same treated cells was subjected to RNA-Seq. All the extracted RNA samples were treated with DNase I to remove potential genomic DNA followed by purification using phenol:chloroform:isoamyl alcohol for RNA-Seq. Raw reads were generated from the Illumina HiSeq2500 sequencer in the Genomic Research Center from University of Rochester Medical Center.

first: Jiangbin

last: Wu

first: Kadiam

last: Venkata Subbaiah

first: Li

middle: H

last: Xie

first: Feng

last: Jiang

first: Deanne

last: Mickelsen

first: Jason

last: Myers

first: Wai

last: Wilson Tang


title: Paraspeckles induced by NEAT1 isoform-switching antisense oligonucleotides: application in high-risk neuroblastoma


title: SPOP mutation reshapes chromatin landscape and transcriptional response to androgens [ChIP-seq]

first: Ivana

last: Grbesa

summary: To define the epigenomic response to AR activation, we employed the 3D organoid model of murine prostate tissue. Control and SPOP-mutant prostate organoids were stimulated with 10 nM dihydrotestosterone (DHT) or vehicle. Next, we performed the transcriptomic analysis (mRNA-seq) together with profiling of the accessibility landscape (ATAC-seq), transcription factor (AR, and FOXA1) binding and H3K4me2 modified nucleosomes.

overall_design: Examination of H3K4me2 histone modifications, and AR and FOXA1 binding in Control (normal) and SPOP-mutant mouse prostate organoids. In case of H3K4me2  and FOXA1 ChIP-seq cells we performed ChIP-seq on  DHT and EtOH treated cells . In case of AR ChIP-eq, only on DHT-treated cells.

first: Christopher

last: Barbieri


title: Hairless regulates heterochromatin maintenance and muscle stem cell function as a histone demethylase antagonist

city: Palo Alto

first: Ling

address: 300 Pasteur Drive

institute: Stanford University


title: Influenza A virus-infection differentially affects conventional and regulatory T cell repertoire

city: Hannover

first: Christoph

last: Binz

state: Niedersachsen

address: Carl-Neuberg-Straße 1

department: Institut für Immunologie

country: Germany

institute: Medizinische Hochschule Hannover

summary: To investigate the impact of Influenza A virus (IAV)  infection on thymic development of mouse regulatory T cells (Tregs) and conventional T cells (Tconv), the TCR repertoire of thymic Tregs and Tconv of IAV-infected and control mice was analyzed.

overall_design: Foxp3hCD2RAGGFP double reporter mice were infected with 666 ffu IAV PR8. A control group of mice received PBS. Thymi were collected at 10 days post infection (dpi). CD4+RAGGFP+CD25+Foxp3hCD2+, CD4+RAGGFP+CD25-Foxp3hCD2-, CD4+RAGGFP-CD25+Foxp3hCD2+, or CD4+RAGGFP-CD25-Foxp3hCD2- cells were sorted from CD8-depleted thymocytes. RNA was isolated from these cells and was analyzed by 5´RACE and PCR amplification followed by illumina-sequencing of Tcrb transcripts. A total of 8 mice received IAV while  5 mice were treated with PBS.

first: Yassin

last: Elfaki


title: RNA-sequencing in KELLY cells with oligonucleotide:leash lipoplexes

first: Jack

last: Cooper

summary: RNA-sequencing has been used to obtain transcriptome-wide differences that occur in paraspeckle-deficient, MYCN-amplified/model high-risk neuroblastoma cell lines with an increase in the long non-coding paraspeckle-associated NEAT1_2 RNA, to decipher the role of paraspeckles in this cancer type.

overall_design: Methods: KELLY cell lines were treated with custom-designed morpholino oligonucleotide:DNA leash lipoplexes, and cells were lysed. RNA-seq was conducted to show transcriptome wide changes occurring due to increased NEAT1_2 levels and subsequent paraspeckle formation. Our study has shown upregulation of differentiation pathways is associated with increased NEAT1_2 RNA and paraspeckle levels.

first: Alina

last: Naveed

first: Ruohan

last: Li

first: Alysia

last: Hubbard

first: Tao


title: Inducible overexpression of zebrafish microRNA-722 suppresses chemotaxis of human neutrophil like cells

city: West Lafayette

first: Qing

last: Deng

state: Indiana

address: 915 W. State Street

department: Department of Biological Sciences

institute: Purdue University

summary: To assess the effect of miR-722 in mature neutrophil like cells driven by and inducible promoter to avoid affecting neutrophil diffrentiation

overall_design: comparing genes that are down regulated during miR-722 overexpression

first: Alan

middle: Y

last: Hsu


title: The role of DELLA protein in tomato plant response to water-deficit stress

city: Rehovot

first: David

last: Weiss

address: Hertzel st.

country: Israel

institute: The Hebrew University of Jerusalem

summary: We previously showed that increased levels of the tomato DELLA protein PROCERA (PRO) promoted ABA responses in guard cells, including ABA-induced stomatal closure and gene expression. Thus we aimed to identifiy DELLA-regulated genes in guard cells in order to study the molecular mechanism by which DELLA promotes stomatal closure.

overall_design: Transcriptome analysis of guard cells isolated from plants expressing DELLA gain-of-function (pro∆17) or from DELLA loss-of-function mutant (pro)

first: Hagai

last: Shohat


title: Single cell sequencing identifies novel sub-populations of breast cancer cells selected under hypoxia

city: Oxford

first: Adam

last: Cribbs

address: Windmill Road

department: NDORMS

country: United Kingdom

institute: University of Oxford

summary: During tumour growth cancer cells are subject to and selected by microenvironmental stress. The selection of such cells allows for continued growth and survival, during hypoxia, acidosis, nutritional deprivation, drug treatment and radiation. However, there is great microenvironmental heterogeneity in every tumour. Must studies of gene regulation in vitro investigate whole cell populations, often by western blotting or mRNA expression. Thus, the individual variability of gene induction that could lead to selection, and basal cell molecular variability on which the selection operates, basic Darwinian principles, are not defined. We previously showed that two distinct populations can often be induced in epithelial tumour cell lines under hypoxia, identified by induction of Carbonic Anhydrase 9 [CA9].Here, we investigated the heterogeneity of breast cancer cells, and the relationship to the CA9 positive population in hypoxia, by using single cell sequencing analysis.

overall_design: Examination of the MCF7 breast cancer cell line using single cell transcriptomics (smartseq2)

middle: P

first: Adrian

last: Harris


title: Nuclear IQGAP1 promotes gastric cancer cell growth by altering the splicing of a cell-cycle regulon in co-operation with hnRNPM

city: Vari

first: Panagiota

last: Kafasla

address: 34 Fleming Str

department: IFBR

country: Greece

institute: B.S.R.C. "Al. Fleming"

summary: Heterogeneous nuclear ribonucleoproteins (hnRNPs) play a decisive role in alternative splicing, regulating the cell proteome and contributing to human diseases. hnRNPs are nuclear proteins but it is still an open question where they localize in the nucleus and what determines their tethering to nuclear assemblies in response to signals. Here we report that IQGAP1, a cytosolic scaffold protein, localizes in the nucleus of gastric cancer cells acting as a tethering module for hnRNPM as well as other spliceosome components. The IQGAP1-hnRNPM interaction alters, among others, the alternative splicing of ANAPC10 and is required for the response of hnRNPM to heat-induced stress signals. Together, IQGAP1 and hnRNPM promote gastric cancer cell growth while their depletion leads to cell cycle arrest and halts tumour progression. We propose that IQGAP1 localizes in the nucleus and coordinates gastric tumour growth by recruiting, in response to stress-signals, spliceosome components that drive cell cycle progression.

overall_design: 3 biological replicates for the parental cells (MKN45) and 2 biological replicates for the IQGAP1-KO cells

first: Malgorzata

last: Rogalska


title: Effect of loss-of-function of ZFP-1, DOT-1.1 and MML-1 on gene expression in C. elegans

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

institute: King’s College London

summary:
Transcriptional control is mediated by interactions of transcription factors with their cognate DNA elements, as well as by epigenetic modifications to chromatin catalyzed by a variety of enzymes. Thus, understanding the crosstalk between transcription factors and epigenetic modifiers is of prime importance. The Dot1-like protein (DOT1L) is an evolutionary conserved methyltransferase with catalytic specificity towards histone 3 lysine 79 (H3K79). DOT1L is essential for mammalian development and has been studied mostly in the context of aggressive leukemias. Recent observations suggest that the role of DOT1L in malignant transformation can be generalized to contexts beyond leukemia. For instance, DOT1L has been implicated in breast cancer progression, and this has been attributed to its cooperation with c-Myc. However, the mechanistic details underlying this association are unknown. Previous work in our lab has shown that DOT-1.1, the C. elegans DOT1L homologue, is recruited to chromatin by ZFP-1 (similarly to DOT1L recruitment by AF10 in mammals), and this complex negatively modulates transcription. Interestingly, promoters of ZFP-1/DOT-1.1 target genes are enriched in E-boxes, the consensus binding motif for c-Myc. Prompted by the exciting hypothesis that DOT-1.1 and MML-1, the C. elegans c-Myc homologue, cooperate genome-wide, we profiled gene expression in wild-type worms and dot-1.1(gk105059), zfp-1(ok554), and mml-1(gk402844) loss-of-function mutants by microarray. We found significant overlaps between genes upregulated in the three mutants, and the same was observed for downregulated genes. A significant global increase of non-coding transcripts was observed in either mutant compared with wild-type. Therefore, ZFP-1/DOT-1.1 and MML-1 co-regulate both coding and non-coding genes and globally inhibit non-coding transcription. Further investigation is underway to uncover the mechanism of cooperation of ZFP-1/DOT-1.1 and MML-1.

Profiling of gene expression in wild-type third larval stage (L3) larvae and zfp-1(ok554), dot-1.1(gk105059) and mml-1(gk402844) mutant worms.

overall_design: A total of 12 total RNA samples were analyzed, 3 for each strain. Pairwise comparisons were performed on each mutant versus wild-type.

first: Rube

first: Alla

last: Grishok


title: Differential requirement for B-cell Receptor signaling during adhesion of different Mantle Cell Lymphoma cell lines to stromal cells

city: Uppsala

first: Gustav

last: Arvidsson

state: Uppsala

address: Husargatan 3

department: Department of Medical Sciences

institute: Uppsala Universitet

summary: Lymphoma cells interact with specific microenvironment cell subsets, such as stromal cells, from which they receive survival and proliferation stimuli. These interactions negatively influence therapeutic response and increase the risk for drug resistance and relapse. It is still not clear why clinically similar tumors in different patients respond differently to established treatment regimens. Objective: The main aim of this study was to identify and compare key signaling pathways related to stromal cell adhesion in different mantle cell lymphoma (MCL) cell lines.Methods: Human MCL cells (JeKo1 and REC1) were cultured alone or in co-culture with mouse MS-5 stromal cells. Differentially expressed genes in adherent cells were identified by RNA sequencing and species-specific read sorting. The cell surface levels of proteins encoded by selected differentially expressed genes were quantified using flow cytometry in adherent and suspension cells. Selective inhibitors or siRNA were used to assess their significance for adherence to stromal cells. Results: Jeko1 and REC1 cells exhibited different time-dependent patterns of adhesion to stromal cells. 590 genes that were differently regulated upon adhesion in each cell line individually, showed significant differences in the extent or direction of regulation between the two cell lines. From this set, there was a significant increase in transcript levels for B-cell Receptor (BCR) pathway signature genes in adherent JeKo1 cell but not in adherent REC1 cells. Inhibition of BCR signaling using siRNA or the clinically approved inhibitor, Ibrutinib, decreased the number of adherent JeKo1 cells but had no such effect on REC1 cells. The cell surface levels of CXCR4 were higher in JeKo1 cells compared to REC1 cells and CXCR4 inhibition disrupted the adhesion of JeKo1 but not REC1 cells to the stromal cells. ICAM1 cell surface levels were induced in JeKo1 cells upon adhesion while REC1 showed a high level of ICAM1 in non-adherent cells. Depletion of ICAM1 levels by siRNA reduced the stromal cell adhesion of both JeKo1 and REC1 cells. Conclusions: The results suggest that different MCL cell lines exhibit different signaling profiles and pathway dependencies during microenvironment interaction. In this study BCR signaling pathways were shown to be important for stromal cell adhesion of JeKo1 cells but not REC1 cells. This provides a possible mechanism to account for the differential responsiveness of MCL patients to treatment with the Bruton’s Tyrosine Kinase inhibitor, Ibrutinib, an inhibitor of BCR signaling that is clinically approved for MCL.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: RNA-seq; four conditions with four replicates per condition, 16 samples in total.

first: Anthony

last: Wright

first: Laia

last: Sadeghi


title: LATS1 is a Central Signal Transmitter for Achieving Full Type-I Interferon Activity

status: Public on Sep 08 2021

city: Suzhou

first: Yibo

last: Zuo

address: Renai road 199

country: China

institute: Soochow university

summary: Interferons (IFNs) possess broad-spectrum antiviral activity to resist virus epidemic. However, IFNs antiviral efficacy needs to be greatly improved. Here, we reveal that LATS1 is a vital signal transmitter governing full type-I-interferon (IFN-I) signaling activity. Importantly, LATS1 deficiency restricts IFN-I signaling and attenuates host antiviral immune response.

overall_design: HEK293T cells were transfected with either control shRNAs (shCON) or shRNAs against LATS1 (shLATS1) and then treated with IFNα (1,000 IU/ml) for 4 hrs. Total RNAs were isolated from HEK293T cells using TRIzol reagent (Invitrogen). The RNA samples were sent to Wuhan BGI for further sequencing and analysis.


title: Gene expression in human keratinocytes cultivated with serum-free medium and serum containing medium

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

summary:
The objective of this study was thus to develop ab initio that chemically defined serum-free medium. We used a statistical design of experiment (DOE) approach to screen a large number of candidate factors, for both their potential individual and synergetic effects, as to identify a formulation which was then tested extensively.
In this study, we present the properties of keratinocyte cultivated with serum-Free medium (Surge SFM) and complemented DME-Ham medium (with serum).

overall_design: Four human keratinocyte populations at passage 2 cultivated with with serum-free medium or serum containing medium until cells attained 80-95% confluence.

first: Sergio

last: Cortez Ghio

first: Martin

last: Barbier

first: Emilie

last: Doucet

first: Imad

last: Debbah

first: Andréanne

last: Cartier

last: Jolibois

first: Amélie

last: Morissette

first: Danielle

last: Larouche

first: Julie

last: Fradette

first: Sylvain

last: Guérin

first: Alain

last: Garnier

first: Lucie

last: Germain


title: Neuronal accumulation of peroxidated lipids promotes demyelination and neurodegeneration though the activation of the microglial NLRP3 inflammasome

city: Bethesda

first: Guohao

last: Wang

state: MD

address: 35 3c1004 Convent Dr.

department: NINDS

institute: NIH

summary: Peroxidated lipids accumulate in the presence of reactive oxygen species and are linked to neurodegenerative diseases. Here we found that neuronal ablation of Arf1, a small GTPase important for lipid homeostasis, promoted the accumulation of peroxidated lipids, lipid droplets and ATP in the mouse brain and led to neuroinflammation, demyelination, and neurodegeneration, mainly in the spinal cord and hindbrain. Ablation of Arf1 in cultured primary neurons led to an increase in peroxidated lipids in co-cultured microglia, the activation of the microglial NLRP3 inflammasome, and the release of inflammatory cytokines in an APOE-dependent manner. Deleting the Nlrp3 gene rescued the neurodegenerative phenotypes in the neuronal Arf1-ablated mice. We also observed a reduction in Arf1 in human brain tissue from amyotrophic lateral sclerosis and multiple sclerosis patients. Together, our results uncover a previously unrecognized role of peroxidated lipids released from damaged neurons in the activation of a neurotoxic microglial NLRP3 pathway that may play a role in human neurodegeneration.

overall_design: Study of Arf1 function in the neurons

first: Weiqin

last: Yin

first: Wei

last: Lu

first: Steven

middle: X

last: Hou


title: Expression data from microdissection isolated epthelium and stroma of the same pateint with benign prostatic hyperplasia

city: Beijing

first: Wujiang

last: Liu

address: 8 Xishiku Xicheng

institute: Peking University

summary:
Although there are great differences between hyperplastic epithelium and stroma, so far, no data show differences in gene expression between epithelium and stroma, which may have a potential great impact on the discovery of drug targets
We performed the microdissection and microarray to uncover the differences in gene expression between epithelium and stroma of the same patient with BPH

overall_design: The same amount of epithelial tissue and stromal tissue were collected, RNA was extracted, post transcriptional markers were used, and the expression differences between the two parts were compared

first: Liu

last: Wujiang

first: Jin

last: Jie

first: Zhou

last: Liqun

first: Guo

last: Yinglu


city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

summary: We report that HNF1B primarily bind promoter regions across the whole genome.

overall_design: ChIP-seq of HNF1B  in prostate cancer cell line DU145 overexpressing HA tagged HNF1B by HA antibody.

first: Jianqing

first: Fei

last: Lan


title: Single-cell transcriptome and cell-specific network analysis reveal the reparative effect of NT-4 supplementation in preantral follicles grown in vitro [gc_RNA-seq]

city: Guangzhou

first: Ying-chun

last: Guo

address: NO.17, Shougouling Rd.

institute: Sixth Affiliated Hospital of Sun Yat-sen University

summary: In-vitro-grow (IVG) of preantral follicles is essential for female fertility preservation, while effective approach to improve it is far from being explored. Here, we report the dynamic location of TRKB in human and mouse ovaries, and a positive relation between human oocyte maturation and NT-4 level in follicular fluid. For the first time, we observe the improving effect of NT-4 on mice preantral follicle IVG, including follicle diameter, hormone production and oocyte maturation. Single-cell transcriptome analysis shows that the reparative effect of NT-4 on oocyte maturation in IVG may be mediated by regulation of PI3K-Akt signaling pathway and subsequent organization of F-actin. Suppression of advanced stimulated complement system in granulosa cells may also contribute to the improvement. Cell-specific network analysis reveals that NT-4 may recover the inflammation damage induced by abnormal lipid metabolism in IVG environment. Collectively, our data suggest that NT-4 is involved in the ovarian physiology and may serve to improve the efficiency of preantral follicle IVG for fertility preservation.

overall_design: Granulosa cell mRNA profiles of 12 to 14-day old Kunming mice; Granulosa cells were derived from preantral follicle grown in vitro ( with or without NT-4 ) for 6 days.

first: Pei-gen

last: Chen

first: Chuan-chuan

last: Zhou

first: Cong

last: Fang


title: Single cell functional genomics reveals plasticity of subcutaneous white adipose tissue (WAT) during early postnatal development

city: Detroit

first: James

middle: G.

last: Granneman

state: mi

address: 6135 Woodward

department: CMMG

institute: Wayne State University

summary: We performed a large-scale single cell transcriptomic (scRNA-seq) and epigenomic (snATAC-seq) characterization of cellular subtypes (adipose stromal cells (ASC) and adipocyte nuclei) during inguinal WAT (subcutaneous; iWAT) development in mice, capturing the early postnatal period (postnatal days (PND) 06 and 18) through adulthood (PND56).

overall_design: Bulk mRNA, scRNA-seq, snATAC-seq of inguinal white adipose tissue stromal cells and adipocytes during development

middle: G

first: Elizabeth

last: Rondini


title: Gene expression of clinical breast cancer cells cultured by sphere and adherent culture methods

city: Tokyo

first: Takahiko

last: Murayama

address: 4-6-1 Shirokanedai Minato-ku

country: Japan

institute: University of Tokyo

summary: Cancer stem-like cells (CSCs) are thought to be responsible for recurrence of tumors and poor prognosis because of their higher tumor initiating ability and drug resistance, though the mechanisms remain still unclear. Here, we show a critical role of mini-chromosome maintenance protein (MCM) 10, a component of DNA replication machinery, in enabling CSCs to deal with DNA replicative stress. Our transcriptomic analysis of patient-derived cultured breast cancer cells revealed that MCM10 is strongly upregulated in CSC-enriched spheroid cells, compared to cancer cells cultured in a regular condition. Elevated MCM10 expression was correlated with worse prognosis of patients with breast cancer. Depletion of MCM10 resulted in not only reduced cell proliferation and tumorigenesis, but also reduced tumor sphere forming efficiency, expression levels of stemness markers, and the tumor initiating ability. These results indicate that MCM10 is essential for maintenance of CSCs as well as for tumor cell proliferation. DNA fiber assay revealed that CSCs have a comparatively high level of DNA replicative stress. Overexpression of MCM10 helped cells to proliferate in a medium containing hydroxyurea (HU), a replicative stress-inducing chemotherapeutic agent. Conversely, MCM10 depletion made cells more fragile to replicative stress induced by HU or mitomycin C (MMC), another replicative stress inducer. Therefore, MCM10 plays critical roles for dealing with the enhanced replicative stress generated in CSCs for their survival, leading to maintenance of tumor initiating ability and drug resistance. We provide a preclinical rationale to target MCM10, the critical mediator for DNA replicative stress, for breast cancer that includes CSCs.

overall_design: Conparison of expression between sphere and adherent cells derived from three breast tumors

first: Kaoru

last: Yamawaki

first: Toyoaki

last: Natsume

first: Tatsunori

last: Nishimura

first: Yuta

last: Kogure

first: Kana

last: Tominaga

first: Asuka

last: Nakata

first: Asako

last: Sasahara

first: Masao

last: Yano

first: Satoko

last: Ishikawa

first: Masashi

last: Inokuchi

first: Tetsuo

last: Ota

first: Kazuhiro

last: Ikeda

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue

first: Masahide

last: Seki

first: Yutaka

last: Suzuki

first: Sumio

last: Sugano

first: Masahiko

last: Tanabe

first: Kei-ichiro

last: Tada

first: Masato

middle: T

last: Kanemaki

first: Koji

last: Okamoto

first: Arinobu

last: Tojo

first: Noriko

last: Gotoh


title: MBD2 and H3K4Me3 CUT&RUN-sequencing in C2C12 cells undergoing myogenic differentiation

city: La Jolla

first: Ukrae

last: Cho

state: CA

address: 10010 N Torrey Pines Rd

department: Molecular and Cell Biology

institute: Salk Institute for Biological Studies

summary: MBD2 genome-binding landscape was assessed by CUT&RUN-sequencing in differentiating C2C12 cells. H3K4Me3 CUT&RUN-sequencing was performed as a positive control. Negative control experiment was also performed using a rabbit isotype control monoclonal IgG.

overall_design: C2C12 cells that have undergone myogenic differentiation were harvested at 0, 1, and 5 days for CUT&RUN-sequencing. C2C12 myotubes and reserve cells were separated by mild trypsinization. CUT&RUN-sequencing library was prepared using a Cell Signaling Technology CUT&RUN assay kit. Sequencing libraries were prepared using NEBNext Ultra II DNA library prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7645 and E7600). Libraries were quantified and analyzed using Qubit dsDNA HS assay kit (Thermo Fisher Scientific) and a TapeStation 2200 with high-sensitivity DNA kit (Agilent). Libraries were sequenced in paired-end 150 base pair mode on the Illumina NovaSeq 6000 platform.  Paired-end fragments were trimmed, mapped to the mm10 genome, and filtered using Trim Galore, Bowtie2 , and SAMtools , respectively. Peaks were identified using MACS2 and further filtered and analyzed with in-house Python scripts that leveraged pyBigWig and pyBedTools packages. GO term analyses (biological processes) were performed on http://metascape.org. Genomic annotation of the peaks was conducted using ChIPseeker. CUT&RUN-sequencing data were plotted using karyoploteR.

first: Cho

last: Ukrae

first: Hetzer

last: Martin


title: Effects of antipsychotics risperidone and olanzapine on the striatum, liver, pancreas and adipose tissue

city: Barcelona

first: Natalia

last: Rodriguez

state: Barcelona

address: Casanova 143

department: Basic Clinical Practice

institute: University of Barcelona

summary:
Analysis of gene expression in the striatum, the liver, the pancreas, and the visceral adipose tissue of mice treated for 28 days with a daily dose of an atypical antipsychotic: risperidone (1 mg/kg) or olanzapine (3.5 mg/kg). Results provide new insights into the molecular mechanisms underlying antipschotic effects, particularly in tissues relevant for antipsychotic-induced metabolic dysregulation.
Antipsychotics are associated with weight gain and other metabolic abnormalities such as hyperglycemia, dyslipidemia and metabolic syndrome. We used microarrays to uncover the underlying molecular mechanisms and identify the key genes involved in AP-induced metabolic effects.

overall_design: Gene expression was assessed by microarray (Affymetrix mouse Clariom S Arrays) in four mice tissues: the striatum, the liver, the pancreas and the adipose tissue. Mice were treated for 28 days with a daily dose of vehicle, risperidone (1 mg/kg) or olanzapine (3.5 mg/kg). Each group included 8 C57BL/6JOlaHsd mice (4 males and 4 females).

first: Albert

last: Martínez-Pinteño

first: Patricia

last: Gassó

first: Llucia

last: Prohens

first: Àlex

last: Segura

first: Mara

last: Parellada

first: Jerónimo

last: Saiz-Ruiz

first: Manuel

last: Cuesta

first: Miguel

last: Bernardo

first: Amalia

last: Lafuente

first: Sergi

last: Mas


title: Next Generation Sequencing Facilitates Quantitative Analysis of IBP Transcriptomes

city: Dalian

first: Shuo

last: Wu

address: Linggong Road No.2

institute: Dalian university of technology

summary: Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived strain GCY transcriptome profiling (RNA-seq) and to evaluate protocols for optimal high-throughput data analysis

overall_design: mRNA profiles of  strain GCY were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Zelong

last: Li


title: Impact of heterozygous SRI mutation (R2483H) of Setd2 (Setd2SRI/wt)

city: Houston

first: Cheryl

middle: L

last: Walker

state: TX

address: 1 Baylor Plaza

department: Center for Precision Environmental Health

institute: Baylor College of Medicine

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

overall_design: Refer to individual Series


title: Single-cell RNA-seq of T cells in B-ALL patients reveals an exhausted subset with remarkably heterogeneity

first: Zongcheng

address: No. 8 East Street, Fengtai District

institute: Fifth Medical Center of Chinese PLA General Hospital

summary: Characterization of functional T cell clusters is key to developing strategies for immunotherapy and predicting clinical responses in leukemia. Here, we performed single-cell RNA sequencing (scRNA-seq) with T cells sorted from the peripheral blood of healthy individuals and patients with B cell-acute lymphoblastic leukemia (B-ALL). Unbiased bioinformatics analysis enabled us to identify 13 T cell clusters in the patients based on their molecular properties. All 11 major T cells subsets in healthy individuals were found in the patients with B-ALL, with the counterparts in the patients universally showing more activated characteristics. Two exhausted T cell populations, characterized by up-regulation of TIGIT, PDCD1, HLADRA, LAG3, and CTLA4 were specifically discovered in B-ALL patients. Of note, these exhausted T cells possessed remarkable heterogeneity, and ten sub-clusters were further identified, which were characterized by different cell cycle phase, naïve states, and GNLY (coding granulysin) expression. Coupled with single-cell T cell receptor repertoire profiling, we suggested diverse originations of the exhausted T cells in B-ALL, and clonally expanded exhausted T cells were likely to originate from CD8+ effector memory/terminal effector cells. Together, these data provide for the first-time valuable insights for understanding exhausted T cell populations in leukemia.

overall_design: Single cell RNA-seq with 28,812 T cells sorted from the peripheral blood of healthy individuals and patients with B cell-acute lymphoblastic leukemia, as well as T-cell receptor repertoire sequencing from one of the healthy individuals and the same patients.

first: Xiaofang

last: Wang

first: Yanjuan

last: Chen

first: Bingyan

last: Huang

first: Ling

last: Xu

first: Jing

last: Lai

first: Yuhong

last: Lu

first: Xianfeng

last: Zha

first: Bing

last: Liu

first: Yu

last: Lan

first: Yangqiu


title: Impact of heterozygous SRI mutation (R2483H) of Setd2 (Setd2SRI/wt) on H3K36me3 patterns in the brains of mouse neonates

summary: We report that only a limited genes have differential H3K36me3 marks in the brains of heterozygous Setd2SRI/wt mice compared to those of wild type mice at P0.

overall_design: Examination of H3K36me3 histone modification in the brains of newborn wild type and heterozygous Setd2SRI/wt mouse littermates

first: In

last: Park

first: Rahul

last: Jangid

first: Matt

last: Konning


title: Transcriptomic response of Xanthomonas campestris pv. campestris after exposure to allyl-isothiocyanate and indol-3 carbinol

city: Pontevedra

first: Pilar

last: Soengas

state: Pontevedra

address: Palacio de Salcedo

department: Brassica Genetic and Biochemistry

institute: CSIC

summary: We performed a transcriptomic analysis of the necrotrophic bacteria Xanthomonas campestris pv. campestris exposed to two different isothiocyanates (allyl-isothiocyanate and indol-3-carbinol), searching for mechanisms of adaptation and detoxification of these chemicals.

overall_design: Three comparisons were performed: allyl-isothiocyanate vs control, indol-3-carbinol vs control and allyl-isothiocyanate vs indol-3-carbinol. Two repetitions of each treatment were performed.

first: Pari

last: Madloo

first: Margarita

last: Lema


title: Transcriptome analysis of primary microglia defecting ASD-related genes.

first: Shogo

last: Tanabe

address: 4-1-1 Ogawahigashicho

institute: National Center of Neurology and Psychiatry

summary: We report the transcriptome analysis by RNAseq for primary microglia defecting ASD-related genes by siRNA treatment.

overall_design: mRNA profiles of microglia after control, Chd8, and Tsc2 siRNA treatment.

first: Rieko

last: Muramatsu


title: Cerium oxide nanoparticle administration to skeletal muscle cells under different gravity and radiation conditions

city: Pontedera (PI)

first: Gianni

last: Ciofani

address: Viale Rinaldo Piaggio 34

country: Italy

institute: Istituto Italiano di Tecnologia

type: Non-coding RNA profiling by high throughput sequencing

summary: For their remarkable biomimetic properties implying strong modulation of the intracellular and extracellular redox state, cerium oxide nanoparticles (also termed “nanoceria”) were hypothesized to exert a protective role against oxidative stress associated to the harsh environmental conditions of spaceflight, characterized by microgravity and highly energetic radiations. Nanoparticles were supplied to proliferating C2C12 mouse skeletal muscle cells under different gravity and radiation levels (microgravity+cosmic radiations or Earth gravity+cosmic radiations on board the International Space Station; Earth gravity on ground). Biological responses were thus investigated at a transcriptional level by RNA next-generation sequencing. Lists of differentially expressed genes (DEGs) were generated and intersected by taking into consideration relevant comparisons, which led to the observation of prevailing effects of the space environment over those induced by nanoceria, possibly due to its administration during spaceflight. In space, up-regulation of transcription was slightly preponderant over down-regulation, and it implied involvement of intracellular compartments, with the majority of DEGs being consistently over- or under-expressed whenever present. Cosmic radiations regulated a higher number of DEGs than microgravity and seemed to promote increased cellular catabolism. By taking into consideration space physical stressors alone, microgravity and cosmic radiations appeared to have opposite effects at transcriptional level despite partial sharing of molecular pathways. Interestingly, gene ontology denoted some enrichment in terms related to vision, when only effects of radiation were assessed. The regulation of mitochondrial uncoupling protein 2 in space-relevant samples suggests perturbation of the intracellular redox homeostasis, and leaves open opportunities to antioxidant treatment for oxidative stress reduction in harsh environments.

overall_design: RNA-seq/miRNA-seq of C2C12 proliferating mouse myoblasts, cultured in the following conditions (n=3): A (without nanoceria, in space without gravity), B (with nanoceria, in space without gravity), C (without nanoceria, in space with gravity), D (with nanoceria, in space with gravity), E (without nanoceria, on land), and F (with nanoceria, on land).

first: Giada

last: Genchi

first: Andrea

last: Degl'Innocenti

first: Chiara

last: Martinelli

first: Matteo

last: Battaglini

first: Daniele

last: De Pasquale

first: Alessandro

last: Mariani

first: Michele

last: Balsamo

first: Valfredo

last: Zolesi


title: Impact of heterozygous SRI mutation (R2483H) of Setd2 (Setd2SRI/wt) on gene expression in the brains of mouse neonates

first: Cheryl

last: Walker

summary: We report that only a limited number of genes are differentially expressed in the brains of heterozygous Setd2SRI/wt mice compared to those of wild type mice at P0.

overall_design: mRNA profiles in the brains of newborn wild type and heterozygous Setd2SRI/wt mouse littermates

first: In

last: Park

first: Matthias


title: Antagonism of mitophagy by Zika virus reveals Ajuba as a regulator of PINK1-Parkin signaling and PKR-dependent inflammation

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

summary: Dysregulated inflammation is a key driver of disease following infection with the globally important human pathogens, Zika virus (ZIKV) and dengue virus. However, specific mechanisms of inflammation are not well defined. Here, we demonstrate that ZIKV antagonizes mitophagy, or the process of selective degradation of damaged mitochondria. The mechanism of antagonism was through interactions between NS5 and the host protein Ajuba to prevent Ajuba translocation to depolarized mitochondria. We further identify a role of Ajuba in mitophagy through augmenting PINK1 kinase activity. Mitophagy suppression in infected Ajuba-/- cells amplified the cellular integrated stress response (ISR) to promote ZIKV replication, and increased pro-inflammatory cytokine expression dependent on the ISR kinase, PKR. Thus, ZIKV suppresses mitophagy to favor replication and this failure of mitochondrial quality control is translated to inflammation by PKR, suggesting new therapeutic targets to treat flavivirus disease.

first: Sanket

middle: S

last: Ponia

first: Shelly

last: Robertson

first: Kristin

last: McNally

first: Gail

last: Sturdevant

first: Matthew

last: Lewis

first: Forrest

last: Jessop

first: Catherine

middle: M

last: Bosio

last: Kendall

first: Dylan

last: Gallegos

first: Arielle

last: Hay

first: Cindi

last: Schwartz

first: Rebecca

last: Rosenke

first: Greg

last: Saturday

first: Sonja

last: Best


title: Loss of Foxc1 and Foxc2 function in chondroprogenitor cells disrupts endochondral ossification.

city: Edmonton

first: Fred

last: Berry

state: AB

address: 3002D Li Ka Shing Centre, University Of Alberta, University Of Alberta

institute: University of Alberta

summary: Endochondral ossification forms and grows the majority of the mammalian skeleton and is tightly controlled through gene regulatory networks. The forkhead box transcription factors Foxc1 and Foxc2 have been demonstrated to regulate aspects of osteoblast function in the formation of the skeleton but their roles in chondrocytes to control endochondral ossification are less clear. We demonstrate that Foxc1 expression is directly regulated by SOX9 activity, one of the earliest transcription factors to specify the chondrocyte lineages. Moreover we demonstrate that elevelated expression of Foxc1 promotes chondrocyte differentiation in mouse embryonic stem cells and loss of Foxc1 function inhibits chondrogenesis in vitro. Using chondrocyte-targeted deletion of Foxc1 and Foxc2 in mice, we reveal a role for these factors in chondrocyte differentiation in vivo.  Loss of both Foxc1 and Foxc2 caused a general skeletal dysplasia predominantly affecting the vertebral column. The long bones of the limb were smaller and mineralization was reduced and organization of the growth plate was disrupted.  In particular, the stacked columnar organization of the proliferative chondrocyte layer was reduced in size and cell proliferation in growth plate chondrocytes was reduced. Differential gene expression analysis indicated disrupted expression patterns in chondrogenesis and ossification genes throughout the entire process of endochondral ossification in Col2-cre;Foxc1Δ/Δ;Foxc2Δ/Δ  embryos.  Our results suggest that  Foxc1 and Foxc2 are required for correct chondrocyte differentiation and function. Loss of both genes results in disorganization of the growth plate, reduced chondrocyte proliferation and delays in chondrocyte hypertrophy that prevents correct ossification of the endochondral skeleton.

overall_design: Total RNA was isolated from the ribs of control (wild type) or Col2-cre;Foxc1-/-;Foxc2-/- mice at 16.5 dpc.  RNA was isolated form three embryos of each genetype for sequencing.

first: Priyanka

last: Maripuri


title: Single-cell transcriptome and cell-specific network analysis reveal the reparative effect of NT-4 supplementation in preantral follicles grown in vitro [oocyte_RNA-seq]

first: Ying-chun

last: Guo

overall_design: oocyte mRNA profiles of 12 to 14-day old Kunming mice; oocytes were derived from preantral follicle IVG ( with or without NT-4, day 6 or day 10) versus in vivo

first: Pei-gen

last: Chen

first: Chuan-chuan

last: Zhou

first: Cong

last: Fang


title: NAT10-mediated β-hydroxybutyrylation  Rewires Genomic 3D Conformation and Replication Timing [Replication-seq]

first: wenhui

last: Zhao

address: 5 Yiheyuan Road, Haidian District

summary: Spatiotemporal regulation of chromatin replication (replication timing, RT) in eukaryotes is critical to maintain the genomic integrity. Here we focused on epigenetic mechanisms in rewiring genomic 3D conformation and replication timing. The results show that the novel lysine β-hydroxybutyrylation (Kbhb) modifications accelerates chromatin replication without inducing replication defects. This effect was mediated by the NAT10, a novel b-hydroxybutyryl-transferase, through regulating the association of NAT10 and CTCF with chromatin. Depletion of NAT10 and NAT10-mediated Kbhb dramatically reduce chromatin-bound NAT10 and CTCF, resulting in reorganization of genomic 3D conformation with enhanced trans- and cis-interaction in Hi-C matrix, with elevated proportion of A compartments, and with reorganized TADs boundaries. Moreover, reorganization of genomic 3D conformation contributes to rewire replication timing. These results support models in which NAT10-mediated β-hydroxybutyrylation coordinates genomic 3D conformation reorganization with replication timing alteration, and emphatically address the concept that epigenetic mechanisms reconcile genomic 3D conformation with replication timing.

overall_design: E/L repli-seq were performed on β-hydroxybutyrate (BHB) treated control (siCtrl) or NAT10 knock-down (siNAT10) U2OS cells.

first: Wenhui

first: Kun

last: Liu


title: A Patient specific iPSC-based model of Hydatidiform mole reveals abnormal BMP4 signaling caused by NLRP7 deficiency

city: Cold Spring Harbor

first: Aybuke

last: Alici

address: 1 Bungtown Rd.

institute: Cold Spring Harbor Laboratory

summary: Complete Hydatidiform Mole (HM) is a gestational trophoblastic disease resulting in hyper proliferation of trophoblast cells and absence of embryo development. Mutations in NLRP7 gene is a  major cause of familial recurrent complete HM, where no embryonic tissue is present during the pregnancy. NLRP7 is a novel protein and its function is poorly understood. Lack of NLRP7 in the mouse genome and challenges in studying  human embryogenesis as well as human trophoblast differentiation has prevented elucidation of the pathophysiology of this disease and the function of NLRP7 in HM. Here, we established an in vitro model of HM using NLRP7 deficient patient-derived human induced pluripotent stem cells (iPSCs). Whole transcriptome profiling during trophoblast differentiation revealed that NLRP7 deficiency results in precocious downregulation of pluripotency factors, activation of trophoblast genes and promotes maturation of differentiated extraembryonic cell types such as syncytiotrophoblasts. We further showed that these phenotypes are dependent on BMP4 signaling and BMP pathway inhibition prevented excessive trophoblast differentiation of HM-iPSCs. Taken together, this novel human iPSC model of a genetic placental disease recapitulates aspect of trophoblast biology and sheds light on early human embryogenesis by identifying NLRP7 as an important regulator of this process.

overall_design: mRNA profiles were obtained from trophoblast-like cells derived from patient specific iPSCs and unrelated healty control iPSCs upon treatment via FGF and ACTIVIN/NODAL inhibitors together with either BMP4 or BMP inhibitor.

last: Alici-Garipcan

first: Burcu

last: Özçimen

first: Tamer

last: Önder

first: Nesrin

last: Özören


title: The Hippo pathway regulates density-dependent proliferation of iPSC-derived cardiac myocytes

city: Nashville

first: Dylan

last: Burnette

state: TN

address: 465 21st Avenue S.

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

summary: Inducing cardiac myocytes to proliferate is considered a potential therapy to target heart disease, however, modulating cardiac myocyte proliferation has proven to be a technical challenge. The Hippo pathway is a kinase signaling cascade that regulates cell proliferation during the growth of the heart. Inhibition of the Hippo pathway increases the activation of the transcription factors YAP/TAZ, which translocate to the nucleus and upregulate transcription of pro-proliferative genes. The Hippo pathway regulates the proliferation of cancer cells, pluripotent stem cells, and epithelial cells through a cell-cell contact-dependent manner, however, it is unclear if cell density-dependent cell proliferation is a consistent feature in cardiac myocytes. Here, we used cultured human iPSC-derived cardiac myocytes (hiCMs) as a model system to investigate this concept. hiCMs have a comparable transcriptome to the immature cardiac myocytes that proliferate during heart development in vivo. Our data indicate that a dense syncytium of hiCMs can regain cell cycle activity and YAP expression and activity when plated sparsely or when density is reduced through wounding. We found that combining two small molecules, XMU-MP-1 and S1P, increased YAP activity and further enhanced proliferation of low-density hiCMs. Importantly, these compounds had no effect on hiCMs within a dense syncytium. These data add to a growing body of literature that link Hippo pathway regulation with cardiac myocyte proliferation and demonstrate that regulation is restricted to cells with reduced contact inhibition.

overall_design: Three independent replicates, five samples each. Dense control and sparse control are control cells plated at different densities (Sparse is 8X fewer cells than dense). Drug-treated samples (XMU, S1P, and XS) were sparsely-plated cells.

first: Abigail

middle: C

last: Neininger

first: Xiaozhuan

last: Dai

first: Qi


title: TNF blockade uncouples toxicity and anti-tumor efficacy induced with an agonist CD40 antibody

city: Philadelphia

first: Jesse

last: Lee

state: PA

address: South Pavilion, Room 8-326

institute: University of Pennsylvania

summary: TNF mechanistically links cytokine release and hepatotoxicity triggered by an agonist CD40 antibody, and toxicity can be suppressed by blockade of TNF without affecting anti-tumor efficacy.

overall_design: mRNA sequencing of bulk liver tissue collected from wild-type mice at 48 hours after treatment with the CD40 agonist FGK45 (compared to control)

first: Meredith

last: Stone

first: Veronica

last: Herrera

first: Kathleen

last: Graham

first: Jae

middle: W

first: Austin

last: Huffman

first: Heather

last: Coho

first: Evan

last: Tooker

first: Max

last: Myers

first: Michael

last: Giannone

first: Yan

last: Li

first: Thomas

last: Buckingham

first: Kristen

last: Long

first: Gregory

last: Beatty


title: Generation of human blastocyst-like structures from pluripotent stem cells

city: beijing

first: zheying

last: min

address: Yiheyuan road NO.5

institute: Peking University

summary: Due to ethical concerns and restricted access to human blastocysts, we lack a comprehensive understanding of early human embryogenesis. A reliable model system that can recapitulate early stages of human embryogenesis would help solve this problem.Here we report a robust three-dimensional (3D), two-step induction protocol for generating blastocyst-like structures (EPS-blastoids) from human extended pluripotent stem (EPS) cells. Morphological and single-cell transcriptomic analyses revealed that EPS-blastoids contain key cell lineages and are transcriptionally similar to human blastocysts. Furthermore, EPS-blastoids also exhibited the developmental potential to undergo post-implantation morphogenesis in vitro to form structures with a cellular composition and transcriptome signature similar to human embryos that had been cultured in vitro for 8 or 10 days. In conclusion, human EPS-blastoids provide a robust new experimental platform for studying early developmental stages of the human embryo.

overall_design: To analyze the transcriptome signature of EPS-blasotids on different developmental days (including day6, day8 and day10).

first: Zheying

last: Min

first: Yong

last: Fan

first: Yang

last: Yu


title: NAT10-mediated β-hydroxybutyrylation  Rewires Genomic 3D Conformation and Replication Timing

city: Beijing

first: wenhui

last: Zhao

summary: Spatiotemporal regulation of chromatin replication (replication timing, RT） in eukaryotes is critical to maintain the genomic integrity. Here we focused on epigenetic mechanisms in rewiring genomic 3D conformation and replication timing. The results show that the novel lysine β-hydroxybutyrylation (Kbhb) modifications accelerates chromatin replication without inducing replication defects. This effect was mediated by the NAT10, a novel b-hydroxybutyryl-transferase, through regulating the association of NAT10 and CTCF with chromatin. Depletion of NAT10 and NAT10-mediated Kbhb dramatically reduce chromatin-bound NAT10 and CTCF, resulting in reorganization of genomic 3D conformation with enhanced trans- and cis-interaction in Hi-C matrix, with elevated proportion of A compartments, and with reorganized TADs boundaries. Moreover, reorganization of genomic 3D conformation contributes to rewire replication timing. These results support models in which NAT10-mediated β-hydroxybutyrylation coordinates genomic 3D conformation reorganization with replication timing alteration, and emphatically address the concept that epigenetic mechanisms reconcile genomic 3D conformation with replication timing.

overall_design: NAT10 ChIP-seq were performed on control (control) or β-hydroxybutyrate (BHB) treated  U2OS cells. CTCT ChIP-seq were performed on β-hydroxybutyrate (BHB) treated control (siCtrl) or NAT10 knock-down (siNAT10) U2OS cells.

first: Wenhui

first: Kun

last: Liu


title: Identification of differentially expressed genes in the hippocampus in the intraamygdala kainic acid mouse model of status epilepticus.

first: Camille

last: Stephan Otto Attolini

state: Select a State or Province

address: Baldiri Reixac 10

department: Biostatistics and bioinformatics Unit

institute: IRB Barcelona

summary: The aim of this work was to identify mRNA expression changes in the ipsilateral hippocampus in the intraamygdala kainic acid (KA) mouse model of status epilepticus. In this model, status epilepticus (prolonged damaging seizures) are triggered by an intraamygdala KA injection. All mice develop epilepsy after a short latency period of 3-5 days. For our experiments, 10-week old mice with a C57BL/6 background were either injected with intraamygdala KA (n = 18) or vehicle (PBS, n = 18). Mice were sacrificed 8 hours following status epilepticus (acute pathology) or 14 days post-status epilepticus (timepoint at which all mice suffer from chronic epilepsy) and ipsilateral hippocampi were quickly dissected and pooled into 3 groups (n = 3 per pooled sample).

overall_design: Total mRNA from ipsilateral hippocampi was extracted, purified and amplified. cDNA was hybridized using the Mouse MG-430 PM Array Strip and CEL files were generated from DAT files using Affymetrix Command Console software. Finally, differential gene expression was calculated.

first: Alberto

last: Parras

last: Stephan-Otto Attolini

first: Tobias

last: Engel


title: LncRNA and mRNA Sequencing Analysis of Left Testis in Experimental Varicocele Rats Treated with Morinda officinalis Polysaccharide

city: Fuzhou

first: Lihong

last: Zhang

state: Fujian

address: No. 1 Xueyuan Road, Minhou County

institute: Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Fujian Medical University

summary:
Purpose: Next-generation sequencing (NGS) was performed to illustrate the genetic molecular mechanism underlying varicocele (VC) pathogenesis and Morinda officinalis polysaccharide (MOP) repair effect.
Methods: The male Sprague–Dawley (SD) rats (about 6-7 weeks old and 200±10g weight) were divided into three groups: 1) control group (Control); 2) experimental varicocele group (VC); 3) 300 mg kg-1 MOP administration group (VC+MOP). The next-generation RNA sequencing were performed to identify the differentially-expressed mRNA and lncRNA in left testicular tissue between each two compared group.
Results: The result show that a total of 144 mRNAs and 63 LncRNAs, 63 mRNAs and 148 LncRNAs , 173 mRNAs and 54 LncRNAs were found differentially expressed between compared group VC vs. Control, VC+MOP vs. VC, and VC+MOP vs. Control respectively.
Conclusions: Our study try to offer a indication for novel diagnose marker and therapeutic method, as well as provide feasible research orientations for further study.

overall_design: Left testicular mRNA and lncRNA profiles of  experimental varicocele rats treated with Morinda officinalis polysaccharide were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000.

first: Xiaozhen

first: Wei

last: Wang


title: RNA-seq of mouse heart with different storage time followed by reperfusion

city: Ann Arbor

first: Paul

last: Tang

state: MI

address: 2800 Plymouth Road

department: Cardiac surgery

institute: University of Michigan

summary: We examine the RNA profile of LV and RV in donor heart with different period of storage (0, 4, and 8 hours) follwed by reperfusion. We find that both LV and RV has activated immune response after prolonged storage compared to 0h.

overall_design: Examination of transcriptomic response to cold storage (0, 4 and 8 hours) and reperfusion in LV and RV of donor heart

first: Tang

last: Paul

first: Lei

last: Ienglam


title: Remodeled single-cell landscape in the metastatic bone marrow in human neuroblastoma unraveled by multi-omics and deep multiplex imaging

status: Public on Sep 07 2021

city: Vienna

first: Fikret

last: Rifatbegovic

address: Zimmermannplatz 10

department: Tumor biology

country: Austria

institute: Children's Cancer Research Institute

summary: Single-cell assessment of bone marrow metastases is essential to decipher the entire spectrum of tumor heterogeneity in solid cancers with bone marrow involvement. We used multi-epitope-ligand cartography (MELC) to spatially profile 20 biomarkers in 35,000 disseminated tumor cells (DTCs), hematopoietic and mesenchymal cells from eight neuroblastoma bone marrow metastases. We developed DeepFLEX, a single-cell image analysis pipeline for MELC data that combines deep learning-based cell and nucleus segmentation and overcomes frequent challenges of multiplex imaging methods. Comparisons of cell type proportions between samples indicated that microenvironmental changes in the bone marrow are associated with tumor cell infiltration and therapy response. Hierarchical clustering of DTCs revealed multiple phenotypes with highly diverse expression of markers such as FAIM2, which we propose as a complementary marker to capture DTC heterogeneity in neuroblastoma. This single-cell atlas is an important step towards a deeper understanding of DTCs and their interactions with the bone marrow niche.

overall_design: mRNA of 38 samples was sequenced and analysed. Some of the RNA-Seq Samples are also available in GEO Series GSE94035.

first: Daria

last: Lazic

first: Florian

last: Kromp

first: Michael

last: Kirr

first: Filip

last: Mivalt

last: Halbritter

first: Marie

last: Bernkopf

first: Andrea

last: Bileck

first: Marek

last: Ussowicz

first: Inge

last: Ambros

first: Peter

middle: F

first: Christopher

last: Gerner

first: Ruth

last: Ladenstein

first: Christian

last: Ostalecki

first: Sabine

last: Taschner-Mandl


title: Exploring heterogeneity of alveolar type 1 cells

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

summary: single cell RNA-sequencing of alveolar type 1 cells

overall_design: scRNA-seq of CD31- CD45- E-cadherin+ tdTomato+ cells from ACID;R26tdTomato mice.

first: Fan

last: Li

first: Beiyun

last: Zhou

first: Zea

last: Borok


title: Smarca4 inactivation promotes lineage-specific transformation and early metastatic features in the lung [Bulk RNA-seq]

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: SMARCA4 (BRG1) encodes for one of two mutually-exclusive ATPases present in SWI/SNF chromatin remodeling complexes, and is among the most frequently mutated genes in human lung adenocarcinoma. Despite its prevalence, the functional consequences of SMARCA4 alterations on lung cancer initiation and progression remain poorly understood. Using genetically engineered mouse models, patient-derived xenografts, and single-cell epigenomic profiling, we demonstrate that loss of Smarca4 sensitizes CCSP+ cells within the lung to malignant transformation and tumor progression, resulting in highly advanced dedifferentiated tumors and increased metastatic incidence. Consistent with these phenotypes, Smarca4-deficient tumors lack lung lineage transcription factor activities and instead show activation of embryonic stem cell-like programs, resembling a metastatic cell state. Thus, the SWI/SNF complex – via Smarca4 – acts as a gatekeeper for lineage-specific cellular transformation and metastasis during lung cancer evolution.

overall_design: Bulk RNA-seq on isolated cancer cells from murine lung adenocarcinoma models of Smarca4 loss

first: Carla

last: Concepcion

first: Sai

last: Ma

first: Lindsay

last: LaFave

first: Arjun

first: Manyuan

last: Liu

first: Lydia

last: DeAngelo

first: Jonathan

last: Kim

first: Isabella

last: Del Priore

first: Adam

middle: J

last: Schoenfeld

first: Manon

last: Miller

first: Vinay

middle: K

last: Kartha

last: Westcott

first: Francisco

last: Sánchez-Rivera

first: Kevin

last: Meli

first: Manav

last: Gupta

first: Roderick

last: Bronson

first: Gregory

last: Riely

first: Natasha

last: Rekhtman

first: Charles

last: Rudin

first: Aviv

last: Regev

first: Jason

middle: D

last: Buenrostro

first: Tyler

last: Jacks


title: Specific endothelical cells govern nanoparticle entry into solid tumours

city: Toronto

first: Warren

last: Chan

state: ON

address: 160 College St.

institute: University of Toronto

summary: We sequenced the transcroptome of isolated nanoparticle positive and nanoparticle negative tumour endothelial cells from mouse 4T1 mammary tumours

overall_design: Tumour endothelial cells were isolated from 2 weeks old 4T1 tumours in female Balb/c mice using immunomagnetic isolation for CD45-, and CD31+ cells. Nanoparticle positive and negative tumour endothelial cells were then sorted by FACS to generate a nanoparticle positive endothelial cell group and a nanoaprticle negative endothelial cell group. This was done in 3 different tumours. RNA was isolated from the cells and processed for sequencing.

first: Benjamin

middle: R

last: Kingston


title: Establishment of Transposase-assisted Low-input m6A Sequencing Technique

city: GuangZhou

first: Yan

last: Li

state: GuangDong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: School of Life Science

institute: Sun Yat-sen University

summary: As the most abundant and best-characterized internal mRNA modification, N6-methyladenosine (m6A) emerges to play a critical regulatory role in wide range of physiological and pathological processes, including gametogenesis, neuronal development, obesity and tumorigenesis. Methylated RNA immunoprecipitation coupled with next-generation sequencing (MeRIP-seq) facilitates transcriptome-wide m6A profiling, also is the most widely used technique to understand the biological significance of m6A. However, it typically requires over 100 μg of total RNA or 107 cells as input materials, hampering its application in limited samples. Here, we develop tMeRIP-seq, a transposase assisted MeRIP-seq method to achieve m6A profiling using ultra-low amount of input RNA. By marrying Tn5 tagmentation to m6A-specific immunoprecipitation, tMeRIP-seq largely improves the efficiency of library construction and reduces the input materials to as little as 60 ng total RNA or 103 cells. We apply this method on a small droplet of human blood and recapitulate the m6A profile previously reported using conventional protocol. We find tMeRIP-seq is a convenient and powerful method to examine m6A in ultra-low input material, potentially providing m6A as a new layer of bio-marker for liquid biopsy.

overall_design: The profiles of mRNA m6A modifications from ultra-low input materials including HEK293T total RNA, HEK293T cells and human peripheral blood.

first: Guan-Zheng

last: Luo

first: Tao

last: Chen


title: Increased glucose uptake in hippocampus as a surrogate biomarker of metabolic reconfiguration of microglia in Alzheimer’s disease

city: Seoul

first: Hongyoon

last: Choi

state: Seoul Teugbyeolsi

address: Daehakro 101, Jongrogu

country: South Korea

institute: Seoul National University Hospital

summary: Microglia is dynamically reprogrammed according to the progression of Alzheimer’s disease (AD). However, clinical translation into biomarker development for functional change in microglia has not been achieved. Here, we find the close association of the metabolic reconfiguration of microglia with increased hippocampal glucose uptake, which can be noninvasively estimated by [18F]fluorodeoxyglucose (FDG) positron emission tomography (PET). We found that increased FDG activity in the hippocampus of an AD mouse model depended on microglial uptake. Single-cell RNA-sequencing of the hippocampus showed the changes of glucose metabolism profiles including glucose transporters, glycolysis and oxidative phosphorylation mainly occurred in microglia. A subset of microglia with high glucose transporters with defective glycolysis and oxidative phosphorylation was increased according to disease progression. Furthermore, we also found a positive association between a soluble TREM2 of cerebrospinal fluid, a marker of microglial activation, and hippocampal FDG uptake as a human study. We identified a reconfiguration of microglial glucose metabolism in the hippocampus of AD and suggested a feasible imaging biomarker based on widely used FDG PET to reflect microglial metabolic profiles.

overall_design: The purified cells obtained from the hippocampus (CA1) were sequenced using the Chromium single cell gene expression platform (10x Genomics). Approximately 1000-1500 cells from each dissected brain were directly loaded into each sample well following manufacturer instructions. All samples were combined into droplets with barcoded beads. Manufacturer specifications were followed for generation of the barcoded libraries and then the samples were sequenced to an average depth of 40,000-60,000 reads on an Illumina Nextseq 500 sequencer.

first: Yoori

first: Youngsun

last: Lee

first: Hyun

last: Kim

first: Seokjun

last: Kwon

first: Do

last: Hwang

first: Dong


title: Oligodendrocyte degeneration triggers the formation of inflammatory brain lesions

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

summary:
Here, we investigated whether cuprizone-induced oligodendrocyte apoptosis is sufficient to trigger peripheral immune cell recruitment into the forebrain. We show that early cuprizone-induced white matter lesions display a striking similarity to early MS lesions, i.e., oligodendrocyte degeneration, microglia activation and absence of lymphocytes. Such early cuprizone lesions are sufficient to trigger peripheral immune cell recruitment.
The lesions are characterized by discontinuation of the perivascular glia limitans, focal axonal damage, and perivascular astrocyte pathology. Time course studies showed that the severity of cuprizone-induced lesions positively correlates with the extent of peripheral immune cell recruitment. Furthermore, results of genome-wide array analyses suggest that moesin is integral for early microglia activation in cuprizone and MS lesions. This study underpins the significance of brain-intrinsic degenerative cascades for immune cell recruitment and, in consequence, MS lesion formation.

overall_design: 8 samples were analyzed, four control samples and four cuprizone samples.

first: Markus

last: Kipp


title: Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling

city: Rome

first: Silvia

last: Campello

state: <None>

address: Via della Ricerca Scientifica

department: Department of Biology

institute: University of Rome, Tor Vergata

summary: Medulloblastoma (MB) is a childhood malignant brain tumour comprising four main subgroups characterized by different genetic alterations and rate of mortality. Among MB subgroups, patients with enhanced levels of the c-MYC oncogene (MBGroup3) have the poorest prognosis. Here we identified a previously unrecognized role of the pro-autophagy factor AMBRA1 in regulating MB. We demonstrated that AMBRA1 expression levels strongly depend on c-MYC expression and correlate with patient poor prognosis; also, knockdown of AMBRA1 reduces MB stem potential, growth and migration of MBGroup3 cells in vitro and in vivo. At a molecular level, AMBRA1 mediates these effects by suppressing SOCS3, an inhibitor of STAT3 activation. In turn, active STAT3 increases c-MYC expression that, in a positive feedback loop, sustains AMBRA1 transcription. Importantly, pharmacological inhibition of autophagy profoundly affects stem potential and metastasization of MBGroup3 cells in vitro and in vivo, and a combined anti-autophagy and anti-STAT3 approach impacts MBGroup3 cell survival. Taken together, our data identified the c-MYC/AMBRA1/STAT3 axis as a strong oncogenic signalling pathway with significance for both patient stratification strategies and targeted treatments of MBGroup3.

overall_design: Characterization of the global gene expression changes induced by AMBRA1 or by ATG7 siRNA-mediated downregulation

first: Franceca

last: Nazio

first: Agnese

last: Po

first: Luana

last: Abballe

first: Francesca

last: Diomedi Camassei

first: Matteo

last: Bordi

first: Caterina

last: Ferraina

first: Antonio

last: Camera

first: Marco

last: Pezzullo

first: Iolanda

last: Boffa

first: Ignazio

last: Caruana

first: Elena

last: Papaleo

first: Biagio

last: De Angelis

first: Evelina

last: Miele

first: Antonella

last: Cacchione

first: Andrea

last: Carai

first: Concetta

last: Quintarelli

first: Angela

last: Mastronuzzi

first: Elisabetta

last: Ferretti

first: Franco

last: Locatelli

first: Francesco

last: Cecconi


title: Chronic stress primes innate immune responses in mice and humans

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

summary: Psychological stress (PS) is associated with systemic inflammation and accelerates inflammatory disease progression (e.g., atherosclerosis). The mechanisms underlying stress-mediated inflammation and future health risk are poorly understood. Monocytes are key in sustaining systemic inflammation, and recent studies demonstrate they maintain memory of inflammatory insults, leading to a heightened inflammatory response upon rechallenge. We show that PS induces remodeling of the chromatin landscape and transcriptomic reprogramming of monocytes skewing them to a primed hyperinflammatory phenotype. Monocytes from stressed mice and humans exhibit a characteristic inflammatory transcriptomic signature and are hyperresponsive upon stimulation with Toll-like receptor ligands. RNA and ATAC sequencing reveal that monocytes from stressed mice and humans exhibit activation of metabolic pathways (mTOR and PI3Kinase) and reduced chromatin accessibility at mitochondrial respiration loci. Collectively, our findings suggest that PS primes the reprogramming of myeloid cells to a hyperresponsive inflammatory state, which may explain how PS confers inflammatory disease risk.

overall_design: RNAseq and ATACseq of isolated bone marrow monoctyes from 6 mice (3 stress, 3 control). RNAseq of isolated bone marrow monocytes stimulated with LPS of 16 pools of 4 mice each (4 pools control unstimulated, 4 pools stressed unstimulated, 4 pools control stimulated, 4 pools stressed stimulated). RNAseq of isolated whole blood monocytes from humans with high and low stress (12 high stress, 15 low stress) from the HARP study.

first: Tessa

last: Barrett

first: Emma

last: Corr

first: Coen

last: van Solingen

first: Emily

last: Brown

first: Graeme

last: Koelwyn

middle: H

last: Lee

first: Lianne

last: Shanley

first: Tanya

last: Spruill

first: Fazli

last: Bozal

first: Annika

last: de Jong

first: Alexandra

last: Newman

first: Kamelia

last: Drenkova

first: Michele

last: Silvestro

first: Bhama

last: Ramkhelawon

first: Harmony

last: Reynolds

first: Judith

last: Hochman

first: Matthias

last: Nahrendorf

first: Filip

last: Swirski

first: Edward

middle: A

last: Fisher

first: Jeffrey

last: Berger

first: Kathryn

last: Moore


title: Genome-wide maps of open chromatin in liver cells of Astyanax mexicanus [ATAC-seq]

city: Kansas City

first: Chris

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

summary: Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.

overall_design: Open chromatin profiles of liver tissue from 2 replicates each of Surface, and Pachon and Tinaja cave variants of Astyanax mexicanus.

first: Jaya

last: Krishnan

first: Ning

last: Zhang

first: Jake

last: VanCampen

first: Robert

last: Peuss

first: Shaolei

last: Xiong

first: Alexander

last: Kenzior

first: Hua

last: Li

first: Joan

last: Conaway

first: Nicolas

last: Rohner


title: RNA-Seq Analysis of liver cells of Astyanax mexicanus.

summary: Organisms adapt to and survive in environments with varying nutrient availability. Cis-regulatory changes play important roles in adaptation and phenotypic evolution. To what extent cis-regulatory elements contribute to metabolic adaptation is less understood. Here we have utilized a unique vertebrate model, Astyanax mexicanus, that survives in nutrient rich surface and nutrient deprived cave water to uncover gene regulatory networks in metabolic adaptation. We performed genome-wide analysis of accessible chromatin and histone modifications in the liver tissue of one surface and two independently derived cave populations, providing the first genome-wide epigenetic landscape in this organism. In parallel, we performed RNA Seq as a read out of gene expression. We find that many cis-regulatory elements differ between surface and the cavefish, while the two independently derived cave populations have evolved remarkably similar regulatory signatures. Changes in gene regulatory networks between the surface and cave morphotypes point to global changes in key metabolic pathways.

overall_design: Stranded mRNA profiles of liver tissue from 2 replicates each of Surface, and Pachon and Tinaja cave variants of Astyanax mexicanus.


title: Cobalt Induced Oxidative Stress Contributes to Alveolar/Bronchiolar Carcinogenesis in B6C3F1/N Mice

city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

summary:
To identify differentially expressed  transcripts between control samples and spontaneous tumors, or control samples and cobalt treated tumors, we collected RNA from male and female B6C3F1 mice from a 2-year inhalation NTP bioassay exposed to 0 or 5 mg/m3 cobalt metal dust.  These samples were interrogated with the Affymetrix Mouse Genome 430 2.0 GeneChip Array.
A total of 11557 gene transcripts were differentially expressed between control samples and spontaneous tumors, and 12420 gene transcripts were differentially expressed between control samples and treated cobalt tumors (false discovery rate (FDR) < 0.05).

overall_design: There were 3 groups and 6x replication for each group, for 18 total samples. The groups were (1) vehicle control, (2) spontaneous tumors, (3) tumors present with cobalt treatment. We compared vehicle control vs spontaneous tumor and control vs treated tumor using ORIOGEN software. The permutation based p-values for each test were significant for FDR≤5%.

first: Arun

last: Pandiri


title: Microarray analysis of OVSAHO and KURAMOCHI cells incubated with simvasatin or L-778123

status: Public on Sep 06 2021

city: Tokyo

first: Yusuke

last: Kobayashi

state: Outside of the US

address: 35 Shinanomachi, Shinjuku-ku

department: Department of Obstetrics and Gynecology

institute: Keio University School of Medicine

summary: To extract genes that are regulated in ovarian cancer cell lines OVSHO and KURAMOCHI when cultured with statin compared to when cultured with L-778123.

overall_design: Total RNA was extracted from OVSAHO and KURAMOCHI cells incubated with simvastatin or L-778123 using RNeasy Mini Kits (Qiagen, Hilden, Germany) in combination with RNase-free DNase (Qiagen). The quality of RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA samples were labeled using Low Input Quick Amp Labeling kits (one-color; Agilent) and then hybridized to the Agilent SurePrint G3 Human Gene Expression version 3.0 Microarray (Agilent) according to the manufacturer’s instructions. The arrays were scanned using the Agilent DNA microarray scanner G2505C (Agilent).

first: Haruko

last: Kunitomi


title: The SRSF4/lncRNA GAS5 axis regulates left ventricular hypertrophy by inhibiting the glucocorticoid receptor

city: Cold Spring Harbor

first: Carlos

last: Martí-Gómez

email: carlos199m1@gmail.com, martigo@cshl.edu

address: 1 Bungtown Rd

department: Quantitative Biology

institute: Cold Spring Harbor Laboratory

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

overall_design: Refer to individual Series


title: Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

city: Seattle

first: Bosiljka

last: Tasic

state: WA

address: 615 Westlake Ave N.

department: Molecular Genetics

institute: Allen Institute for Brain Science

summary: Abundant evidence supports the presence of at least three distinct types of thalamocortical (TC) neurons in the primate dorsal lateral geniculate nucleus (dLGN) of the thalamus, the brain region that conveys visual information from the retina to the primary visual cortex (V1). Different types of TC neurons in mice, humans, and macaques have distinct morphologies, distinct connectivity patterns, and convey different aspects of visual information to the cortex. To investigate the molecular underpinnings of these cell types, and how these relate to differences in dLGN between human, macaque, and mice, we profiled gene expression in single nuclei and cells using RNA-sequencing. These efforts identified four distinct types of TC neurons in the primate dLGN: magnocellular (M) neurons, parvocellular (P) neurons, and two types of koniocellular (K) neurons. Despite extensively documented morphological and physiological differences between M and P neurons, we identified few genes with significant differential expression between transcriptomic cell types corresponding to these two neuronal populations. Likewise, the dominant feature of TC neurons of the adult mouse dLGN is high transcriptomic similarity, with an axis of heterogeneity that aligns with core vs. shell portions of mouse dLGN. Together, these data show that transcriptomic differences between principal cell types in the mature mammalian dLGN are subtle relative to the observed differences in morphology and cortical projection targets. Finally, alignment of transcriptome profiles across species highlights expanded diversity of GABAergic neurons in primate versus mouse dLGN and homologous types of TC neurons in primates that are distinct from TC neurons in mouse.

sample_organism:
Macaca fascicularis
Macaca nemestrina
Homo sapiens
Mus musculus

overall_design:
Single-cell RNA-seq data from mouse dLGN, LP, and LGv. Single-nucleus RNA-seq data from Macaque dLGN and pulvinar. Single-cell RNA-seq data from human.
>>> Submitter declares that the human raw data will be deposited in dbGaP due to patient privacy concerns. <<<

first: Trygve

middle: E

last: Bakken

first: Cindy

last: van Velthoven

first: Vilas

last: Menon

first: Rebecca

last: Hodge

first: Zizhen

last: Yao

first: Thuc

middle: N

last: Nguyen

first: Lucas

last: Graybuck

first: Gregory

last: Horwitz

first: Darren

last: Bertagnolli

first: Jeff

last: Goldy

first: Anna

last: Yanny

first: Emma

last: Garren

first: Sheana

last: Parry

first: Tamara

last: Casper

first: Soraya

middle: I

last: Shehata

first: Eliza

last: Barkan

first: Aaron

last: Szafer

first: Boaz

middle: P

last: Levi

first: Nick

last: Dee

first: Kimberly

last: Smith

first: Susan

last: Sunkin

first: Amy

last: Bernard

first: John

last: Phillips

first: Michael

last: Hawrylycz

first: Christof

last: Koch

first: Gabe

last: Murphy

first: Ed

last: Lein

first: Hongkui

last: Zeng


title: Global transcriptomic profiling of Mycobacterium tuberculosis (Mtb) H37Rv in phosphate limited or phosphate enriched media

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

country: India

institute: Bose Institute

summary: Transcriptomic profiling of Mtb grown in phosphate limited or phosphate enriched media showed differential expression of a large set of genes, giving insight into how Mtb remodels its transcriptome depending on the concentrations of phosphate available in its environment.

overall_design: Replicate cultures of Mtb were grown either in phosphate limited or phosphate enriched medium and global transcriptomes were compared.

first: Amar

last: Mahatha

first: Joyoti

last: Basu

first: Sudipto

last: Saha


title: RNA-Seq analysis of SRSF4 KO hearts compared to controls.

first: Carlos

last: Martí-Gómez

summary: The goal of this study is to analyse the transcriptome of control hearts vs hearts lacking SRSF4 expression.

overall_design: SRSF4 KO and control hearts were extracted at 2months of age. Three different hearts were included for each condition.

first: Javier

last: Larrasa-Alonso

first: Enrique

last: Lara-Pezzi


title: Genome-wide maps of chromatin state in liver cells of Astyanax mexicanus [ChIP-seq]

first: Chris

last: Seidel

overall_design: Chromatin profiles of H3K4me3, H3K27Ac, and H3K27me3 by immunoprecipitation in liver tissue from 2 or 3 replicates each of Surface, and Pachon and Tinaja cave variants of Astyanax mexicanus.

first: Jaya

last: Krishnan

first: Ning

last: Zhang

first: Jake

last: VanCampen

first: Robert

last: Peuss

first: Shaolei

last: Xiong

first: Alexander

last: Kenzior

first: Hua

last: Li

first: Joan

last: Conaway

first: Nicolas

last: Rohner


title: iCLIP analysis of SRSF4 binding profile in neonatal cardiomyocytes

summary: The goal of this study is to analyse binding preferences of SRSF4 in cardiac myocytes.

overall_design: Neonatal cardiomyocytes were extracted from C57BL/6 mice at P0 or P1.23 A total of 8 million cells were plated in 10 cm2 plates. The following day, cells were transfected with 15 μg of SRSF4-GFP modRNA using 21 μL Lipofectamine 2000. At 48 h post-transfection, cells were irradiated once with 100 mJ UV light (254 nm), and iCLIP was performed

last: Larrasa

first: Michaela

last: Müller-McNicoll