title: Identification and Characterization of the Determinants of Copper Resistance in the Acidophilic Fungus Acidomyces richmondensis MEY-1 Using the CRISPR/Cas9 System

status: Public on Nov 14 2022

city: Tianjin

first: Jinyang

last: Li

address: No. 32, Xiqi Road, Tianjin Airport Economic Park

institute: Chinese Academy of Sciences

summary: Copper (Cu) homeostasis has not been well-documented in filamentous fungi, especially extremophiles. Acidophilic fungus Acidomyces richmondensis MEY-1 has extremely high Cu tolerance among filamentous fungi, and the transcription factor ArAceA has been shown to be involved in this process. The ArAceA deletion mutant (ΔArAceA) exhibits specific growth defects at Cu concentrations of ≥ 10 mM. To gain genomic insight into the Cu tolerance mechanism and the role of ArAceA in Cu tolerance, we treated the ΔArAceA mutant and WT strains with or without 15 mM CuCl2 for 6 h. Transcriptional profiling analysis revealed that ΔArAceA mutant is transcriptionally more sensitive to Cu than the wild-type strain. Our findings provide insights into the molecular basis of Cu tolerance in acidophilic filamentous fungi.

overall_design: Arthroconidia of WT and ∆ArAceA strain were inoculated into 100 mL of liquid MMC and grown at 30°C and 200 rpm for 4 days. The mycelium was washed twice with sterilized water and then transferred to 100 mL of MMC, with or without addition of 15 mM CuCl2, for 6 h before RNA extraction. Triplicate cultures were sampled in each condition.

first: Huiying

last: Luo


title: CRISPR-based targeted haplotype-resolved assembly of a megabase region [EPIC]

status: Public on Nov 15 2022

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

country: China

institute: Fudan University

summary: Constructing high-quality haplotype-resolved genome assemblies has substantially improved the ability to detect and characterize genetic variants. A targeted approach providing readily access to the rich information from haplotype-resolved genome assemblies will be appealing to groups of basic researchers and medical scientists focused on specific genomic regions. Here, using the 4.5 megabase, notoriously difficult-to-assemble major histocompatibility complex (MHC) region as an example, we demonstrated an approach to construct haplotype-resolved assembly of the targeted genomic region with the CRISPR-based enrichment. Compared to the results from haplotype-resolved genome assembly, our targeted approach achieved comparable completeness and accuracy with reduced computing complexity, sequencing cost, as well as the amount of starting materials. Moreover, using the targeted assembled personal MHC haplotypes as the reference both improves the quantification accuracy for sequencing data and enables allele-specific functional genomics analyses of the MHC region. Given its highly efficient use of resources, our approach can greatly facilitate population genetic studies of targeted regions, and may pave a new way to elucidate the molecular mechanisms in disease etiology.

overall_design: 10x linked-reads, CCS reads and WGBS for Enriched MHC, RNA-seq sequencing and Illumina Human Methylation 850 BeadChip for NA12878

first: Taotao

first: Duo

last: Du

first: Dandan

last: Zhang


title: Transcriptomes of cultured human hematopoietic stem cells.

status: Public on Nov 13 2022

city: 4 Shiroganedai, Minato-ku

first: Masatoshi

last: Sakurai

state: Tokyo

department: Stem Cell Biology and Regenerative Medicine

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

type: Expression profiling by high throughput sequencing

summary:
We compared transcriptomes of CD34(high)EPCR-positive with CD34(high)EPCR-negative cells after 10-days culture in PCL-PVAc-PEG based 3a medium.
It was because our culture condition had not previously reported and so we demonstrated that phenotypic HSCs were concentrated in EPCR-positive fraction as conventional UM171-based culture system.
As a result, CD34(high)EPCR-positive cells highly expressed HSC markers (HLF, AVP, PRDM16 and FGD5) compared with CD34(high)EPCR-negative cells.

overall_design: mRNA profile of CD34(high)EPCR-positive and CD34(high)EPCR-negative cells derived from 10-days cultured cord blood CD34+ cells.

first: Kantaro

last: Ishitsuka


title: Single cell transcriptome sequencing of expanded human hematopoieic stem/progenitor cells cultured in PCL-PVAc-PEG based 3a medium and StemSpan with UM171/SR-1 medium.

summary: We demonstrated that chemically difined PCL-PVAc-PEG based 3a medium was superior to conventional StemSpan besed medium in expansion of human hematopoietic stem cells. In fact, more phenotypic HSCs (CD34+EPCR+CD90+CD45RA-ITGA3+) were expanded in our culture condition and higher donor chmerism was achieved in transplantation assay using humanized mice. But detail transcriptome profiles of expanded HSCs was unknown and therefore single-cell RNA sequencing was done to reveal it. As a result, expanded cells in our medium had more HSPC featured cells. Interestingly, erythroid/megakaryocyte progenitors was more expanded in our condition. On the other hands, other culture condition made more myeloid progenitor cells but few HSPC featured cells. This result support the idea that our new medium are able to selectively expand HSCs.

overall_design: Transcriptome analysis of expanded cells at single-cell level to compare efficiency of chemically difined our new medium with conventional StemSpan and cytokine besed medium.

first: Kantato


title: Multi-omic analysis of homologous recombination deficient, end-stage ovarian cancer

status: Public on Nov 12 2022

city: Melbourne

first: Elizabeth

middle: Louise

last: Christie

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

type: Methylation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Expression data from MCF10A cells treated with TGFβ for multiple time points [scRNA-seq]

status: Public on Nov 11 2022

city: Boston

first: Andrew

last: Emili

state: MA

address: 72 East Concord St

department: Biochemistry

country: USA

institute: Boston University

summary: We combine state-of-the-art data acquisition platforms and bioinformatics tools to devise PAMAF, a workflow that simultaneously examines twelve omics modalities, i.e., protein abundance from whole-cells, nucleus, exosomes, secretome and membrane; N-glycosylation, phosphorylation; metabolites; mRNA, miRNA; and, in parallel, single-cell transcriptomes. Here we apply PAMAF in an established in vitro model of TGFβ-induced epithelial to mesenchymal transition (EMT) to quantify >61,000 molecules from 12 omics and 10 timepoints over 12 days. Bioinformatics analysis of this EMT-ExMap resource allowed us to identify; –unexpected topological coupling between omics, –four distinct cell states during EMT (E, E/M-1, E/M-2, M), –omics-specific kinetic paths, –stage-specific multi-omics characteristics, –distinct regulatory classes of genes, –ligand–receptor mediated intercellular crosstalk using an innovative pipeline integrating scRNAseq and subcellular proteomics, and –novel combinatorial drug targets (e.g., Hedgehog signaling and CAMK-II) to inhibit EMT, which we validate using a 3D mammary duct-on-a-chip platform. Overall, while this study provides an unprecedented resource on TGFβ signaling and EMT, PAMAF-like workflows can be applied to generate comprehensive molecular landscapes of other multifaceted biological processes.

overall_design: MCF10A cells treated with TGFβ for multiple time points.

first: Indranil

last: Paul


title: Expression data from MCF10A cells treated with TGFβ for multiple time points [miRNA-4]


title: Mapping and understanding the function of RNA in octopus brain

city: Berlin

first: Grygoriy

last: Zolotarov

address: Hannoversche Strasse 28

department: Berlin Institute of Medical Systems Biology

country: Germany

institute: Max Delbruck Center for Molecular Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Coleoid cephalopods possess a highly complex nervous system and a rich behavioral repertoire that is unique within the invertebrates and is comparable to – but evolved independently from – the vertebrates (Shigeno et al. 2018). To explain this complexity, previous studies have implicated a unusually high level of mRNA editing in transcripts expressed in both the octopus and squid nervous system (Albertin et al. 2015; Alon et al. 2015; Liscovitch-Brauer et al. 2017). We have sequenced RNA across 18 tissues from the octopus O. vulgaris, and analyzed the extent of mRNA isoform usage as well as the expression of microRNAs in the nervous system in comparison to non-neuronal tissues.

overall_design: Messenger RNA and small RNA profiles of 18 tissues of a common octopus (Octopus vulgaris). In this study, the replicates are present for small RNA expression dataset, where the same set of 18 tissues has been analyzed using 2 different library preparation protocols. With few exceptions, there are matching polyA RNA-seq and totalRNA-seq datasets for the tissues in the study. Finally, the same tissue combinations have been profiled by both FLAM-seq and Iso-seq full-length mRNA sequencing methods.

first: Ivano

last: Legnini

first: Nikolaus

last: Rajewsky


title: Expression data from MCF10A cells treated with TGFβ for multiple time points [HuGene-2_0]

first: Paul

last: Indranil

first: Emili

last: Andrew


title: RNA sequencing of astrocytes purified from adult brain cortices of TwKOastro mice (Knockout of Twnk in astrocytes generated with Gfap73.12:Cre driver, Jackson stock 012886)

city: Berkeley

first: Olesia

last: Ignatenko

state: CA

address: Morgan Hall

institute: UC Berkeley

summary: To investigate astrocyte responses to mitochondrial dysfuncation, we induced a knockout of Twnk (encodes mitochondrial DNA helicase Twinkle) in mouse brain astrocytes (TwKOastro mice). This leads to depletion of mitochondrial genome copy number and its expression.

overall_design: Transcriptomes of 5 TwKOastro astrocyte preparations were compared to 6 control preparations. Astrocytes were purified from 3-3.5 months old control and TwKOastro mice using magnetic beads coated with ACSA-2 antibody (cortices from 3-4 mice per one preparation were used). RNA sequencing was done in the BGI Genomics, China. mRNA was enriched by Oligo dT selection, and reverse transcription was done using random N6 primer. End repair and adaptor ligation were followed by PCR amplification of the library. Quantification of transcript abundance was done using kallisto software, differential expression analysis was done using sleuth (PMID:27043002; PMID:28581496).     TwKOastro mice = Gfap73.12Cre+;Twnkloxp/loxp or Gfap73.12Cre+;Twnkloxp/null. Control mice = Gfap73.12Cre-;Twnkloxp/loxp or Gfap73.12Cre-;Twnkloxp/null.      TwKOastro mice are characterised in PMID:29302033.  Generation of Twnkloxp/loxp mice is described in PMID:26924217.  LoxP sites are located in the introns 1 and 3 of Twnk, Cre expression leads to a frameshift.    Gfap73.12-Cre mice = JAX:012886.

first: Gulayse

last: Ince-Dunn

first: Anu

last: Suomalainen


title: Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders

status: Public on Nov 08 2022

city: Greenwood

first: Rebecca

middle: A

last: MacPherson

state: SC

address: 114 Gregor Mendel Circle, Dr. Trudy Mackay

department: Center for Human Genetics

institute: Clemson University

summary: Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma‐Related Gene‐1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.

overall_design: RNAseq (post rRNA depletion) of whole body Drosophila melanogaster, sexes separately, in the genetic background TRiP (y1, sc1, v1, sev21) (control), where mutant samples have ubiquitous Ubi156-GAL4-mediated UAS-GAL4 system knockdown of brm, osa, Snr1, SMC1, SMC3, and vtd. Three biological replicates per sex per line.

first: Vijay

last: Shankar

first: Robert

middle: R

last: Anholt

first: Trudy

middle: F

last: Mackay


title: Transcriptomic profiling of blood and adipose-resident eosinophils from mice

status: Public on Nov 10 2022

city: UNSW Sydney

first: Kate

last: Quinlan

state: NSW

address: Room 3102, Level 3, Biosciences South Building (E26)

department: School of Biotechnology and Biomolecular Sciences

institute: UNSW Sydney

summary: Eosinophils are immune effector cells with beneficial homeostatic roles in fat. Here, bulk RNA-seq profiling revealed distinct transcriptomic signatures in fat-resident eosinophils and circulating eosinophils.

first: Manan

last: Shah

first: Alexander

middle: J

last: Knights

first: Emily

last: Vohralik

first: Annalise

middle: M

last: Psaila

middle: G


title: TEFM variants impair mitochondrial transcription elongation causing childhood-onset neurological disease

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

summary: We report that TEFM variants are associated with mitochondrial respiratory chain deficiency. We show that patient's cells have reduced levels of promoter distal mitochondrial RNA transcripts.

overall_design: Patient's fibroblasts and muscle samples as well as control samples were analysed by RNA-Seq


title: Single cell transcriptomics of the tumor immune microenvironment from checkpoint blockade-treated B16 tumors edited with control or TBK1-targeting sgRNAs.

status: Public on Nov 07 2022

first: Seth

middle: Allen

last: Anderson

address: 75 Ames Street

department: Cancer Program

institute: Broad Institute of MIT and Harvard

summary: To examine the effect of tumor-specific TBK1 loss on the tumor immune microenvironment, we performed scRNA-seq on CD45+ cells from B16 tumors from mice treated with anti-PD-1 compared to mice treated with isotype control (IgG).

overall_design: B16 tumors were treated with irradiated GM-CSF-secreting B16 (GVAX) cells on days 1 and 4 post tumor challenge and anti-PD1 monoclonoal antibody by IP injection on days 6, 9, and 12 post tumor challenge. CD45+ cells were isolated from B16 tumors and analyzed using scRNA-seq (10X Genomics, 3' chemistry).

first: Thomas

last: Davis

first: Sarah

last: Kim

middle: T

last: Manguso

first: Russell

middle: W

last: Jenkins


title: Whole transcriptome analysis of critically ill elderly patients with sepsis

status: Public on Nov 03 2022

city: Taichung City

first: thh

last: lab

address: 1650 Taiwan Boulevard Sect. 4, Taichung, Taiwan 40705, ROC

country: Taiwan

institute: TCVGH

summary: Sepsis is a frequent complication in critically ill patients and highly heterogeneous that is associated with high morbidity and mortality rates, especially in the elderly population. Utilizing RNA-Sequencing (RNA-Seq) to analysis biological pathways is widely used in clinical and molecular genetics studies, but in elderly patients with sepsis are still lacking. Hence, we aim to investigate the mortality-relevant biological features and transcriptomic features in elderly patients who were admitted to intensive care unit (ICU) for sepsis.

overall_design: We enrolled 37 elderly patients with sepsis at a tertiary referral hospital in central Taiwan. Blood samples and clinical/laboratory data were collected on day-1 and day-8 for RNA-Seq analysis. We implemented the DVID enrichment analysis and Gene Set Enrichment Analysis to identify the dynamic transcriptome and enriched pathway of day-8/day-1 differentially expressed genes, respectively. Finally, we utilized the MiXCR to analyze the diversity of T cell repertoire.

first: I-Chieh

last: Chen

first: Hsin-Hua

first: Yu-Han

last: Jiang

first: Tzu-Hung

last: Hsiao

first: Tai-Ming

last: Ko

first: Wen-Chen

last: Chao


title: Prostate cancer cell-platelet bidirectional signaling promotes calcium mobilization, invasion and apoptotic resistance via distinct receptor-ligand pairs

status: Public on Nov 05 2022

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I street NW, Ross Hall, Suite 731

institute: George Washington University

summary: Platelets play a crucial role in cancer and thrombosis. The receptor-ligand repertoire mediating prostate cancer (PCa) cell-platelet interactions have not been fully elucidated. Microvilli emanating from the plasma membrane of PCa cell lines (RC77 T/E, MDA PCa 2b) directly contacted individual platelets and platelet aggregates, thereby stimulating calcium mobilization in platelets and promoting translocation of P-selectin and integrin aIIbb3 onto the platelet surface. Platelets in turn dose-dependently stimulated PCa cell invasion and apoptotic resistance. PCa cells were exceedingly sensitive to activation by platelets, occurring at platelet:PCa cell ratios ~20,000-fold lower than normally encountered in blood. Candidate platelet-PCa cell signaling axis partners responsible for these cellular events were identified by RNA-Seq and could be broadly divided into 4 categories: i) integrin-ligand, ii) EPH receptor-ephrin, iii) immune checkpoint receptor-ligand, and iv) miscellaneous receptor-ligand interactions. PCa cell-stimulated calcium mobilization was mediated by a fibronectin1 (FN1; PCa side)-aIIbb3 (platelet side) axis. Reciprocally, platelet-stimulated PCa cell invasion was facilitated by a CD55 (platelet side)-adhesion G-protein coupled receptor E5 (ADGRE5; PCa side) axis, with contribution from platelet cytokines CCL3L1 and IL32. Platelet-stimulated PCa cell apoptotic resistance relied on ephrin-EPH receptor and lysophosphatidic acid (LPA)-LPA receptor (LPAR) signaling. Of the participating partners, FN1 and LPAR3 overexpression was observed in PCa specimens compared to normal prostate, while high expression of CCR1 (CCL3L1 receptor), EPHA1 and LPAR5 in PCa was associated with poor patient survival. These findings emphasize that non-overlapping receptor-ligand pairs participate in oncogenesis and thrombosis, highlighting the complexity of any contemplated clinical intervention strategy.

overall_design: Gene expression profiling via RNA-seq of prostate cancer cell lines MDA PCa 2b and RC77 T/E.

first: Norman

middle: H

last: Lee


title: Deciphering immune responses primed by a bacterial lipopeptide in wheat towards Zymoseptoria tritici

status: Public on Nov 04 2022

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

country: France

institute: University of Lille

summary: We revealed that mycosubtilin, a lipopeptide from Bacillus subtilis, protects wheat against the hemibiotrophic fungal pathogen Zymoseptoria tritici. Foliar application of the biomolecule primes, during the early stages of infection, the expression of genes associated with sixteen functional groups, including responses to pathogens, abiotic and oxidative stresses, secondary metabolism, cell-wall structure and function, and primary metabolic pathways (carbohydrate, amino acid, protein, lipid, and energy metabolisms).

overall_design: Wheat plants treated with mycosubtilin (M) or not (control, C), and inoculated with Z. tritici (i) or not (Ni) were analyzed for their gene expression.

first: Rémi

last: Platel

first: Ali

last: Siah


title: Oxidative phosphorylation selectively orchestrates tissue macrophage homeostasis

status: Public on Oct 31 2022

city: Madrid

first: Stefanie

middle: K

last: Wculek

address: C. de Melchor Fernández Almagro, 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III

summary: In vitro studies associated oxidative phosphorylation (OXPHOS) with anti-inflammatory macrophages, while pro-inflammatory macrophages rely on glycolysis. However, the metabolic needs of macrophages in tissues (TMFs) to fulfil their homeostatic activities are incompletely understood. Here, we identified OXPHOS as highly discriminating process among TMFs from different tissues in homeostasis by analysis of RNAseq data, in both human and mouse. Impairing OXPHOS in TMFs via Tfam deletion differentially affected TMF populations. Tfam deletion resulted in reduction of alveolar macrophages (AMs) due to impaired lipid-handling capacity, leading to increased cholesterol content and cellular stress, causing cell cycle arrest in vivo. In obesity, Tfam depletion selectively ablated pro-inflammatory lipid-handling white adipose tissue macrophages (WAT-MFs), preventing insulin resistance and hepatosteatosis. Thus, OXPHOS, rather than glycolysis, distinguishes TMF populations and is critical for the maintenance of TMFs with a high lipid-handling activity, including pro-inflammatory WAT-MFs. This could provide a selective therapeutic targeting tool.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of 4 pools each of Tfam-fl/fl (control samples or WT) or CD11c-Cre Tfam-fl/fl (experimental samples or KO) alveolar macrophages isolated from 3-5 3-week-old mice per sample by FACS/flow sorting.

first: Ignacio

last: Heras-Murillo

first: Diego

last: Mañanes

first: David

last: Sancho


title: FMT improve spleen function

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: FMT from AOS treated mice rescue busulfan disrupted spleen

overall_design: Mice treated with busulfan, then dosed with FMT from AOS treated mice (A10-FMT) or from control mice (Con-FMT)

first: Hongfu

last: Zhang

first: Pengfei

first: Ruqing

last: Zhong

first: Tao

last: Xu


title: Drug perturbation RNA sequencing of 2 prostate cancer cell lines

city: New York City

first: Alessandro

last: Vasciaveo

state: NY

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

institute: Columbia University

summary: Prioritizing cancer treatments at the individual patient level remains challenging, and performing co-clinical studies using patient-derived models in real-time is often not unfeasible. To circumvent these challenges, we introduce OncoLoop, a precision medicine framework to predict and validate drug sensitivity sensitivity in both a human tumors and in its their pre-existing high est-fidelity (cognate) (cognate) model(s)—for contextual in vivo validation—) by leveraging perturbational profiles of clinically-relevant oncology drugs. As proof-of-concept, we applied OncoLoop to prostate cancer (PCa) using a series of genetically engineered mouse models (GEMMs) that capture the broad spectrum of disease states, including metastatic, castration-resistant, metastatic, and neuroendocrine prostate cancer. Interrogation of published cohorts revealed that most patients were represented by at least one cognate GEMM-derived tumor (GEMM-DT), based on upon Master Regulator (MR) conservation analysis. Drugs recurrently predicted to recurrently invert MR protein activity in patients and their cognate GEMM-DTs were successfully validated, including in two cognate allografts and one cognate patient derived xenograft (PDX). OncoLoop is highly generalizable and can be extended to other cancers and potentially other pathologdiseasesies.

overall_design: 1728 RNAseq profiles of perturbed cell-lines with FDA-approved drugs and late-stage experimental compounds. Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.   Samples were prepared and sequences in batches of 96 that included 6 vehicle (DMSO) and 6 water controls.  2 replicates were taken for each drug-cell-line pair.

first: Eugene

last: Douglass

first: Andrea

last: Califano

first: Mariano

last: Alvarez

first: Charles

last: Karan

first: Ronald

last: Realubit


title: Expression data from MCF10A cells treated with TGFβ for multiple time points

first: Andrew

last: Emili

platform_organism:
Homo sapiens
synthetic construct


title: Differential expression and correlation analysis of miRNA–mRNA profiles in longissimus dorsi of different stage goats

status: Public on Nov 09 2022

city: Nanning

first: Sanbao

address: No.100,Daxue East Road

institute: Guangxi University

summary: MicroRNAs (miRNAs) are small non-coding RNAs that regulate the post transcriptional control of several pathway intermediates, and essential for regulation in skeletal muscle of many species, such as mice, cattle, pig and so on. However, a little number of miRNAs have been reported in the muscle development of goat. In this study, the longissimus dorsi transcripts of goat at 1- and 10-month-old were analyzed for RNA-seq and miRNA-seq. The results showed that 10-month-old Longlin goat expressed 327 up- and 419 down-regulated differentially expressed genes (DEGs) compared with the 1-month-old were founded. In addition, 20 co-up-regulated and 55 co-down-regulated miRNAs involved in muscle fiber hypertrophy of goat were identified in 10-month-old Longlin and Nubian goat compared with 1-month-old. Five miRNA–mRNA pairs (chi-let-7b-3p-MIRLET7A, chi-miR193b-3p-MMP14, chi-miR-355-5p-DGAT2, novel_128-LOC102178119, novel_140-SOD3) involved in the goat skeletal muscle development were identified by miRNA–mRNA negative correlation network analysis. Our results provided an insight into the functional roles of miRNAs of goat muscle-associated miRNAs, allowing us to better understand the transformation of miRNA roles during mammalian muscle development.

first: Qinyang

last: Jiang

first: Mingsheng

first: Qiongwen


title: Single cell transcriptomics of the tumor immune microenvironment from checkpoint blockade-treated and/or TBK1 inhibitor-treated B16-OVA tumors

first: Seth

last: Anderson

summary: Recent studies have demonstrated critical roles for TBK1 in regulation of activity of numerous immune cell types, including T cells, B cells, dendritic cells, and macrophages. To examine the effect of TBK1 inhibition on the tumor immune microenvironment, we performed scRNA-seq on CD45+ cells from B16-OVA tumors from mice treated with anti-PD-1, TBK1i, or anti-PD-1 plus TBK1i, compared to isotype control (IgG).

overall_design: B16-OVA tumors were treated with either anti-PD1 monoclonoal antibody or isotype IgG by IP injection on days 1, 2, 4, 6, 8, and 11 post tumor challenge and either TBK1 inhibitor or vehicle by oral gavage daily for 18 days post tumor challenge. CD45+ cells were isolated from B16-OVA tumors and analyzed using scRNA-seq (10X Genomics, 3'v2 chemistry).

first: Robert

last: Manguso

first: Russell

last: Jenkins


title: RNAseq and the histone acetylated chromosome immunoprecipitation of U87 or GBM stem cells(GSC) treated with bulk control/0.5mM 8-cpt-cAMP/1nM MS275 or a combination

status: Public on Oct 17 2022

city: Guangzhou

first: liu

last: xincheng

address: zhongshan Road 74 Street

institute: sysu

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Transcriptomics and the ChIP-seq revealed that the combination of 8-cpt-cAMP and MS275 could maximize the glioma differentation compared to control or use either drug alone

overall_design:
U87 cells/Glioblastoma stem cells were treated with bulk control(V)/0.5mM 8-cpt-cAMP(C)/1nM MS275 (M) or a combination (CM) for 48 hours. Total RNA was extracted from 1×10^6 cells with TRIzol Reagent (Thermo Fisher Scientific) and was sent for RNA sequencing.

Submitter states that the raw data files for the ChIP-seq samples have been lost.

first: Xincheng

last: Liu


title: A human STAT3 gain-of-function variant confers T cell dysregulation without predominant Treg dysfunction in mice

status: Public on Oct 14 2022

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Center of lesional skin gene expression in plaque type psoriasis

status: Public on Oct 11 2022

city: Klong Luang

first: Onjira

last: Jumlongpim

state: Pathumthanii

address: Chulabhorn international college of medicine, 99 Moo 18

department: Dermatology

country: Thailand

institute: Chulabhorn International College of Medicine, Thammasat University

summary:
Purpose: To identify the gene expression and upstream regulator at lesional skin of psoriasis vulgaris
Methods:Full-thickness skin biopsies at lesional skin and uninvolved skin were taken from psoriasis patients. Transcriptomic profiling was constructed by high-throughput next-generation sequencing (NGS) technology
Result:The total of 1328 DEGs are identified. Among these 1328 DEGs, 648 were upregulated and 680 were down regulated . Upstream regulators involving in keratinocyte proliferation was predicted to be activated.  These DEGs and upstream regulator may be associated with psoriasis pathogenesis
Conclusion: This study revealed upstream regulator that may be involved in psoriasis pathogenesis

overall_design: Expression profile lesion and uninvovled skin mRNA

first: Suphagan

last: Boonpetkaew

first: Jitlada

last: Meephansan

first: Sasin

last: Charoensuksira

first: Pattarin

last: Tangtanatakul

first: Jongkonnee

last: Wongpiyabovorn

first: Mayumi

last: Komine


title: Multi-omic analysis of homologous recombination deficient, end-stage ovarian cancer [Expression]

city: Melbourne

first: Elizabeth

last: Christie

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary: High grade serous ovarian cancer (HGSC) is frequently characterized by homologous recombination (HR) DNA repair deficiency, and while most such tumors are sensitive to initial treatment, acquired resistance is common. We undertook a multi-omics approach to interrogate the molecular diversity in end-stage disease, using multiple autopsy samples collected from 15 women with HR-deficient HGSC. Patients had polyclonal disease, and several resistance mechanisms were identified within most patients, including reversion mutations and HR restoration by other means. We also observed frequent whole genome duplication, and global changes in immune composition with evidence of immune escape. This analysis highlights diverse evolutionary changes within HGSC that conspire to evade therapy and ultimately overwhelm individual patients.

overall_design:
Transcriptomic profiling was done on 45 end stage high grade serous ovarian cancer samples, 41 of which were autopsy tumors, 3 primary tumors and 1 ascites sample. 38 primary samples and 6 autopsy samples from GSE209964 were also used as part of the cohort.
NOTE: the raw FASTQ files are still being uplaoded to EGA so we will update the GEO submission later once we have the study ID for the raw data

first: Nikki

last: Burdett

first: Ahwan

last: Pandey

first: David

last: Bowtell


title: Tumor-specific immunity is enhanced by differentiation of stem-like memory T cells in the bone marrow

status: Public on Oct 01 2022

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

summary: Expanding stem-like memory T cells and depleting exhausted alloreactive T cells is the key to enhancing graft-versus-tumor effects.

overall_design: 2 samples

first: Simone

last: Minnie

first: Geoffrey

last: Hill


title: Oligodendrocyte-lineage cell-secreted L-type prostaglandin D synthase promotes oligodendrocyte differentiation and myelination

city: los angeles

first: lin

last: Pan

address: 2203 glendon avenue

department: Psychiatry

institute: UCLA

summary: We used RNA sequencing to examine the transcriptional changes in differentiated oligodendrocytes, oligodendrocyte precursor cells, astroctytes, and microglia after blocking exocytosis from oligodendrocyte-lineage cells

overall_design: Examine the transcriptional changes in differentiated oligodendrocytes, oligodendrocyte precursor cells, astroctytes, and microglia bettween control mice and Pdgfra-creER:ibot mice

first: Lin

first: Ye

last: Zhang


title: Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity

status: Public on Nov 01 2022

city: Paris

last: Bikard

address: 28 rue du Dr Roux

institute: Institut Pasteur

overall_design: Refer to individual Series


title: Multiscale fractal shape cues support hierarchical assembly and maturation of podocytes via curvature-induced extracellular matrix patterning

status: Public on Oct 06 2022

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: Nature efficiently self-organizes cells and tissues into complex fractal forms. Whether fractal patterning contributes functionally to maturation, and how cells sense and interpret such shape cues, is not well understood. Using kidney podocytes as a model system, bioinspired templating of glomerular histology was leveraged to design controlled fractal 2½ -D surfaces for cell culture. Microcurvature was associated with charge density gradients in space, found to direct extracellular matrix protein organization resulting in hierarchical assembly of cell structures and fractally-branching podocyte morphology in vitro, outlined with a novel fluorescent assaying technique. Shape simulation was uniquely associated with mature-like foot processes on an organized ECM. In applications of drug testing, coronavirus infection, and a cells-as-sensors approach to patient serum diagnostics, fractally stimulated cells were more responsive than flat cultures. Fractal frameworks may thus provide a functional role in podocyte maturation and could serve to advance other bioengineered systems.

overall_design: Biomimetic fractal topography modulates charge density gradients to orchestrate cell attachment and drive development.

first: Anastasia

last: Korolj

first: Praful

last: Aggarwal

first: Teng

last: Cui

first: Xin

last: Song

first: Laleh

last: Shamaei

first: Naimeh

last: Rafatian

last: Radisic

first: Sonia

last: Rodriguez-Ramirez

first: Chuan

last: Liu

first: Matthew

last: Li

first: Karl

last: Wagner

first: Sergi

last: Clotet-Freixas

last: Virlee

first: Mohtada

last: Sadrzadeh

first: Tobin

last: Filleter

first: Ana

last: Konvalinka

first: Milica


title: Glycation-mediated tissue-level remodeling of brain meningeal membrane by aging

status: Public on Oct 26 2022

city: Daejeon

first: Hyo Min

last: Kim

address: 291 Daehak-ro

department: Department of Bio and Brain Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: We performed bulk transcriptomic analysis to examine how glycation-modified collagen further impacts the function of meningeal fibroblasts. We preprocessed raw data to align bulk RNA-seq using STAR (detailed in Experimental Section) and identified differentially expressed genes (DEGs), especially ECM-related gene sets.

overall_design:
One biological sample of human leptomeninges-derived fibroblast cells was analyzed for each of 2 conditions:
VC – vitrified collagen membrane without glycation
GVC – vitrified collagen membrane with glycation

first: Pilnam


title: Extended longevity geometrically-inverted proximal tubule organoids

status: Public on Oct 07 2022

city: Atlanta

first: Shuichi

last: Takayama

state: GA

address: 950 Atlantic Dr NW

department: Biomedical Engineering

institute: Georgia Institute of Technology

summary: This study reports the cellular self-organization of primary human renal proximal tubule epithelial cells (RPTECs) around a minimal Matrigel scaffold to produce basal-in and apical-out proximal tubule organoids (tubuloids). These tubuloids are produced and maintained in hanging drop cultures for 90+ days, the longest such culture of any kind reported to date. The tubuloids upregulate maturity markers, such as aquaporin-1 (AQP1) and megalin (LRP2), and exhibit less mesenchymal and proliferation markers, such as vimentin and Ki67, compared to 2D cultures. They also experience changes over time as revealed by a comparison of gene expression patterns of cells in 2D culture and in day 31 and day 67 tubuloids. Gene expression analysis and immunohistochemistry reveal an increase in the expression of megalin, an endocytic receptor that can directly bind and uptake protein or potentially assist protein uptake. The tubuloids, including day 90 tubuloids, uptake fluorescent albumin and reveal punctate fluorescent patterns, suggesting functional endocytic uptake through these receptors. Furthermore, the tubuloids release kidney injury molecule-1 (KIM-1), a common biomarker for kidney injury, when exposed to albumin in both dose- and time-dependent manners. While this study focuses on potential applications for modeling proteinuric kidney disease, the tubuloids may have broad utility for studies where apical proximal tubule cell access is required.

overall_design: Total RNA was isolated from renal proximal tubule epithelial cells (RPTECs) grown in 2D well-plate culture, day 31 and Day 67 RPTEC organoids grown in hanging drop culture.

first: Eric

last: Parigoris

first: Ji-Hoon

last: Lee

first: Amy

first: Xueying

last: Zhao


title: Gene expression profile at single cell level of PBMC from a CID patient (P) caused by IRF4 p.T95R heterozygous mutation and an age-matched healthy control (HC)

status: Public on Oct 24 2022

city: Shanghai

first: Qing

last: Min

address: DongAn Road

institute: Fudan University

summary: To assess the global changes in PBMC subsets distribution and gene expresion of a CID patient (P) caused by IRF4 p.T95R heterozygous mutation, we performed single-cell RNA sequencing (scRNA-seq) of PBMC isolated from P and HC

overall_design: PBMC were isolated with the use of Ficoll density gradient centrifugation and analyzed using scRNAseq.

first: Ji-Yang

last: Wang

first: Xiaochuan

first: Bijun

last: Sun


title: Dose-specific Efficacy of Adipose-derived Mesenchymal Stem Cells in Septic Mice

status: Public on Oct 05 2022

city: Chengdu

first: Tao

state: Sichuan

address: No.1, Keyuan 4 Rd

department: Regenerative Medicine Research Center

institute: Sichuan University West China Hospital

summary: Mesenchymal stem cells (MSCs) therapy for sepsis has been extensively studied in the past decade, however, the treatment regimen and mechanism of action of MSCs remain elusive. Here, we attempted to understand the efficacy and mechanism of action of MSCs on rescuing mice with sepsis. A mouse model of sepsis was produced by cecal ligation and puncture (CLP). Allogeneic adipose-derived MSCs (ADSCs) were administered by intravenous infusion at 6 h after CLP, and dose-related effects of ADSCs on these mice were determined by survival rate, histopathological changes, biochemical and coagulation parameters, bacterial load, and plasma levels of endotoxin and inflammatory cytokines. The tissue distribution of intravenously infused ADSCs in septic mice was investigated by pre-labeling ADSCs with the lipophilic membrane dye PKH26. RNA sequencing analysis was performed to assess the transcriptional changes in peripheral blood mononuclear cells (PBMCs) and the liver. A significant therapeutic effect of ADSCs at a dose of 2×107 cells/kg in septic mice was evidenced by a remarkable reduction in mortality (36% vs 9% survival rate), blood bacterial burden, systemic inflammation, and multiple organ damage. In contrast, ADSCs at a lower dose (1×107 cells/kg) failed to achieve any beneficial outcomes, while ADSCs at a higher dose (4×107 cells/kg) caused more early death within 24 hours after CLP, retaining a steady survival rate of 21% thereafter. PKH26-labeled ADSCs were predominantly localized in the lungs of septic mice after intravenous infusion, with only a smaller proportion of PKH26-positive signals appearing in the liver and spleen. RNA-sequencing analysis identified that insufficient phagocytic activity of PBMCs in addition to a hyperactivation of the hepatic immune response was responsible for the ineffectiveness of low-dose ADSCs therapy, and acute death caused by high-dose ADSCs infusion was associated with impaired coagulation signaling in PBMCs and exacerbated hepatic hypoxic injury. Our findings demonstrate a dose-specific effect of ADSCs on the treatment of sepsis due to dose-related interactions between exogenous stem cells and the host’s microenvironment. Therefore, a precise dosing regimen is a prerequisite for ADSCs therapy for sepsis.

overall_design: Different doses of ADSCs (1×107, 2×107 or 4×107 cells/kg, resuspended in 0.2 mL of 1% albumin solution) or vehicle (1% albumin) were administered intravenously at 6 h after CLP surgery via the tail vein. To determine the dose-related mechanisms of action of ADSCs, RNA-sequencing analysis was performed in PBMCs and liver in CLP mice at 6 h after vehicle or different doses of ADSCs treatment.

first: Kui

first: Rui

first: Fulai

last: Xue

first: Guodan

last: Zeng

first: Jingyao

last: Zhang

first: Yuan

last: Ma

first: Li

last: Feng

first: Y

last: Kang


title: Distinct pathogenic roles for resident and monocyte-derived macrophages in lupus nephritis

city: Brisbane

first: Zewen Kelvin

last: Tuong

state: QLD

address: 62 Graham Street, Centre for Children's Health Research (CCHR), South Brisbane, QLD, 4101

institute: The University of Queensland

summary: Lupus nephritis is a serious complication of systemic lupus erythematosus, mediated by IgG immune complex (IC) deposition in kidneys, with limited treatment options. Kidney macrophages are critical tissue sentinels that express IgG-binding Fcγ receptors (FcγRs), with previous studies identifying prenatally seeded resident macrophages as major IC responders. Using single-cell transcriptomic and spatial analyses in murine and human lupus nephritis, we sought to understand macrophage heterogeneity and subset-specific contributions in disease. In lupus nephritis, the cell fate trajectories of tissue-resident (TrMac) and monocyte-derived (MoMac) kidney macrophages were perturbed, with disease-associated transcriptional states indicating distinct pathogenic roles for TrMac and MoMac subsets. Lupus nephritis–associated MoMac subsets showed marked induction of FcγR response genes, avidly internalized circulating ICs, and presented IC-opsonized antigen. In contrast, lupus nephritis-associated TrMac subsets demonstrated limited IC uptake, but expressed monocyte chemoattractants, and their depletion attenuated monocyte recruitment to the kidney. TrMacs also produced B cell tissue niche factors, suggesting a role in supporting autoantibody-producing lymphoid aggregates. Extensive similarities were observed with human kidney macrophages, revealing cross-species transcriptional disruption in lupus nephritis. Overall, our study suggests a division of labor in the kidney macrophage response in lupus nephritis, with treatment implications — TrMacs orchestrate leukocyte recruitment while MoMacs take up and present IC antigen.

overall_design:
Kidney MNPs were isolated by Fluorescence-activated cell sorting (FACS) according to F4/80 and CD11b expression pattern and 10x Genomics 3' single-cell sequencing was performed on sorted cells.

Please note that the processed data file for the GSM6630647 MRL-Lpr sample has been replaced on Mar 14, 2023.

first: Zewen

first: Nathan

last: Richoz

first: Menna

last: Clatworthy


title: Selective disruption of NRF2-KEAP1 interaction leads to NASH resolution and reduction of liver fibrosis in mice

status: Public on Sep 07 2022

city: Croissy-sur-Seine

first: Fabien

last: MELCHIORE

address: 125 chemin de Ronde

institute: Servier IdRS

summary: The transcription factor NRF2 and its negative regulator KEAP1 are master regulators of redox, metabolic and protein homeostasis, detoxification and appear therefore as attractive drug targets for the treatment of NASH. S217879 a small molecule disrupting the KEAP1-NRF2 interaction has been highly characterized using various molecular and cellular assays. It was then evaluated in two different NASH-relevant preclinical models, and RNAseq data were obtained with samples from Diet-induced Obesity NASH (DIO NASH) mouse model. In DIO NASH mice, S217879 treatment resulted in a significant improvement of established liver injury with clear reduction in both NAS score as well as liver fibrosis. Alpha SMA and Col1A1 staining as well as quantification of liver hydroxyproline levels confirmed the reduction in liver fibrosis in response to S217879. RNA seq analyses revealed major alterations in the liver transcriptome in response to S217879 with activation of NRF2-dependent gene transcription as well as a marked inhibition of key signaling pathways driving disease progression

overall_design: Comparative gene expression profiling analysis of RNA-seq data from liver samples of ctrl or pharmacologically treated mice (DIO induced NASH mouse model)

first: Klaus

last: Seedorf

first: Csaba

last: Weber

first: Cedric

last: Vinson

first: Sylvie

last: Berger

first: Laurent-Michel

last: Vuillard

first: Arpad

last: Kiss

first: Stephanie

last: Creusot

first: Olivier

last: Broux

first: Anne

last: Geant

first: Catherine

last: Ilic

first: Karine

last: Lemaitre

first: Julien

last: Mahieux

first: Virginie

last: Martigny

first: Didier

last: Durand

last: Melchiore

first: Miklos

last: Nyerges

first: Nicolas

last: Provost

first: Valérie

last: Duvivier

first: Philippe

last: Delerive


title: A 3´ UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria

status: Public on Sep 28 2022

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

summary: Increasing numbers of small, regulatory RNAs (sRNAs) corresponding to 3´ untranslated regions (UTR) are being discovered in bacteria. One such sRNA, denoted GlnZ, corresponds to the 3´ UTR of the Escherichia coli glnA mRNA encoding glutamine synthetase. Several forms of GlnZ, processed from the glnA mRNA, are detected in cells growing with limiting ammonium. GlnZ levels are regulated transcriptionally by the NtrC transcription factor and post-transcriptionally by RNase III. Consistent with the expression, E. coli cells lacking glnZ show delayed outgrowth from nitrogen starvation compared to wild type cells. Transcriptome-wide RNA-RNA interactome datasets indicated that GlnZ binds to multiple target RNAs. Immunoblot and assays of fusions confirmed GlnZ-mediated repression of glnP and sucA, encoding proteins that contribute to glutamine transport and the citric acid cycle, respectively. Although the overall sequences of GlnZ from E. coli K-12, Enterohemorrhagic E. coli and Salmonella enterica have significant differences due to various sequence insertions, all forms of the sRNA were able to regulate the two targets characterized. Together our data show that GlnZ promotes survival of E. coli under low nitrogen conditions by modulating genes that affect carbon and nitrogen flux.

overall_design: Application of MS2 affinity purification followed by RNA-seq (MAPS) to strains expressing MS2-GlnZ or MS2 control, in order to identify GlnZ RNA binding partners.

first: Lauren

last: Walling

first: Andrew

middle: B

last: Kouse

first: Svetlana

last: Shabalina

first: Hongen

last: Zhang

first: Gisela

last: Storz


title: Gene expression profile at single cell level of peripheral blood B cells from a CID patient (P) caused by IRF4 p.T95R heterozygous mutation and an age-matched healthy control (HC)

first: Qing

last: Min

summary: To assess the global changes in B cell maturation and differentiation of a CID patient (P) caused by IRF4 p.T95R heterozygous mutation, we performed single-cell RNA sequencing (scRNA-seq) of peripheral B cells isolated from P and HC

overall_design: Peripheral B cells of P and HC were sorted by Fluorescence-activated cell sorting (FACS) according to the expression of CD19 and analyzed using scRNAseq.

first: Ji-Yang

last: Wang

first: Xiaochuan

first: Wenjie


title: A human STAT3 gain-of-function variant confers T cell dysregulation without predominant Treg dysfunction in mice [single cell RNA-seq]

first: Megan

last: Cooper

summary: Primary immune regulatory disorders (PIRD) are a group of disorders characterized by immune dysregulation, presenting with a wide range of clinical disease including autoimmunity, autoinflammation, or lymphoproliferation. Autosomal dominant germline gain-of-function (GOF) variants in STAT3 result in a PIRD with a broad spectrum of clinical features and prior studies have documented a decreased frequency of Foxp3+ regulatory T (Treg) cells and an increased frequency of Th17 cells is some patients. However, the precise mechanisms of disease pathogenesis in STAT3 GOF syndrome remain largely unknown. We developed a knock-in mouse model harboring a de novo pathogenic human STAT3 variant (p.G421R) and found these mice developed T cell dysregulation, lymphoproliferation and CD4+ Th1 cell skewing. Surprisingly, Treg cell numbers, phenotype, and function remained largely intact, however mice had a selective deficiency in the generation of iTreg cells. In parallel, we performed single-cell RNA-sequencing on T cells from patients with STAT3 GOF syndrome. We demonstrate only minor changes in the Treg cell transcriptional signature and an expanded, effector CD8+ T cell population. Together, these finding suggest Treg cells are not the primary driver of disease and highlight the importance of preclinical models in the study of disease mechanisms in rare PIRD.

overall_design: 3 healthy age- and sex-matched donors (C1-C3) and 3 patients with STAT3 GOF syndrome (P1-P3)

first: Erica

last: Schmitt

first: Ana

last: Kolicheski


title: Alteration of the N6-methyladenosine Epitranscriptome Profile in Synthetic Phthalate-treated Human Induced Pluripotent Stem Cell-Derived Endothelial Cells

status: Public on Oct 10 2022

city: Chicago

first: Jordan

last: Jousma

state: Illinois

address: 909 South Wolcott

department: Pharmacology and Regenerative Medicine

institute: University of Illinois


title: A human STAT3 gain-of-function variant confers T cell dysregulation without predominant Treg dysfunction in mice [bulk RNA-seq]

overall_design: bulk RNA-seq


title: Cerivastatin synergizes with trametinib and enhances its efficacy in the therapy of Uveal Melanoma

status: Public on Aug 31 2022

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

summary: Background and Aims:  Uveal melanoma (UM), the most common primary intraocular tumor in adults, is characterized by marked variability in its ability to metastasize. In fact, up to half the patients with UM develop distant metastases, most commonly to the liver. Mutations in alpha G-protein subunits, GNAQ and GNA11, are found in most primary UM, in a mutually exclusive pattern. Also, mutations in SF3B1, EIF1AX, and BAP1, are associated with markedly distinct prognoses Targeted therapy with MAP kinase inhibitors has been unsuccessful in the treatment of uveal melanoma (UM). The constitutive activation of GNAq and GNA11, typical of MU, determines the activation not only of the MAP kinases but also of the transcription factors YAP / TAZ. It is known that when statins are used to inhibit the HMGCR activity in the mevalonate pathway, the nuclear localization and transcriptional activity of YAP-TAZ are also inhibited mediating a potential anti-cancer activity  Methods: We investigated the sensitivity to drugs of a panel of 6 lines of MU, two metastatic and 4 derived from primary tumors, of the latter two were monosomic. We established the IC50s of the individual drugs and the effects of the combinations. The synergistic effects of drugs were studied using MTT proliferation tests, cell cycle and apoptosis. The most synergistic combination was tested in vivo in NSG mice.  Results: The synergistic concentrations of trametinib and cerivastatin (T+C) induced a massive arrest of proliferation and cell cycle and an increase of apoptosis 72 hours after the start of treatment particularly in the monosomic, BAP1 mutated UPMM3 cell line. The synergistic effect of T+C was reached after 7 instead of 3 days. In the metastatic OMM2.5 cell line. T+C treatments reduced ERK and AKT phosphorylation and increased the cytoplasmatic, inactive form of YAP. T+C treatment of NSG mice transplanted with the monosomic UM cell line reduced significantly tumor growth.  Conclusion: This study suggests that statins potentiate the efficacy of MEK inhibitors in the therapy of UM

overall_design: Twelve different uveal melanoma cell lines UPMM3. Cell were treated with  Trametinib 10nM; Cerivastatin 0.125 microM; Cerivastatin 0.125 microM+Trametinb  10nM for 24 hours. Cell were analyzed in triplicate.

first: Rosaria

last: Gangemi

first: Laura

last: Emionite

first: Gilberto

last: Filaci

first: Patrizio

last: Castagnola

first: Martine

last: Jager

first: Ulrich

last: Pfeffer

first: Michela

last: Croce


title: Cohesin regulates alternative splicing alone or with BRD4

first: Dinah

middle: S.

last: Singer

address: Building 10, Room 4B-17

department: Division of Cancer Biology

institute: National Cancer Institute

summary: By targeted depletion of Cohesin (RAD21 subunit) or BRD4 alone or together, we have established that cohesin alone or with BRD4 regulates the alternative splicing of a large subset of genes under both physiological and heat shock conditions.

overall_design: We examined by RNA-seq the effect on gene expression and alternative splicing of cohesin and BRD4 deletion alone or together under physiological and heat shock conditions. Targeted degradation of RAD21 was mediated by an auxin-inducible degron (AID) system (HCT116RmAC cells, RAD21 alleles are fused with a minimal AID tag) and the targeted depletion of BRD4 in HCT116RmAC cells was achieved by treating with MZ1, a proteolysis targeted chimera (PROTAC), under conditions leading to selective degradation of BRD4.

first: A

last: Singh

first: Q

last: Chen

first: D

last: Meerzaman


title: Novel estrogen-responsive genes (ERGs) for the evaluation of estrogenic activity

status: Public on Aug 26 2022

city: Fukuoka

first: Kentaro

last: Nishi

address: 2-3-1 Matsukadai Higashi-ku

department: Life Science

institute: Kyushu sangyo university

summary: Estrogen action is mediated by various genes including estrogen-responsive genes (ERGs). ERGs have  been used as markers for gene expression and as reporter-genes, while gene expression profiling using a set  of ERGs has been used as statistically reliable transcriptomic assays, such as DNA microarray assays and  RNA-seq. However, the quality of ERGs has not been extensively examined. Here, we found a set of 300  ERGs newly identified by six sets of RNA-seq data obtained from estrogen-treated and control human  breast cancer MCF-7 cells. The ERGs exhibited statistical stability as judged by the coefficient of variation  (CV) analysis, and their usefulness as markers for estrogenic activity by examining the stability of data in  the study of correlation analysis, and functional association with estrogen action through database searches.  A set of the top 30 genes based on CV ranking were further evaluated quantitatively by RT-PCR and  qualitatively by a functional analysis using GO and KEGG databases and by a mechanistic analysis to  classify ERα/β-dependent or ER-independent types of transcriptional regulation. The 30 ERGs were  characterized by (1) the enzymes, such as metabolic enzymes, proteases and protein kinases, (2) the genes  with specific cell functions, such as cell-signaling mediators, tumor-suppressors and the roles in breast  cancer, (3) the association with transcriptional regulation, and/or (4) estrogen-responsiveness. Therefore,  the ERGs identified here could represent various cell functions and cell signaling pathways including  estrogen signaling, and thus, would be useful to evaluate estrogenic activity.

overall_design: MCF-7 cells at a density of 1.0×10^6 cells per well were cultured in RPMI1640 supplemented with 10% DCC-FBS for 3 days under the conditions of 37°C in 5% CO2. The cells were treated in RPMI1640 including 10 nM E2, 1 µM ICI or 0.1% DMSO (vehicle) for 2 more days.

first: Wenqiang

last: Fu

first: Ryoiti

last: Kiyama


title: Transcriptomic analysis of acute stress in goats

status: Public on Aug 14 2022

city: fort valley

first: phaneendra

last: batchu

state: georgia

address: 1005 State univerity drive

department: Animal Science

institute: fort valley state university

summary: Transportation stress causes significant changes in physiological responses in goats; however, studies exploring the transcriptome of stress are very limited.  This study was conducted to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology.  Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control). Blood samples were collected before and after treatment for stress hormone, metabolite, and transcriptomic analysis. RNA-Seq technology was used to obtain the transcriptome profiles of blood.  Analysis of physiological data using SAS showed that plasma cortisol concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group. A similar effect was noticed in plasma non-esterified fatty acid concentrations.  Glucose concentrations were the lowest in the control group, highest in the 180 min group, and intermediate in the 30 min group (P < 0.01, while plasma creatine kinase concentrations were not significantly influenced by TRT.  Neutrophil counts were higher (P < 0.01) and lymphocyte counts were lower (P < 0.01) in 180 min group compared to 30 min or control groups.  The DESeq2 software identified a total of 430 DEGs for control vs. 30 min comparison, of which 127 genes were upregulated.  For 180 min vs. control comparison, 741 DEGs were upregulated.  Enrichment analysis of DEGs related to transportation stress through Gene Ontology and KEGG databases revealed that the DEGs related to inflammatory pathways, caspases, and apoptosis such as IL1R2, CASP14, CD14, TLR4, and MAPK14 were highly expressed in the transported group of goats compared to non-transported goats.  Stress in goats leads to a sequence of events at cellular and molecular levels that causes inflammation and apoptosis and is also reflected in blood metabolites and leukocyte counts.

overall_design: The protocols for this research were approved by the Animal Care and Use Committee at Fort Valley State University prior to beginning of the experiment. A total of fifty-four uncastrated male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (i) transported for 30 min (approx. 50 km), (ii) transported for 180 min (approx. 200 km), or (iii) held in pens (control), on two different days. A livestock trailer with internal floor dimensions of 4.5 × 1.8 m were used to transport the goats. The ambient temperatures were -3.0 ± 1.0 ºC and 1.0 ± 1.0 ºC on day 1 and 2, respectively. Prior to the experiment, goats were primarily raised on free range pasture with a grain supplement and with ad libitum access to hay and water. Feed was withheld overnight prior to the day of the experiment.

first: Aditya

last: Naldurtiker

first: Phaneendra

last: Batchu

first: Brou

last: Kouakou

first: Thomas

last: Terrill

first: G

last: McCommon

first: Govind

last: Kannan


title: Whole genome functional characterization of RE1 silencers using a modified massively parallel reporter assay BRB-seq

status: Public on Sep 30 2022

city: Bar Harbor

first: Kousuke

last: Mouri

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

summary: Both upregulation and downregulation by cis-regulatory elements help establish precise gene expression. Our understanding of how elements repress transcriptional activity is far more limited than activating elements. To address this gap, we characterized RE1, a group of transcriptional silencers bound by REST, on a genome-wide scale using an optimized massively parallel reporter assay (MPRAduo). MPRAduo empirically defined a minimal binding strength of REST required by silencer (REST m-value), above which multiple cofactors colocalize and act to directly silence transcription. We identified 1,500 human variants that alter RE1 silencing and found their effect sizes are predictable when they overlap with REST binding sites above the m-value. In addition, we demonstrate that non-canonical REST binding motifs exhibit silencer function only if they precisely align two half sites with specific spacer length. Our results show mechanistic insights into RE1 silencer which allows us to predict its activity and effect of variants on RE1, providing a paradigm for performing genome-wide functional characterization transcription factors binding sites.

overall_design: We knocked out RE1 silencers in HCT116 cells by using CRISPR-Cas9 and measured differential gene expression using BRB-seq.

first: Hannah

last: Dewey

first: Ryan

last: Tewhey


title: RNA sequencing of mouse kidney response to rilmenidine

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

summary: This dataset consists of kidney gene expression profiles of young UM-HET3 mice subjected to rilmenidine for 1 month. Corresponding age-, sex- and strain-matched littermate controls are also presented.  Using this data, we assessed association between gene expression response to rilmenidine in kidney and established signatures of lifespan-extending interventions and aging. This dataset complements corresponding liver data stored at GSE131868.

overall_design: 3-month old UM-HET3 male mice from University of Michigan Medical School were subjected to rilmenidine (10 ppm) for 1 month. Their littermate controls of the same age and sex were also used for the analysis. 4 biological replicates were used for the rilmenidine group, and 6 biological replicates were used for the control group. In all cases, interventions continued until the animals were sacrificed.

first: Vadim

last: Gladyshev


title: Multi-omic analysis of homologous recombination deficient, end-stage ovarian cancer [Methylation]

status: Public on Nov 12 2022

city: Melbourne

first: Elizabeth

last: Christie

state: Victoria

address: 305 Grattan St

institute: Peter MacCallum Cancer Centre

summary:
High grade serous ovarian cancer (HGSC) is frequently characterized by homologous recombination (HR) DNA repair deficiency, and while most such tumors are sensitive to initial treatment, acquired resistance is common. We undertook a multi-omics approach to interrogate the molecular diversity in end-stage disease, using multiple autopsy samples collected from 15 women with HR-deficient HGSC. Patients had polyclonal disease, and several resistance mechanisms were identified within most patients, including reversion mutations and HR restoration by other means. We also observed frequent whole genome duplication, and global changes in immune composition with evidence of immune escape. This analysis highlights diverse evolutionary changes within HGSC that conspire to evade therapy and ultimately overwhelm individual patients.
Methylation profiling was done on 29 end stage high grade serous ovarian cancer samples. 38 primary tumours, 6 autopsy tumours and 7 fallopian tube normals from GSE65820 were also used as part of the cohort.

overall_design: Genome wide DNA methylation profiling of 29 tumours of end stage high grade serous ovarian cancer. The Illumina Infinium MethylationEPIC BeadChip was used to obtain DNA methylation profiles across approximately 850,000 CpGs. 38 primary tumours, 6 autopsy tumours and 7 fallopian tube normals from GSE65820 were also used as part of the cohort.

first: Nikki

last: Burdett

first: Ahwan

last: Pandey

first: David

last: Bowtell


title: Single-Cell RNA-Seq Analysis Reveals Macrophage Involved in Pathogenesis of Human sporadic type A aortic dissection

status: Public on Sep 23 2022

city: Guangzhou

first: Bin

last: Zhang

state: Guangdong

address: 107 Yanjiang West Road

department: Department of Cardiovascular Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

summary: Macrophages play an important role in the progression of sporadic acute type A aortic dissection (ATAAD). The aim of this study was to characterize the cellular heterogeneity of macrophages in AD tissues by scRNA-seq. Ascending aortic wall tissue from 6 ATAAD patients and 3 heart transplant donors were assessed by scRNA-seq, then analyzed and validated by various bioinformatics algo-rithms and histopathology experiments. The results revealed the proportion of macrophages in AD tissues (24.51%) was significantly higher than that in normal tissues (13.69%). Among the 6 macro-phage subclusters, pro-inflammatory macrophages accounted for 14.96% in the AD group, and 0.18% in the normal group. Chemokine and inflammation related genes (CCL2, CCL20, S100A8, and S100A9) were expressed more intensively in macrophages in AD tissue than that in the normal tissues. Ad-ditionally, intercellular communication analysis and transcription factor analysis indicated activation of inflammation and degradation of the extracellular matrix in AD tissues. Finally, immunohisto-chemistry, immunofluorescence and western blot experiments confirmed the overexpression of macrophage marker genes (CD68 and CD163) and matrix metalloproteinases (MMP9 and MMP2) in AD tissues. Collectively, our study provides a preliminary evaluation of the role of macrophages in AD and potentially aid in the development of therapeutic options in the future.

overall_design: We performed scRNA sequencing to understand macrophage function in in Pathogenesis of Human sporadic type A aortic dissection. We analyzed and validated by various bioinformatics algorithms and histopathology experiments.

first: Kuan

last: Zeng

first: Ruicong

last: Guan

first: Yanqi

last: Yang


title: 5-methylcytosine (m5C) RNA modification controls the innate immune response to virus infection by regulating type I interferons

status: Public on Sep 26 2022

first: Li-Sheng

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

summary: Cytosine-5 methylation (m5C) is one of the most prevalent modifications of RNA, playing important roles in RNA metabolism, nuclear export, and translation. However, the potential role of RNA m5C methylation in innate immunity remains elusive. Here we show that depletion of NSUN2, an m5C methyltransferase, significantly inhibits the replication and gene expression of a wide range of RNA and DNA viruses. Notably, we found that this antiviral effect is largely driven by an enhanced type I interferon (IFN) response. The antiviral signaling pathway is dependent on the cytosolic RNA sensor RIG-I but not MDA5. Transcriptome-wide mapping of m5C following NSUN2 depletion in human A549 cells revealed a marked reduction in the m5C methylation of several abundant non-coding RNAs (ncRNAs). However, m5C methylation of viral RNA was not noticeably altered by NSUN2 depletion. In NSUN2-depleted cells, the host RNA polymerase (Pol) III transcribed ncRNAs, in particular RPPH1 and 7SL RNAs, were substantially upregulated, leading to an increased level in unshielded 7SL RNA in cytoplasm, which served as direct ligands for the RIG-I mediated IFN response. In NSUN2 depleted cells, inhibition of Pol III transcription or silencing of RPPH1 and 7SL RNA dampened IFN signaling, partially rescuing viral replication and gene expression. Finally, depletion of NSUN2 in an ex vivo human lung model and a mouse model inhibits viral replication and reduces pathogenesis which is accompanied by enhanced type I IFN responses. Collectively, our data demonstrate that RNA m5C methylation controls antiviral innate immunity through modulating m5C methylome of ncRNAs and their expression.

overall_design: [dataset1] 16 samples (Sample 1-16): Duplicates for bisulfite-seq for RNA m5C detection in total RNA from wild-type and NSUN2-knockout A549 cells, under RSV or VSV infection.  [datase2] 16 samples (Sample 21-36): Duplicates for RIP-seq of RIG-I IP-enriched RNA from wild-type and NSUN2-knockout A549 cells, under RSV or VSV infection. [datase3] 12 samples (Sample 37-48): Triplicates for RNA-seq of "RNA input" and "anti-dsRNA antibody IP-enriched dsRNA" from wild-type and NSUN2-knockout A549 cells.

first: Yuexiu

first: Chuan

last: He

first: Jianrong

last: Li


title: Expanding the prostate cancer cell line repository: insights into the first Caribbean cell line, ACRJ-PC28

status: Public on Sep 15 2022

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I street NW, Ross Hall, Suite 731

institute: George Washington University

summary: Prostate cell lines from diverse backgrounds are important to addressing disparities in prostate cancer (PCa) incidence and mortality rates among Black men. ACRJ-PC28 was developed from a transrectal needle biopsy and established via inactivation of the CDKN2A locus and simultaneous expression of human telomerase. Characterization assays included growth curve analysis, immunoblots, IHC, 3D cultures, immunofluorescence imaging, confocal microscopy, flow cytometry, WGS and, RNA-Seq. RNA-Seq confirmed the expression of prostate specific genes alpha-methylacyl-CoA racemase (AMACR) and NKX3.1 and Neuroendocrine specific markers, synaptophysin (SYP) and enolase 2 (ENO2) and IHC confirmed the presence of AMACR. WGS confirms the absence of exonic mutations and the presence of intronic variants that appear to not affect function of AR, p53 and pRB. RNA-Seq data revealed numerous TP53 and RB1 mRNA splice variants and the lack of AR mRNA expression. The novel cell line described here should advance research addressing the disparity in prostate cancer among Black men.

overall_design: Gene expression profiling via RNA-seq of a prostate cancer cell line derived from a Black Caribbean male patient.

first: Simone

last: Badal

first: Norman

last: Lee


title: Human transthyretin (TTR) gene expression is markedly increased in repair phenotype of hereditary ATTR Schwann cell model

city: Kurashiki

first: Tatsufumi

last: Murakami

address: 577 Matsushima

institute: Kawasaki Medical School

summary: TTR is markedly expressed in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (S-DMEM)-incubated TgS1 cells compared with Schwann cell medium (SCM)-incubated cells. c-Jun, Gdnf, and Sox2 were upregulated in S-DMEM-incubated TgS1 cell compared with SCM-incubated cells, while Mpz is suppressed in them.

overall_design: Total RNA was isolated from SCM and S-DEMEM-incubated TgS1 cells. RNA sequence library preparation, sequencing, mapping, and gene expression analysis were performed.

first: Yuri

last: Ito


title: The immune microenvironment of HPV-negative oral squamous cell carcinoma from never-smokers and never-drinkers patients suggests higher clinical benefit of IDO1 and PD1/PD-L1 blockade

status: Public on Aug 02 2022

city: Lyon

first: PIERRE

last: SAINTIGNY

address: 28 Rue Laennec

institute: Centre Léon Bérard

summary: Background: Never-smokers and never-drinkers patients (NSND) suffering from oral cavity squamous cell carcinoma (OCSCC) are epidemiologically different from smokers drinkers (SD). We therefore hypothesized that they harbored distinct gene expression profiles. Patients and methods: Data from The Cancer Genome Atlas (TCGA) (discovery set), Gene Expression Omnibus and Centre Léon Bérard (CLB) (three validation sets) with available gene expression profiles of HPV-negative OSCC from NSND and SD were mined. Protein expression profiles and genomic alterations were also analyzed from TCGA, and a functional pathway enrichment analysis was carried out. Formalin-fixed paraffin-embedded samples from 44 OSCC including 20 NSND and 24 SD treated at CLB were retrospectively collected to perform targeted-sequencing of 2,559 transcripts (HTG EdgeSeq system). Enrichment of a six-gene interferon-γ signature of clinical response to pembrozulimab (PD-1 inhibitor) was evaluated in each sample from all cohorts, using the single sample gene set enrichment analysis method. Results: A total of 854 genes and 29 proteins were found to be differentially expressed between NSND and SD in TCGA. Functional pathway analysis highlighted an overall enrichment for immune-related pathways in OSCC from NSND, especially involving T-cell activation. Interferon-γ response and PD1 signaling were strongly enriched in NSND. IDO1 and PD-L1 were overexpressed and the score of response to pembrolizumab was higher in NSND than in SD, although the mutational load was lower in NSND. Conclusion: The main biological and actionable difference between OSCC from NSND and SD lies in the immune microenvironment, suggesting a higher clinical benefit of PD-L1 and IDO1 inhibition in OSCC from NSND.

overall_design:
In 40 patients HPV-negative oral cavity squamous cell carcinoma, gene expression profiles were generated using formalin-fixed paraffin embedded biopsies or archival surgically resected specimens collected prior to treatment initiation. Gene expression profiles were generated using HTG EdgeSeq technology and the Oncology Biomarker Panel (OBP).

>>>Submitter states that raw data are currently unavailable. They are working with the sequencing company to retrieve the raw files<<<

first: Jean-Philippe

last: Foy

first: Valery

last: Attignon

first: Lucas

last: Michon

first: Philippe

last: Zrounba

first: Pierre

last: Saintigny


title: Identification of Homoharringtonine as a potent inhibitor of glioblastoma cell proliferation and migration.

status: Public on Jul 29 2022

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

institute: università di padova

summary:
We previously demonstrated that Annexin A2 (ANXA2) is a pivotal mediator of the pro-oncogenic features displayed by glioblastoma (GBM) tumors, the deadliest adult brain malignancies. In GBM, ANXA2 sustains a transcriptional program involved in cell stemness, proliferation and invasion, negatively impacting patient prognosis. Transcriptional signatures obtained by the modulation of ANXA2 activity/levels were functionally mapped through the QUADrATiC bioinformatic tool for compound identification. Selected compounds were screened by cell proliferation and migration assays in primary GBM cells. Screening of compounds selected through QUADrATiC identified HHT as a potent inhibitor of GBM cell motility and proliferation. A further molecular characterization of the effects displayed by HHT, confirmed its ability to inhibit a transcriptional program involved in cell migration and invasion. Moreover, we demonstrated that the multiple antitumoral effects displayed by HHT are correlated to the inhibition of a PDGFRα-dependent intracellular signaling through the impairment of STAT3 and RhoA axes.
Homoharringtonine is a potent inhibitor of GBM cell proliferation and migration

overall_design: Gene expression was measured using Affymetrix platform in primary GBM cells transfected with siNEG or anti-ANXA2 siRNA, and in GBM cells treated or not with homoharringtonine (HHT).

first: Silvia

last: Bresolin

first: Luca

last: Persano


title: Characterization of the Intracellular Behavior of Mirror Image L-Oligonucleotides Reveals the Potent Cytotoxicity of G-Rich L-RNA

status: Public on Sep 01 2022

city: College Station

first: Jonathan

middle: Thomas

last: Sczepanski

state: Texas

address: 580 Ross Street

department: Chemistr y

institute: Texas A&M University

summary: Due to their bioorthogonal properties, such as nuclease resistance, L-oligonucleotides are being increasingly employed in biomedical applications including L-aptamers, microarrays, molecular sensors, and live cell imaging probes. Given the large number of proteins that have been shown to bind nucleic acids in a nonspecific or “promiscuous” manner, it is reasonable to predict that interactions across the mirror are abundant, potentially leading to undesired effects. However how they interact with these environments and their potential consequences is not well studied. In this study, we conducted the first detailed characterization of how L-oligonucleotides interact with biological systems at the cellular level, revealing important stereochemistry-dependent behaviors of L-oligonucleotides. Notably, we show that G-rich L-oligonucleotides have potent cytotoxicity and a dramatic impact on gene expression, suggesting they make extensive interactions with endogenous proteins. In conclusion, the data presented here demonstrates that, similar to chemical modifications, stereochemistry can have a profound effect on the behavior of oligonucleotides in living systems. This work should motivate similar investigations into other modified oligonucleotides, such as XNAs, that are also perceived to be highly bioorthogonal, which may reveal unforeseen biological effects.

overall_design: Comparative gene expression of HeLa cell upon various L-RNA transfection.

first: Chen-Hsu

last: Yu


title: Epigenome-Wide Association Study of Bacillus Calmette Guerin vaccination in human circulating monocytes

city: Parkville

first: Boris

last: Novakovic

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

institute: Murdoch Children's Research Institute

summary: Trained immunity is a phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study profiled genome-wide DNA methylation in purified human monocytes 15 months after BCG vaccination.

overall_design: Newborns were vaccinated with the BCG vaccine within the first 10 days of life and 14-24 months later peripheral blood mononuclear cells were collected. Monocytes were isolated using FACS (CD14+/-, CD16+/-) and genome-wide DNA methylation was measured using the Infinium HumanMethylation EPIC array.

first: Samantha

last: Bannister

first: Richard

last: Saffery

first: Nigel

last: Curtis


title: Epigenome analysis of glycine chloramine treated Jurkat T cells

status: Public on Jul 31 2022

city: Wellington

first: Aarib

middle: John

last: Stevens

address: 23a Mein Street

department: Pathology and Molecular Medicine

country: New Zealand

institute: University of Otago Wellington

summary: Genome wide DNA methylation profiling of Jurkat T lymphoma cell lines, using the human DNA methylationEPIC 850K array. All cells were blocked using a thymidine block, and DNA methylation was analysed 4 hrs post release from the block (S-Phase) or 72 hours later.  Samples are either untreated control (PBS) or treated with Glycine chloramine. Cells were exposed to Glycine chloramine in two independent time points: pre replication (same time as release from block, 3 replicates) or during S-phase (four replicates, 2 hrs post block release). These two exposures were assessed in two independent experiments and therefore have their own controls. Each replicate used cells from a different passage number, and was performed independently.

overall_design: Bisulphite converted DNA from the cells were hybridised to the Illumina Infinium 850K Human MethylationEPIC Beadchip

first: Aaron

first: Annika

last: Seddon


title: Epigenome and gene expression analysis of glycine chloramine treated Jurkat T cells

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

overall_design: Refer to individual Series


title: Gene expression changes associated with reducing Sox2 expression in ovarian cancer cell line PA1 under anchorage independence

status: Public on Jul 26 2022

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

department: Pathology

institute: UAB

summary: Sex-determining region Y- box 2 (Sox2) is a single-exon transcription factor essential for development and in cancer that has been shown to be overexpressed broadly in many cancers including multiple ovarian cancer subtypes. The objective of this study is to examine the effect of changing Sox2 expression under the conditions of anchorage independent growth that is known to drive the expression of survival genes. We compared genome wide gene expression profiles of the ovarian tumor cell line PA1 upon transient knockdown of Sox2 expression using siRNA and compared to negative silencer control siRNA cells. Cells grown in biological triplicates were transfected under steady state 2D growth conditions and then transferred to poly-hema coated plates to prevent attachment. After 72 hrs, RNA was collected from siSox2 and sicontrol cells followed by verification of reduction in Sox2 levels at the protein and RNA levels . Our analysis of the RNA seq results revealed 59 differentially expressed genes (DEG) between sicontrol and siSox2 cells (p-value ≤ 0.05) of which 52 were protein coding. Of the 59, 35 genes were upregulated in siSox2 and 24 genes were downregulated in the siSox2 cells .  Gene set enrichment analysis of all the differentially expressed genes from the RNA-seq data revealed enrichment of 8 gene sets based on an FDR value <25% and included ‘hallmark of Apoptosis’, ‘TGF-β signaling’, and ‘Epithelial-Mesenchymal transition’ in siSox2 cells and hallmark interferon alpha response and interferon gamma response in sicontrol cells. Several transcription factors with prior established relationships to Sox2 including several PARP family members and TRIM family members were present in these gene sets.

overall_design:
mRNA sequencing of human ovarian ovarian teratocarcinoma (PA1) cells, control and Sox2 reduction with siRNA
Two siRNAs to human Sox2 or negative silencer control obtained from Ambion used to transfect PA1 cells grown in 2D. After 24 hrs, cells were transferred to poly hema coated non adherent plates for 3D growth for an additional 72 hrs followed by RNA extraction.

first: Mythreye

last: Karthikeyan

first: C

first: Abigail

last: Shelton

first: Zainab

last: Shonibare

first: Mehri

last: Monavarian


title: Gene expression profiling in PA1 ovarian cancer cells under anchorage independence either in the presence of vehicle or BMP9 treatment for 24 hours

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

summary: BMP9 promotes anoikis sensitivity in cancer cell lines. Here we examine the changes in gene expression in response to BMP9 in cells under anoikis to identify potential pathways associated with anoikis sensitivity.

overall_design: 6 total samples were analyzed. We performed a pairwise comparison of PA-1 cell line in presence or absence of BMP9. Genes with a p-valued < 0.05 and a fold-change ≥ 2.0 were selected.


title: Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements  [ChIP-seq]

status: Public on Jul 19 2022

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

institute: National Chengchi University

summary: CTCF and Cp190 proteins are implicated at many insulator elements throughout Drosophila genome. Here we compared Hi-C maps, transcriptomes and binding of multiple insulator proteins in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos.

overall_design: ChIP-seq experiments in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos. Two experiments started from independently grown cell cultures were performed for each genetic background and antibody.

first: Tatiana

last: Kahn

first: Mikhail

last: Savitsky

first: Caroline

last: Jacquer

first: Giacomo

last: Cavalli

first: Yuri

last: Schwartz


title: Validation of mRNA markers differentiating among human ARDS subgroups in an ovine model of ARDS phenotypes

status: Public on Jul 27 2022

city: Brisbane

first: Kieran

last: Hyslop

state: Queensland

address: Lvl 3, Clinical Sciences Building 627 Rode Road CHERMSIDE

department: Faculty of Medicine

institute: University of Queensland

summary: Comparison of a subset of mRNA markers previously discribed in leukocytes of human ARDS patients with lung tissue expression in ovine ARDS phenotype 1 and phenotype 2 models

overall_design: 23 anesthetized sheep on mechanical ventilation were randomly allocated to one of two ARDS phenotypes (phenotype 1 (Ph1), hypoinflammatory or phenotype 2 (Ph2), hyperinflammatory) and observed for between 6 and 24 hours.

first: Karin

last: Wildi


title: Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements


title: Topological screen identifies hundreds of Cp190 and CTCF dependent Drosophila chromatin insulator elements [HiC]

overall_design: HiC experiments in cultured Drosophila cells derived from CTCF-KO, Cp190-KO and control embryos. Two experiments started from independently grown cell cultures were performed for each genetic background.


title: Identifying the Key Genes Regulating Mesenchymal Stem Cells Chondrogenic Differentiation: an in virto study

status: Public on Aug 13 2022

first: fei

middle: peng

last: li

address: Zhongshan second road

institute: Sun Yat-Sen University

summary: Mesenchymal stem cells (MSCs) possess the potential of differentiating into chondrocytes, which makes it an ideal source in healing cartilage defects. Here, we want to find out the key genes that participate in MSCs chondrogenesis. Human MSCs were induced for chondrogenesis for 7, 14, and 21 days using high-density micromass culture system and RNA was extracted for RNA-seq. A total of 6247 differentially expressed gene (DEGs) were identified at day 7, and 85 DEGs were identified at day 14. However, no significant DEGs was identified in day 21. The top 30 DEGs at day 7, including COL9A3, COL10A1, and CILP2, are closely related to extracellular matrix organization. While the top 30 DEGs at day 14 revealed that genes related to inflammation were enriched, including CXCL8, TLR2, and CCL20. We also conducted protein-protein interaction (PPI) networks analysis using search tool for the retrieval of interacting genes (STRING) database and identified key hub genes including CXCL8, TLR2, CCL20, and MMP3. The transcriptional factors were also analyzed, and identified top 5 TFs: LEF1, FOXO1, RORA, BHLHE41, SOX5. We demonstrated one particular TF, RORA, in promoting early MSCs chondrogenesis. Taken together, our result suggested that these DEGs may have a complex effect on MSCs chondrogenesis both synergistically and solitarily.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the chondrogenesis process of human mesenchymal stem cells

first: Tongzhou

last: Liang

first: Pengfei

last: Li

first: Bo

last: Gao


title: RNA sequencing of wild-type and TRα (-/-) hindlimb with and without T3 Treatment

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

institute: National Institutes of Health

summary: Conclusions: Our study represents the first detailed analysis of hindlimb transcriptomes in wild-type and TRα (-/-) tadpoles, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: Examination of 3 technical replicate from the same RNA sample which extracted and merged from the several Xenopus tropicalis tadpoles.

first: Yuta

last: Tanizaki

first: Hongen

last: Zhang

first: Yun-Bo

last: Shi


title: ChIP sequencing of wild-type and TRα (-/-) hindlimb with and without T3 Treatment

summary: Our study represents the first detailed analysis of thyroid hormone binding to the genome in the hindlimb of wild-type and TRα (-/-) tadpoles, with biological replicates, generated by ChIP-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of TR binding profiles.


title: Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway

summary: Our study represents the first detailed analysis of thyroid hormone binding to the genome in the intestine of wild-type and TRα (-/-) tadpoles, with biological replicates, generated by ChIP-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of TR binding profiles.

overall_design: Examination of 3 technical replicates from the same ChIP-DNA sample which extracted and merged from the several Xenopus tropicalis tadpoles.


title: Finding genomic targets of transcription factor Six3 in neural stem cells.

status: Public on Jul 17 2022

city: Cold spring harbor

first: Padmina

last: Shrestha

state: NY

address: 1 bungtown road

institute: Cold spring harbor

summary: Pro-neural transcription factor Six3 has been implicated in neuronal differentiation. We established primary neural stem cell with Six3 overexpression, and utilized CUT&RUN to profile genomic loci bound by Six3.

overall_design: We cultured primary neural stem cells from mice and overexpressed Six3 in the cell lines. We differentiated the stem cells into neural lineage and performed CUT&RUN to profile genomic regions bound by Six3.

first: Shrestha

last: Padmina

first: Mills

last: Alea


title: Glycine Chloramine directed gene expression changes in Jurkat T cell lines

first: Aarib

last: Stevens

summary: The goal of the current study was to determine whether chloramine exposure results in long-term alterations in transcriptional output. Proliferating Jurkat T-lymphoma cells were exposed to sublethal doses of glycine chloramine and RNA expression was profiled at 4, 24, 48 and 72 hours.

overall_design: Examination of Glycine chloramine on gene expression in jurkat cells

first: Aaron

first: Annika

middle: R

last: Seddon


title: Effect of depletion of Chd5 on gene expression during neuronal differentiation.

summary: To study the function of Chd5 in neuronal differentiation, we cultured primary neural stem cells from WT and Chd5 deficient embryos.

overall_design: We then differentiated the neural stem cells for 3 and 48 hours and performed an RNA-seq to obtain differentially expressed genes in Chd5 deficient cells.


title: MCF-7 Cell Derived Soluble Factors Define Growth of Vascular and Lymphatic Endothelial Cells: Modulatory Role of miR193a

status: Public on Jul 13 2022

city: Schlieren

first: Giovanna

last: Azzarito

address: Wagistrasse 14

department: Reproductive endocrinology

country: Switzerland

institute: University Hospital Zurich

summary: Angiogenesis and Lymphangiogenesis plays a key role in promoting tumor growth and breast cancer progression as well as metastasis. Active angiogenic process within the tumor tissue is known to promote cancer/tumor growth via nutrient supply, moreover, soluble molecules secreted by lymphatic endothelial cells (ECs) promotes tumor growth.  Hence is feasible that paracrine factors generated by breast cancer cells play a role in regulating tumor neovascularization by lymphatic and vascular ECs. Here using cultured  VECs and LECs assessed the paracrine impact of  MCF-7 breast cancer derived soluble factors on LEC and VEC growth (cell number), gene expression (micro array) and angiogenic proteins (protein array). Moreover, we explored the modulatory actions of miR193 on LEC and VEC growth driven by MCF-7 derived conditioned medium (MCF7-CM). We demonstrate that MCF7-CM differentially modulates VEC and LEC growth, i.e.  induces VEC growth and inhibits LEC growth. Moreover, the growth actions of MCF7-CM were accompanied with differential modulation VEC and LEC growth regulatory genes, that were further altered by miR193 a pretreatment of MCF7 cells. Our findings provide in-depth analysis of MCF7-CM  altered genes relevant for angiogenesis and lymphogenesis. The fact that vascular capillaries support growth and lymphatic capillaries play a role counteracting cancer growth (kill cancer cells), together with our observation in VECs and LECs,  suggests that MCF-7 breast cancer cells differentially modulate vascular and lymphatic growth to facilitate their survival and growth. Since miR193a abrogates the effects of MCF7-CM, it may be an effective therapeutic tool against breast cancer.

overall_design: Proliferation, migration and angiogenesis arrays were performed to investigate the effects of the MCF7-CM on VECs and LECs.Microarray analysis was conducted to determine the genes involved in the differentilly effects on both endothelial cells. Additionally the cells were exposed to consitioned medium collected from MCF-7 cells pre-treated with and without E2 or pre-transfected with miR193a to determine possible effects of the sex hormone and estradiol sensitive miRs.  CM (conditioned medium).

first: Raghvendra

last: Dubey

first: Lisa

last: Kurmann


title: Time-resolved transcriptomes of BCG vaccine induced trained immunity in human monocytes

first: Boris

last: Novakovic

summary: Trained immunity is the phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study profiled the transcriptomes of human monocytes responding to two different BCG vaccine strains.

overall_design: Time-course in vitro culture of human monocytes. Trained immunity was induced in culture through an initial exposure of primary human monocytes to BCG Denmark and BCG Bulgaria strains for 24 hours, followed by removal of stimulus and differentiation to macrophages for an additional 5 days. Cells were collected at baseline (day 0), 4 hour, 24 hour, 6 days and 6 days + 4h LPS re-stimulation.

first: Richard

last: Saffery

first: Mihai

last: Netea

first: Nigel

last: Curtis


title: DNA methylation dynamics during monocyte-to-macrophage differentiation and BCG vaccine induced trained immunity

summary: Trained immunity is a phenomenon whereby innate immune cells such as monocytes or macrophages undergo functional reprogramming after exposure to certain microbial components, altering their responses to future exposures. This study profiled the transcriptomes of human monocytes responding to two different BCG vaccine strains.