title: The interferon-rich skin environment regulates Langerhans cell ADAM17 to promote photosensitivity in lupus [array]

status: Public on Apr 10 2023

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

type:
Expression profiling by array
Third-party reanalysis

summary: The autoimmune disease lupus erythematosus (lupus) is characterized in part by photosensitivity, where patients can develop inflammatory skin lesions with even ambient ultraviolet radiation (UVR) exposure. Evidence points to a role for type I interferon (IFN-I) in photosensitivity, but mechanistic understanding remains limited. We have shown that photosensitivity in lupus models is at least in part attributable to Langerhans cell (LC) dysfunction. Healthy LCs limit photosensitivity via a disintegrin and metalloprotease 17 (ADAM17), a sheddase that normally limits UVR-induced skin inflammation by releasing soluble epidermal growth factor receptor (EGFR) ligands to support keratinocyte survival. On the other hand, LCs from lesional and even non-lesional lupus model skin show reduced ADAM17 activity and mRNA expression. Non-lesional human lupus skin also showed evidence of LC dysfunction, and, here, we asked how the lupus skin environment contributes to this dysfunction. We show that non-lesional skin in human CLE and multiple photosensitive lupus models share gene expression patterns consistent with a high IFN environment and LC dysfunction. IFN-I inhibits murine and human LC ADAM17 activity, and anti-IFNAR1 in lupus models restores LC ADAM17 function and reduces photosensitivity in EGFR and LC ADAM17-dependent manners. Reactive oxygen species (ROS) are a mediator of ADAM17 activity, and we show that lupus models have reduced UVR-induced LC ROS generation that is restored by anti-IFNAR1. Our findings suggest shared pathogenic mechanisms of photosensitivity in human and murine lupus skin and a model whereby the IFN-I-rich microenvironment in non-lesional lupus skin inhibits UVR-induced ADAM17 activity, predisposing to photosensitivity. Our data also suggest that the beneficial effects of the recently FDA-approved anifrolumab (anti-IFNAR1) on human lupus skin could act in part by restoring LC function.

overall_design: Non-lesional and lesional skin samples were from the same patients.

first: Thomas

middle: M

last: Li

first: Noa

last: Schwartz

first: Ali

last: Jabbary

first: David

last: Oliver

first: Yurii

last: Chinenov

first: Theresa

last: Lu


title: Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes

status: Public on Apr 27 2023

city: Houston

first: Pavel

last: Sumazin

state: TX

address: 1102 Bates St

department: Pediatric

country: USA

institute: Baylor College of Medicine

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: An integrative multiomics framework for identification of therapeutic targets in pulmonary fibrosis

status: Public on Apr 11 2023

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg


title: An integrative multiomics framework for identification of therapeutic targets in pulmonary fibrosis [TimeSeries]

summary: Pulmonary fibrosis (PF) is a progressive disease with a poor prognosis and lack of effective treatments. Therefore, identifying effective therapeutic modalities is required to improve outcome. However, the lack of predictive progressive disease biomarkers in the clinic causes a significant gap in the preclinical to clinical translational process. Here, we assessed and identified progressive alterations in pulmonary function, transcriptomics, and metabolomics in mice lungs at 7, 14, 21, and 28 days after a single dose of oropharyngeal bleomycin. By integrating multi-omics data, we identified two central gene subnetworks associated with multiple critical pathological changes in transcriptomics and metabolomics as well as pulmonary function. We presented a multi-omics-based framework to establish a translational link between the bleomycin-induced PF model in mice and human idiopathic pulmonary fibrosis to identify druggable targets and test therapeutic candidates. Our study also indicated peripheral CB1R antagonism as a rational therapeutic target for clinical translation in PF.

overall_design: We measured Pulmonary Function Tests and performed genome-wide transcriptomics and metabolomics analysis on lung tissue obtained from control and fibrotic lungs at 7-, 14-, 21- and 28-days post-bleomycin.

first: Abhishek

last: Basu

first: Kaelin

last: Wolf

first: Joshua

middle: K

last: Park

first: Lenny

last: Pommerolle

first: Madeline

last: Beehee

first: Bernadette

middle: R

last: Gochuico

first: Resat

last: Cinar


title: Alleviating iatrogenic effects of paclitaxel-coated balloons via anti-inflammatory treatment

status: Public on Mar 02 2023

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Background: Paclitaxel is touted as an essential medicine due to its extensive use as a chemotherapeutic for various cancers and an antiproliferative agent for restenosis. Due to recent concerns related to long-term mortality, paclitaxel (PTX)-based endovascular therapy is now surrounded by controversies.  Objective: Examine the inflammatory mediators driven by the systemic administration of PTX and explore the means to suppress these effects.  Methods: RNAseq analysis, cell and mouse models.  Results: RNAseq analysis of primary human endothelial cells (ECs) treated with PTX demonstrated transcriptional perturbations of a set of pro-inflammatory mediators, including monocyte chemoattractant protein-1 (MCP-1) and CD137, which were validated in EC lysates. These perturbations were abrogated with dexamethasone, a prototypic anti-inflammatory compound. The media of ECs pre-treated with PTX showed a significant increase in MCP-1 levels, which were reverted to baseline levels with DEX treatment. A group of mice harvested at different time points after PTX injection were analyzed for immediate and delayed effects of PTX. A 3-fold increase in MCP-1 was noted in blood and aortic ECs after 12 hours of PTX treatment. Similar changes in CD137 and downstream mediators such as tissue factor, VCAM-1 and E-selectin were noted in aortic ECs.  Conclusions: Our study shows that systemic PTX exposure upregulates atherothrombotic markers, and co-delivery of DEX can subdue the untoward toxic effects. Long-term studies are needed to probe the mechanisms driving systemic complications of PTX-based therapies and evaluate the clinical potential of DEX to mitigate risk.

overall_design: Human umbilical vascular endothelial cells (HUVECs) were treated with DMSO or with 5, 50, or 500 nM paclitaxel (PTX) for 24h.

first: Mengwei

last: Zhang

first: Vijaya

last: Kolachalama

first: Vipul

last: Chitalia


title: Next Generation Sequencing  of Wild Type and CMG2-/- Rat Lung Transcriptomes

status: Public on Dec 13 2022

city: Beijing

first: Xiaoyan

last: Liu

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

country: China

institute: Beijing Chao-Yang Hospital

summary:
Purpose:Pulmonary arterial hypertension secondary to congenital heart disease (CHD-PAH) with systemic-to-pulmonary shunt is characterized by proliferative vascular remodeling. Capillary morphogenesis gene-2 (CMG2) exhibits roles in cell proliferation and apoptosis. The purpose of this study was to determine the possible roles of CMG2 in the pathogenesis of systemic-to-pulmonary shunt induced PAH.
Methods Lung tissue sections from CHD-PAH patients, systemic-to-pulmonary shunt induced PAH rat model, CMG2-/- rats, and PASMCs were used. Immunohistochemistry, real time polymerase chain reaction, Western blot, proliferation, apoptosis, and next generation sequencing (NGS) were performed in this study.
Results CMG2 expression was reduced in lung tissues and pulmonary arterioles from Eisenmenger’s syndrome patient and rats with systemic-to-pulmonary shunt induced PAH. CMG2-/- rats exhibited heavier PAH and pulmonary vascular remodeling following exposure to systemic-to-pulmonary shunt for 8 weeks. Over-expression of CMG2 in cultured human PASMCs inhibited cell proliferation and promoted apoptosis, while knockdown of CMG2 promoted cell proliferation and inhibited apoptosis. A total of 1319 genes were found to be dysregulated in CMG2-/- rat lungs as detected by NGS. Biological processes influenced by these differentially expressed genes include regulation of blood vessel diameter, vasoconstriction, regulation of blood vessel size, vascular process in circulatory system, etc., and the most prominent pathway regulated is PI3K-Akt signaling pathway.
Conclusion Our work identifies a novel role for CMG2 in systemic-to-pulmonary shunt induced PAH based on the findings that CMG2 deficiency could exacerbate systemic-to- pulmonary shunt induced vascular remodeling in the development of PAH. CMG2 may be a potential target for CHD-PAH treatment.

overall_design: Lung mRNA profiles of 8-week old wild type (WT) and CMG2-/- rats were generated by deep sequencing, in sextuplicate, using Illuminna Novaseq.

first: Liukun

last: Meng

first: Wen

last: Yuan

first: Hongjie

last: Chi

first: Jian

first: Jiuchang

last: Zhong


title: Oxidized 5-methylcytosine modulates synthetic lethality to poly-ADP-ribose polymerase inhibitors in acute myeloid leukemia

status: Public on Nov 12 2022

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Identification of downstream target genes of transcription factor ZEB1, lncRNA FGD5-AS1 and miR-34a-5p in gastric cancer

status: Public on Feb 23 2023

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

summary: As one of the most abundant lncRNAs in cells, the biological function of lncRNA FGD5-AS1 remains largely unclear in cancers, especially in gastric cancer (GC). In addition, the reason for such high levels of FGD5-AS1 in cells remains unknown. In this study, FGD5-AS1 was proved to be a ZEB1-related lncRNA which was overexpressed and predicted poor prognosis in GC. Knockdown of FGD5-AS1 decreased GC proliferation in vitro and in vivo.

overall_design: To reveal the molecular mechanism by which FGD5-AS1 drives gastric cancer progression, we established GC cell lines knocked down the expression of FGD5-AS1. The transcriptome sequencing studies were performed by deep sequencing. Exploration of downstream target genes of transcription factor ZEB1 in gastric cancer cell lines. The GC cell lines were transfected with miR-34a-5p mimics and negative control siRNAs. After effective transcrection, the genes downregulated by miR-34a-5p were screened by RNA sequencing.

first: Shanshan

last: Qin

first: Dandan

last: Li


title: Chloroplast nucleoid is organized by membrane association of transcribed genes

status: Public on May 10 2023

city: Coyoacan

first: V Miguel

last: Palomar

state: Mexico City

address: Circuito Exterior SN

department: Biochemistry

country: Mexico

institute: School of Chemistry, UNAM

type: Genome binding/occupancy profiling by high throughput sequencing


title: MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis

status: Public on Feb 11 2023

city: Riverside

first: Meng

last: Chen

state: CA

address: 2150 Batchelor Hall, 900 University Ave.

institute: University of California, Riverside

type: Non-coding RNA profiling by high throughput sequencing


title: Disruption of glucagon receptor increase α-cell glucagon expression and secretion beyond hyperplasia in zebrafish

status: Public on Oct 26 2022

city: Shanghai

first: jihong

last: zheng

state: Shanghai

address: Siping Road, Yangpu District

institute: Tongji University

summary: Glucagon receptor (GCGR) is a potential target for diabetes therapy. Several emerging GCGR antagonism-based therapies are under pre-clinical and clinical development. However, the GCGR antagonism as well as GCGR deficient animal accompanied with α-cell hyperplasia and hyperglucagonemia, which may limit the application of GCGR antagonism. To better understand the physiological changes in the α cells during the GCGR disruption, we performed the single cell sequencing of α cells isolated from control and gcgr-/- zebrafish. We found that α cells in gcgr-/- zebrafish dramatically increased glucagon (both gcga and gcgb) expression, we also found that several transcriptional factors that regulate glucagon expression were also increased. Based on the sequencing data, we further experimentally confirmed that gcgr-/- up-regulated glucagon mRNA level by in situ hybridization, and the gcgr-/- increased glucagon promoter activity indicated by reporter line Tg(gcga: GFP). Moreover, our results also revealed that α cells increased glucagon granule population and glucagon level in gcgr-/- zebrafish. These data suggested that hyperglucagonemia in the organism of GCGR antagonism not only contributed by the α-cell hyperplasia but also contributed by the increased glucagon expression and secretion from α cells. Our study provided more comprehensive understanding of physiological changes of α-cell during the GCGR disruption.

overall_design: The 7 dfp (days post fertilization) zebrafish larvae α cells were subjected to single cell RNA-sequencing. We obtained 576 cells sequencing data (384 gcgr-/- and 192 control), After quality control and excluded the potential contaminated β cells and δ cells, 285 high-quality cells were obtained for subsequent analysis (197 gcgr-/- and 88 control).

first: Qi

last: Kang

first: Jihong

last: Zheng

first: Jianxin

last: Jia

first: Ying

last: Xu

first: Xuanxuan

last: Bai

first: Xiaokun

first: Chao

first: Mingyu


title: A circular RNA Edis-Relish-castor axis regulates neuronal development in Drosophila

status: Public on Oct 04 2022

city: St Petersburg

first: Rui

last: Zhou

state: FL

address: REB 4130, 501 6th Ave S

institute: Johns Hopkins University

summary: Circular RNAs (circRNAs) are a new group of noncoding and regulatory RNAs that are particularly abundant in the nervous system, although their physiological functions are underexplored. Here we report that the brain-enriched circular RNA Edis (Ect4-derived immune suppressor) plays an essential role in neuronal development in Drosophila, as its depletion causes defective axonal projection of mushroom body (MB) neurons in the brain, as well as impaired locomotor activity and shortened lifespan of adult flies. In addition, we show that the castor gene, which encodes a transcription factor involved in neurodevelopment, is upregulated in Edis knockdown neurons. Notably, castor overexpression phenocopies Edis knockdown, and reducing castor levels suppresses the neuronal developmental phenotypes in Edis-depleted neurons. Furthermore, chromatin immunoprecipitation analysis reveals that the immune transcription factor Relish occupies two sites at the castor promoter, and that both sites are required for optimal castor gene activation induced by either immune challenge or Edis depletion. Lastly, Relish mutation rescues both the castor hyperactivation phenotype and neuronal defects in Edis knockdown animals. We conclude that the circular RNA Edis acts through Relish and castor to regulate neuronal development.

overall_design: Identification of genes that display changes in expression levels upon depletion of the circular RNA Edis in neurons in Drosophila melanogaster.

first: Wei

last: Liu

first: Weihong

last: Liang

first: Xiao-Peng

last: Xiong

first: Jian

middle: L


title: The Circular RNA Edis Regulates Neurodevelopment and Innate Immunity

summary: Circular RNAs (circRNAs) are widely expressed in eukaryotes. However, only a subset have been functionally characterized. We identify and validate a collection of circRNAs in Drosophila, and show that depletion of the brain-enriched circRNA Edis causes hyperactivation of antibacterial innate immunity both in cultured cells and in vivo. Notably, Edis depleted flies display heightened resistance to bacterial infection and enhanced pathogen clearance. Conversely, ectopic Edis expression blocks innate immunity signaling. In addition, inactivation of Edis in vivo leads to impaired locomotive activity and shortened lifespan. Remarkably, these phenotypes can be recapitulated with neuron-specific depletion of Edis, accompanied by defective neurodevelopment. Importantly, restoration of Edis expression suppresses both innate immunity and neurodevelopment phenotypes elicited by Edis depletion. We provide evidence that Edis encodes a functional protein that associates with and compromises the processing of the immune transcription factor Relish. Consistent with these observations, inactivation of Relish suppresses the innate immunity hyperactivation phenotype in the fly brain and rescues the neurodevelopment defects in Edis knockdown neurons. Thus, our study establishes the circRNA Edis as a key regulator of neurodevelopment and innate immunity.

overall_design: Identification of circular RNAs in cultured Drosophila S2 cells.

first: Xiao

middle: P

first: Shiyu

first: Antonio

last: Tito

first: Julia

last: Situ

first: Daniel

last: Martinez

first: Chunlai

last: Wu

first: Ranjan

middle: J

last: Perera

first: Sheng

last: Zhang


title: Species-specific regulation of XIST by the JPX/FTX orthologs

status: Public on Feb 01 2023

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Hélène Brion

country: France

institute: Université Paris Cité

summary: X chromosome inactivation (XCI) is a developmental regulatory process that initiates with remarkable diversity in various mammalian species. Here we addressed the contribution of XCI regulators, most of which are lncRNA genes (LRGs) characterized in the mouse, to this mechanistic diversity. By combining analysis of single-cell RNA-seq data from early human embryogenesis with various functional assays in pluripotent stem- and differentiated cells, we demonstrate that the function of Ftx is not conserved, while JPX stands a major regulator of XIST expression in human and in mouse. However, the underlying mechanisms differ radically between species and require Jpx RNA in the mouse and the act of transcription of the JPX locus in the human. Moreover, biogenesis of XIST is affected at different regulatory steps between these species. This study illustrates how diversification of LRG modus operanti during evolution provide opportunities for innovations within constrained gene regulatory networks.

overall_design: Two technical replicates of capture HiC sequencing from H9 human Embryonic Stem Cells

first: Olga

last: Rosspopoff

first: Emmanuel

last: Cazottes

first: Christophe

last: Huret

first: Agnese

last: Loda

first: Amanda

last: Collier

first: Miguel

last: Casanova

first: Peter

last: Rugg-Gunn

first: Edith

last: Heard

first: Jean-François

last: Ouimette


title: A novel peptide hydrogel of metal ion clusters for accelerating bone defect regeneration

status: Public on Sep 01 2022

city: Nanjing

first: Liu

last: Xu

address: No.138,Xianlin Avenue,Qixia District,Nanjing City

institute: Nanjing University of Chinese medicine

summary: We explore the genes and pathways related to metal ions involved in extracellular matrix, cell adhension and migration, expression of cytokine, antibacterial, inflammation, and cell signaling.

overall_design:
To investigate the potential osteogenic mechanism of PPH, we performed an mRNA expression profiling microarray. Male Sprague Dawley rats (10 weeks old, 320-350 g weight) were used to test the engineered hydrogels in vivo. For gene expression profiling microarray analysis, tibias were harvested at week 2.
Comparative gene expression profiling of RNA-seq data of processed pyritum hydrogel (PPH)-treated and model groups

first: Shan

first: Tangyong

last: Xiang


title: Transcriptome changes in Olig1 over-expression retina ganglion cells (RGCs) by AAV-Olig1

status: Public on Dec 30 2022

first: Xiuqing

last: Fu

address: 393 Middle Huaxia Road, Pudong

department: School of Life Science and Technology (SLST)

institute: ShanghaiTech University

summary: To gain mechanistic insights into the effects of Olig1, we performed gene expression profiling analysis in RGCs. Transcriptome changes in Olig1 over-expression RGCs showed up-regulating genes related to axon projection development and regeneration-associated genes (RAGs), such as Stmn2, Gal, Gap43, and Sprr1a.

overall_design: Adult male mice were anesthetized with avertin (300-500mg/kg) and positioned in a stereotaxic apparatus. Under microscopic illumination, injections were made through the sclera and retina with a 5μL Hamilton syringe with a 32-gauge needle, avoiding injuring lens for excluding the false-positive possibility of regeneration. In this work, all packaged AAV2 virus (10^13 gc/mL, 1.5μL) were injected into the vitreous chamber to infect RGCs. 7 and 14 days after ONC, we separated RGCs, which were transfected with AAV-Olig1 or AAV-GFP, by magnetic beads coupled with CD90.2 antibody and picked 15~20 cells by Unipick in each sample.

first: Wenrong

last: Zhan

first: Weiya

last: Tian

first: Pengming

last: Zeng

first: Zhenge

last: Luo


title: MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis (RNA-Seq)

first: Meng

last: Chen

summary: MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remains ambiguous. Here we show that HYPONASTIC LEAVES1 (HYL1) – a key component of microRNA biogenesis – acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 (dcl1) allele, dcl1-24, that rescues hyl1-2’s defects in miRNA biosynthesis and warm temperature-induced hypocotyl elongation. Genome-wide miRNA and transcriptome analysis reveal microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-LIKE 9 (SPL9) as critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, the miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miRNA156/SPL9 module as a previously-uncharacterized genetic circuitry that enables plant growth plasticity in response to environmental temperature and light changes.

overall_design: We compared global mRNA levels in 4-d-old Col-0, hyl1-2, pif457, 35S:mim156 and dcl1-24/hyl1-2 seedlings grown in 50 umol m-2 s-1 red light at either 21  C or 27  C.

first: Xuemei


title: Transcriptional responses of Neisseria gonorrhoeae to glucose and lactate: implications for resistance to oxidative damage and biofilm formation

status: Public on Dec 31 2022

city: Atlanta

first: Julio

middle: C.

last: Ayala

state: Georgia

address: 1600 Clifton Rd NE Rm 3-642

department: Division of STD Prevention

institute: Centers for Disease Control and Prevention

summary: Carbon catabolite repression (CCR) is a gene regulation process that allows bacteria to use carbon-energy sources in a hierarchical manner. Thus, the presence of a preferred sugar, usually D-glucose, results in downregulation of genes participating in the transport and catabolic pathways of secondary carbon sources. Further, CCR controls the expression of global regulators that control expression of many genes involved in multiple aspects of bacterial physiology such as stress response proteins and virulence factors. The human-restricted pathogen Neisseria gonorrhoeae can rely upon a limited number of carbon-energy sources, including glucose and lactate and both are available within its infection niches. We recently reported that expression of the L-lactate permease-encoding gene lctP is subjected to glucose repression within physiological concentrations. However, the transducing mechanism or the gene that connect glucose with lctP promoter repression remained unknown. To address this issue, we performed an RNA-Seq analysis to determine the transcriptional landscape of gonococci due to changes in glucose or lactate concentrations in the growth media. Glucose was found to regulate 144 genes (5.5% of total genes in the genome) while lactate influenced the expression of 434 (16.5%) genes with an overlap of 97 genes between the two sugars. Both, glucose and lactate were found to upregulate genes involved in protein translation, a high energy consumption cellular function. Individually, glucose enhanced genes participating in glycolysis and repressed genes in the tricarboxylic acid (TCA) cycle, while lactate enhanced genes encoding respiratory enzymes and ATP synthase. Interestingly, lactate was found to repress expression of several genes encoding known gonococcal virulence factors such as tbpAB encoding the transferrin-binding proteins; the tonB and exbBD genes encoding the membrane energy transfer complex TonB-ExbB-ExbD required for many outer membrane transport systems; katA encoding an important H2O2-inducible catalase and to upregulate mtrR encoding the master repressor of the mtrCDE antimicrobial efflux pump genes. Moreover, glucose repressed mntC encoding a Zn/Mn ABC transporter and lctP, both required for resistance to killing by H2O2. These results set the framework to determine important gonococci virulent factor genes whose expression can be modulated by CCR as well as to discover the corresponding CCR regulators that control such genes.

overall_design: Total RNA samples (8 samples) were isolated from N. gonorrhoeae strain FA19 grown to mid-exponential phase (OD600 0.5-0.7), depleted from ribosomal RNA and subjected to single-end high throughput sequencing on the Illumina NextSeq 500 platform (Illumina Inc., San Diego, CA). Transcript differential expression analyses were conducted between the transcriptomes of FA19 cells grown in GC-broth supplemented with two D-glucose concentrations 1 and 10 mM, and between bacteria grown in GC-broth supplemented with L-lactate 1 or 10 mM. Each condition (sugar concentration) was sequenced in duplicates.

middle: C

first: William

last: Shafer

first: Jacqueline

middle: T

last: Balthazar


title: Transcriptome analysis of the binucleate ciliate Tetrahymena thermophila with asynchronous nuclear cell cycles

status: Public on Jan 11 2023

city: Bryan

first: GEOFFREY

last: KAPLER

address: 4209B Medical Research Education Building II

institute: Texas A&M University

summary:
As a prototypic ciliated protozoan, Tetrahymena thermophila harbors two functionally and physically distinct nuclei within a shared cytoplasm. During the vegetative phase of the life cycle, the S phases of the diploid germline micronucleus and polyploid somatic macronucleus are temporally offset. Here we report the first RNA-Seq analysis across the cell cycle of a binucleated ciliated protozoan.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: RNA was isolated at 30 min intervals across 1.5 vegetative cell cycles, starting with a G1 population synchronized by centrifugal elutriation.

first: Linying

last: Zhang

first: Marcella

last: Cervantes

first: Simin

last: Pan


title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [RNA-seq]

status: Public on Apr 28 2023

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

summary: During development, Hox genes are activated in a time sequence following their relative positions on their clusters, leading to the proper identities of structures along the rostral to caudal axis. To understand the mechanism operating this Hox timer, we used ES-cells derived stembryos and show that the core of the process involves the start of transcription at the anterior part of the cluster, following Wnt signaling, and a concomitant loading of cohesin complexes enriched on the transcribed DNA segments, i.e., with an asymmetric distribution in favor of the anterior part the gene cluster. Chromatin extrusion then occurs with, along with time, successively more posterior CTCF sites acting as transient insulators, thus generating a progressive time-delay in the activation of more posterior-located genes due to long-range contacts with a flanking TAD. Mutant stembryos support this model and reveal that the iterated presence of evolutionary conserved and regularly spaced intergenic CTCF sites control the precision and the pace of this temporal mechanism.

overall_design: RNA-seq data of wt and mutant stembryos

first: Hocine

last: Rekaik

first: Bénédicte

last: Mascrez

first: Célia

last: Bochaton

first: Alexandre

last: Mayran

first: Denis

last: Duboule


title: Gene expression profile of brain tissue in wild-type and MSA Tg mice at the age of 24 weeks

status: Public on Jul 28 2022

city: Fukuoka

first: Hiroo

last: Yamaguchi

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

department: Department of Neurology

country: Japan

institute: Neurological Institute, Graduate School of Medical Sciences,  Kyushu University

summary: RNA was extracted from each brain of 3 WT and 3 Tg mice at the age of 24 weeks and pooled into one in each genotype group, and microarray analysis was performed.

overall_design: Gene expression profile of MSA Tg mice brainstem/cerebellum and spinal cord at the age of 24 weeks was compared against the wild type mice tissue.

first: Yamaguchi

last: Hiroo


title: Single-cell RNAseq data from mouse ON direction-selective ganglion cells

status: Public on Aug 19 2022

city: Baltimore

first: Alex

last: Kolodkin

state: Maryland

address: 725 N Wolfe St

department: Neuroscience

institute: Johns Hopkins University School of Medicine

summary: The goal of this study was to characterize the transcriptomes of ON direction-selective ganglion cells tuned to different directions

overall_design: Each sample contains sequenced mRNA from a single direction-selective ganglion cell. We focused on direction-selective ganglion cells that prefer upward or downward motion. Cells were taken at P4, P5, P7, P8, P10, and P12.

first: Timour

last: Al-Khindi

first: Michael

last: Sherman

first: Takashi

last: Kodama

first: Preethi

last: Gopal

first: Zhiwei

first: James

last: Kiraly

first: Hao

first: Loyal

middle: A

last: Goff

first: Sascha

last: du Lac


title: Functional Recovery from Human Pluripotent Stem-Derived Dopamine Neuron Grafts is Dependent on Neurite Outgrowth

status: Public on Jun 30 2022

city: La Jolla

first: Jeanne

last: Loring

state: California

address: 10550 North Torrey Pines Road

department: The Center for Regenerative Medicine

institute: Scripps Research

summary: We conducted bulk RNAseq to understand changes in the transcriptome of in vitro dopaminergic progenitor cells as their duration of differentiation changes. We obtained gene expression estimates from Day 13, (n=2), Day 18 (n=2), and Day 25 (n=2) cell cultures.

overall_design: Two Parkinson's Disease patients provided skin cells that were reprogrammed -> fibroblasts -> iPSC -> Dopaminergic neurons. At Days 13, 18 and 25 of dopeminergic neuron differentiation, cells were isolated for bulk RNA-seq. Paired-end RNA sequencing was performed on the Illumina HiSeq 2000 platform, with TruSeq_v2 library preparation chemistry.

first: Jim

last: Mossman

middle: F

first: Roy

last: Williams


title: AATF/Che-1 localizes to paraspeckles and suppresses R-loops accumulation and interferon activation in Multiple Myeloma

status: Public on Jul 06 2022

city: Rome

first: Maurizio

last: Fanciulli

address: Via Elio Chianesi 53

department: Department of Research, Advanced Diagnostic, and Technological Innovation

country: Italy

institute: IRCCS Regina Elena National Cancer Institute

summary: We investigated the interactions of AATF/Che1 with paraspeckles complex in Multiple Myeloma(MM) cells by looking at its relationship with lncRNA NEAT1_1(NEAT1) and the essential paraspeckles proteins. By analyzing ChIP- and ChIRP-sequencing of MM cells, we assessed that the interaction between AATF/Che1 and NEAT1 occurs also onto DNA and detected the sites where they co-localize. To better characterize the interaction, we studied the effects of interfering AATF/Che1 or NEAT1 on co-localizing sites through ChIP-seq with NEAT1 interfered (GapmerNEAT1) and ChIRP-seq with AATF/Che1 interfered (siChe). We found that NEAT1 is essential in maintaining the paraspeckles complex onto those sites. Moreover, by exploring DRIP-seq data with siChe, we also detected that AATF/Che1 and NEAT1 localize on R-loops, RNA:DNA hybrid structure involved in DNA transcription and repair. A depletion of AATF/Che1 causes a further increase of those hybrid structures and the activation of the immune response in MM, in particular the interferon (IFN) activation. To further explore these findings, we performed RNA-seq with siChe and GapmerNEAT1 which confirm that AATF/Che-1 down-regulation induces a strong up-regulation of genes involved in IFN response.

overall_design: Examination of RNA-seq, ChIRP-seq, DRIP-seq and ChIP-seq in KMS27 cell lines before and upon Che1 interference. RNA-seq, ChIP in KM27 cell lines before and upon gapmer NEAT1.

first: Tiziana

last: Bruno

first: Giacomo

last: Corleone

first: Clelia

last: Cortile

first: Francesca

last: De Nicola

first: Valeria

last: Catena


title: Single cell gene expression profile of hPSC-derived nephric duct spheroids (day 7) and collecting duct organoiods (day 18)

status: Public on Jun 20 2022

city: Boston

first: Kyle

last: McCracken

state: Massachusetts

address: 4 Blackfan Circle

institute: Brigham and Women's Hospital

summary: We performed directed differentiation of human pluripotent stem cells (hPSCs) into ureteric bud (UB) organoids and performed single cell transcriptomics to analyze different stages of development. At day 7, the spheroids exhibited a nephric duct (ND) signature, and we identified there is also a population of stromal progenitor cells within the cluster. At day 18, the organoids comprise more differentiated collecting duct (CD) cell types including principal cells.

overall_design: During directed differentiation, structures at different timepoints were collected and dissociated into single cells for library preparation using the BD Rhapsody platform. Numerous spheroids/organoids were pooled for for analysis at each developmental stage.

middle: W

first: Joseph

middle: V

last: Bonventre


title: Induction of resistance to NTRK inhibitors via mevalonate pathway by HMGCS2

status: Public on Mar 10 2023

city: Tokyo

first: Yasuhiro

last: Kato

state: Bunkyo Ku

address: Sendagi 1-1-5

department: Pulmonary Medicine and Oncology

institute: Nippon Medical School

summary:
Paretal KM12 and NTRK inhibitor resistant cells established from KM12 in our laboratory was compared to search for and analyze significant factors related to resistance mechanism. To investigated the mechanism of resistance to NTRK-TKI, we establish resistant cells to three type NTRK-TKIs (Larotrectinib, Entrectinib and Selitrectinib) by step -wise methods using KM12 with TPM5-NTRK1 rearrangement for 6 months. (KM12-LR, KM12-ER and KM12-SR) 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2) over expression was observed commonly in three resistance cells. Lower expression of SREBP2 and PPARα in two cells (KM12-ER and KM12-SR) in which HMGCS2 was more overexpressed than parental KM12 and KM12-LR.
In resistant cells, knockdown of HMGCS2 using small interfering RNA improved NTRK-TKIs sensitivity, but further treatment with mevalonolactone after knockdown HMGCS2 reintroduced NTRK-TKIs resistance. In addition, simvastatin and silibinin had synergic effect with NTRK-TKIs to resistant cells and delayed tolerance was observed after sustained exposure to clinical concentrations of NTRK-TKI and simvastatin against KM12. These results suggested that HMGCS2 overexpression induces resistance to NTRK-TKI via the mevalonate pathway. In addition, statin inhibited mevalonate pathway may be useful for overcoming this mechanism resistance.

overall_design: We established resistance cells to three types NTRK inhibitor using KM12.We analyzed differences RNA expression between parental cell and three resistant cells for RNA extraction and hybridization on Affymetrix microarrays.

first: Masahiro

last: Seike

first: Masaru

last: Matsumoto


title: Identify a panel of transcripts that exhibited differential expression between spinal cord motor neurons (spMNs) with low and high regenerative abilities

first: Xiuqing

last: Fu

summary: The mammalian neurons in the central nervous system (CNS) fail to regenerate their axons after injury, while the adult peripheral nervous system (PNS) neurons can regenerate their axons robustly. Promoting the intrinsic regenerative capacity of CNS neurons after injury is potential way to solve this difficulty. For this purpose, we have identified a panel of transcripts that exhibited differential expression between spinal cord motor neurons (spMNs) with low and high regenerative abilities by using retrograde tracing and single-cell RNA sequencing.

overall_design: We classified spinal cord MNs with different regeneration abilities into two groups by labeling their injured axon terminals at the proximal and distal sites of the sciatic nerve with retrograde labeling dyes. That is, fast DIO (Green), which can retrograde diffuse to the soma of spMNs through the injured axonal cell membrane, was injected at the proximal site on the day of operation (Day 0) and labeled all the injured spMNs. Two days after injury (Day 2), we injected fast DiI (Red) into the distal site of the sciatic nerve to mark those spinal cord MNs, whose regenerated axons reached the distal site firstly.

first: Wenrong

last: Zhan

first: Weiya

last: Tian

first: Pengming

last: Zeng

first: Zhenge

last: Luo


title: Single-cell transcriptome analysis of aging brain

status: Public on Nov 18 2022

first: Junjie

last: Gao

address: 600 Yishan Road

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

summary: Single-cell transcriptome analysis of 1-month, 6-month, 20-month  brain

overall_design: Examination of mouse brain

first: Changqing

last: Zhang


title: Gene expression profile of brain tissue in wild-type and MSA Tg mice at the age of 16 weeks

status: Public on Jun 10 2022

first: Hiroo

last: Yamaguchi

summary: RNA was extracted from each brain of 3 wild-type and 3 MSA Transgenic mice at the age of 16 weeks and microarray analysis was performed on each sample.

overall_design: Gene expression profile of MSA Tg mice brain at the age of 16 weeks was compared against wild type mice brain.

first: Yamaguchi

last: Hiroo


title: Maternal allergic sensitization affects the T cell modulatory capacity of milk derived extracellular vesicles

status: Public on Oct 30 2022

city: Utrecht

first: Martijn

last: van Herwijnen

address: Yalelaan 2

country: Netherlands

institute: Universiteit Utrecht

summary:
Background: Human milk extracellular vesicles (EVs) affect various cell types in the gastrointestinal tract, including T cells, and play a role in the development of the newborn’s immune system by delivering specific molecular cargo to target cells. Although maternal allergic sensitization alters the composition of milk, it is unknown whether this impacts the function of milk EVs. Therefore, we analyzed the T cell modulatory capacity and compared the protein and miRNA cargo of EVs from milk of allergic and non-allergic mothers.
Methods: EVs were isolated from human milk from allergic and non-allergic donors by differential centrifugation, density gradient floatation and size exclusion chromatography. Functional modulation of primary human CD4+ T cells by EVs was assessed in vitro. Proteomic analysis and small RNA sequencing was performed on milk EVs to evaluate protein and miRNA abundance and to identify cellular targets of this EV cargo in relevant T cell signaling pathways.
Results: T cell proliferation, activation and cytokine production were suppressed in the presence of milk EVs. Remarkably, milk EVs from allergic mothers modulated T cell activation to a lesser extent than EVs from non-allergic mothers. Integrative multi-omics analysis identified EV cargo of which the cellular targets could be linked to T cell activation-associated processes.
Conclusions: Milk EVs from non-allergic mothers are stronger inhibitors of T cell activation compared to milk EVs from allergic mothers. This altered functionality might be linked to small changes in modulation of certain T cell signaling pathways.

overall_design: Collection of human milk and was done as previously described [Zonneveld, JEV. 2021; PMID: 33732416].  Milk EVs were isolated as previously described [van Herwijnen, MCP. 2016; PMID: 27601599 ]using differential centrifugation and sucose density gradient separation. Milk EVs were isolated from 3.5-4 ml 10,000g milk. EV-enriched fractions from sucrose gradient isolation were diluted with PBS and pelleted at 192,000 g. EV pellets were resuspended in 700 µl Qiazol and frozen at -80°C until sRNA isolation for sequencing. Small RNA (< 200 nt) was isolated using the miRNeasy micro kit (Qiagen) according to manufacturer’s instructions. Input quantity of sRNA for library preparation was based on equal volume of purified milk EVs and ranged between 10-150 ng of sRNA per sample. The Illumina® Truseq small RNA Sample Prep Kit was used to process the samples according to the kit-specific guidelines. Small RNA sequencing was done on the Illumina NextSeq 500 platform with 75 bp single-end sequencing. Samples were sequenced in 1 flow cell with 4 lanes. Samples with less than 7 million reads were sequenced in a second flow cell and data from 2 flow cells were combined. For each individual sample, 4 lanes were combined in a single fastq file. Subsequently, files for those samples which were sequenced in 2 different flow cells were combined. In total 40 fastq files, 20 from non-allergic donors and 20 from allergic donors were obtained. FastQC (version 0.11.5) was used to perform quality control checks on sequencing data. Remaining TruSeq small RNA adapter sequences were checked and clipped from all reads at the 3' end using cutadapt (version 2.8). Remaining adapters were removed from the 5’ end of the reads using cutadapt and the low quality bases were trimmed from all sequence reads using sickle (version 1.33). all sequence reads shorter than 15 bases were discarded. The processed reads were aligned to human reference genome GRCh38 from Ensembl and the number of aligned reads per annotated sRNA was calculated. These processes were performed by Manatee algorithm (version 1.2) applying bowtie to align reads (version 1.0.1), allowing for alignments to a maximum of 50 loci and reporting 3 of them, with equal alignment scores, and a maximum of 3 mismatches. Manatee counts output was rounded and used as raw expression data. The small RNA annotation track was obtained from miRBase (version 22.1), GtRNAdb (version 2.0, January 2016) and Ensembl 99 in order to analyse the miRNAs.

first: Marca

middle: H

last: Wauben


title: Comparison of transcriptome, small RNA and degradome of self grafting and distant grafting in Vitis vinifera

status: Public on Nov 30 2022

city: Zhengzhou

first: Gao-Pu

last: Zhu

state: Henan

address: No. 3, Weiwu Road

department: Non-timber Forest Research and Development Center

institute: Chinese Academy of Forestry

summary: Long distance transfers on genetic material (mRNA, miRNA, Protein, etc.) and metabolites (Hormone) between rootstock and scion is also well documented in the homo-grafting hybrids, but the process in distant-grafting is not reported where rootstock and scion belonging to different Familly. We repeatedly grafted the Vitis vinifera scion onto the Schisandra chinensis stock and got 20 interfamily vegetative hybrids ― Vitis vinifera / Schisandra chinensis (Vs) that could grow normally over 25 years. We found the phonotype leaf, internode, fruit of Vs upper the graft union transformed to intermediate stage between V. vinifera and S. chinensis, and the new traits was inherited by vegetative propagation. To expose the reason, using the simultaneous self-rooted Vitis vinifera (Vv) as control, differences of transcriptomics, miRNAs, degradome between Vv and Vs were analyzed by high-throughput sequencing, and the metabolome by liquid Chromatograph Mass Spectrometer (LC-MS). The results showed that a total of 2113 differentially expressed genes (DEGs), GO annotation and KEGG pathway enrichment analysis found that DEGs function mainly included oxidation-reduction process, metabolic process, etc. 79 differentially expressed miRNAs (DEMs) contains 27 known miRNAs and 52 novel miRNAs were identificated, the main functions of DEMs were defense response, biosynthetic process, etc. The target gene detected by degradome sequencing were mainly regulation of transcription & DNA-templated, auxin-activated signaling pathway, etc. And the degradation group detected 840 target genes corresponding to 252 miRNAs, of which 12 DEMs and the corresponding target gene expression levels were mostly negatively correlated. Meanwhile, 1188 differentially metabolic compounds were identified, the most common of which were sputum metabolism, arginine and proline metabolism, and ABC transporters. Especially the metabolites schizandrin was significantly down regulated and gomisin was up regulated in Vs that were main medicinal ingredients in Schisandra. KEGG pathway enrichment analysis of differential metabolites found more than 30 differential metabolic pathways of Vv-Vs. Our data demonstrate the impact of interfamily graft on the genetic materials and metabolites for the scion and the traits can stable inherited by vegetative propagation, providing an important reference and basis for future breeding through select target gene type rootstocks.

sample_organism:
Vitis vinifera
Schisandra chinensis

platform_organism:
Vitis vinifera
Schisandra chinensis

overall_design: RNA-Seq and miRNA-Seq for self-grafted Vitis vinifera and distantly grafted Vitis vinifera, using Illumina HiSeq 2500 and HiSeq 4000.

first: Junhui

last: Zhao


title: eIF4F complex dynamics are important for the activation of the integrated stress response

status: Public on Jan 25 2023

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

department: Biology

institute: Washington University in St. Louis

summary: In response to stress, eukaryotes activate the integrated stress response (ISR) via phosphorylation of eIF2α to promote the translation of pro-survival effector genes, such as GCN4 in yeast. Complementing the ISR is the Target of Rapamycin (TOR) pathway, which regulates eIF4E function. Here we probe translational control in the absence of eIF4E in Saccharomyces cerevisiae. Intriguingly, we find that loss of eIF4E leads to de-repression of GCN4 translation. In addition, we find that de-repression of GCN4 translation is neither accompanied by eIF2α phosphorylation nor reduction in initiator ternary complex. Our data suggest that when eIF4E levels are depleted, GCN4 translation is de-repressed via a unique mechanism that may involve faster scanning by the small ribosome subunit due to increased local concentration of eIF4A. Overall, our findings suggest that relative levels of eIF4F components are key to ribosome dynamics and may play important roles in translational control of gene expression.

overall_design: Genome and Transcriptome Mapped ribosome profiling and RNA-seq reads. Genome mapping was done using STAR and analyzed using FeatureCounts and python scripts. Transcriptome mapping was done using Salmon and analyzed using DESeq2.

first: Kyusik

middle: Q

last: Kim

first: Ankanahalli

middle: N

last: Nanjaraj Urs

first: Victor

last: Lashinde

first: Alison

last: Greenlaw

first: Benjamin

last: Hudson

middle: S


title: Pseudogenes limit the identification of novel common transcripts generated by their parent genes

status: Public on Oct 15 2022

city: London

first: Emil

middle: Karl

last: Gustavsson

address: 20c Guilford St

country: United Kingdom

institute: University College London

summary: Genomic sequences with high sequence similarity, such as parent-pseudogene pairs, cause short sequencing reads to align to multiple locations, thus complicating genomic analyses. However, their impact on transcriptomic analyses, including the estimation of gene expression and transcript annotation, has been less studied. Here, we investigated the impact of pseudogenes on transcriptomic analyses.

overall_design: Human Poly A+ RNA of healthy individuals that passed away from sudden death/trauma derived from frontal lobe and hippocampus were commercially purchased through Clontech. A total of 100ng of Poly A+ RNA per sample was used for initial cDNA synthesis and subsequent library preparation according to the direct cDNA sequencing (SQK-DCS109). Sequencing was performed on the PromethION using one R9.4.1 flow cell per sample and base-called using Guppy (v 4.0.11; Oxford Nanopore Technologies—ONT, Oxford, UK). Resulting fastq files were processed through the “pipeline-nanopore-ref-isoforms” (https://github.com/nanoporetech/pipeline-nanopore-ref-isoforms). Gene abundances was calculated implementing the -A parameter in StringTie (v 2.1.1 RRID:SCR_016323).

first: Mina

last: Ryten


title: Nanostring based analysis of CBF-AML patients

status: Public on Mar 08 2022

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

summary:
miR-130a is captured as part of a 798 gene probe set on a microarray plate for 48 CBF patients
In the group of patients defined here, survival characteristics and relapse information was collected to unbiasedly assess the impact of any miRNA on survival

overall_design: Microarray analysis of peripheral blood blast samples - Nanostring

first: Martino

last: Gabra

first: Leonardo

last: Salmena


title: Human Somitoids Generated by Reprogramming Pax8+ Urine Cells

status: Public on Sep 01 2022

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

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

overall_design: Refer to individual Series


title: Genome-wide characterization of aquaporins in Spirodela polyrhiza and expression of aquaporin gene family under high temperature stress

status: Public on Jun 28 2022

city: Bin Zhou

first: Shuai

last: Shang

address: Huang he road  391

institute: Binzhou university

summary: To investigate the expression of aquaporin gene family under high temperature stress

overall_design:
We then performed gene expression profiling analysis using data obtained from Different processing groups
Comparative gene expression profiling analysis of RNA-seq data formiddle temperature, high temperature and control group

first: Xuexi

last: Tang


title: Transcriptomic Analysis of Pubertal and Adult Virgin Mouse Mammary Epithelial and Stromal Cell Populations

status: Public on Sep 20 2022

city: Amsterdam

first: Renee

last: van Amerongen

address: Science Park 904

department: Swammerdam Institute for Life Sciences

institute: University of Amsterdam

summary: The mammary gland is a dynamic tissue that mainly develops postnatally under the influence of fluctuating hormone levels. This dataset contains bulk RNAseq data of different mouse mammary gland cell populations (basal, luminal and stromal) that were isolated either during puberty or at different stages of the adult virgin estrous cycle. These data are of interest to researchers in the mammary gland and breast cancer biology field as they allow studies on spatiotemporal, lineage specific changes in gene expression.

overall_design: Primary mouse mammary epithelial cell populations were isolated by enzymatic digestion followed by fluorescence activated cell sorting. For the puberty time point, mammary glands were isolated from 34-36 day old FVB/N mice. The 3rd and 4th glands of 4 individual mice from 3 different litters (P34. P35, P36) were isolated, pooled per mouse and processed to single cells. After sorting, the 4 individual samples from each litter were pooled per cell population (resulting in 3 replicate samples of each cell population). Ultimately, 2 replicate samples were used for RNAseq. These replicates were chosen based on RNA quality. For the adult time point, we tracked the estrous cycle of 32 adult FVB/N mice (age distribution 14-16 weeks) every day for at least 10 days to ensure that samples were isolated from mice that were stably cycling. The 3rd and 4th mammary glands were isolated, pooled per mouse and processed to single cells.  Adult samples were divided into 'early' and 'late' proestrus, estrous, metestrous and diestrus based on our interpretation of the accompanying vaginal cytology and histology. In case we did not observe a clear difference between early or late stages, we used the cell numbers of the different sorted populations as a second criterium. Ultimately, this resulted in 2 replicates per estrous cycle stage for each of the different cell populations, with each replicate containing the pooled cells from 2 or 3 mice. RNAseq for the puberty and adult timepoints was done in two different runs.

first: Renée


title: Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [miR130aKD_Kasumi]

summary: Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSC) point to shared core stemness properties. However, discordance between mRNA and protein signatures underscores an important role for post-transcriptional regulation by miRNAs in governing this critical nexus. Here, we identified miR-130a as a regulator of HSC self-renewal and differentiation. Enforced expression of miR-130a impaired lymphoid differentiation and expanded long-term HSC. Integration of protein mass spectrometry and chimeric AGO2 eCLIP-seq identified TBL1XR1 as a primary miR-130a target, whose loss of function phenocopied miR-130a overexpression. Moreover, we found that miR-130a is highly expressed in t(8;21) AML where it is critical for maintaining the oncogenic molecular program mediated by AML1-ETO. Our study establishes that identification of the comprehensive miRNA targetome within primary cells enables discovery of novel genes and molecular networks underpinning stemness properties of normal and leukemic cells.

overall_design:
Characterization of gene expression changes following miR-130a knock-down in Kasumi-1 cells.

>>>Submitter states: Raw data is being submitted separately to the EGA as we require controlled access for some data.<<<

first: Gabriela

last: Krivdova

first: Alex

first: John

middle: E

last: Dick


title: Global Identification of the miR-130a targetome in  human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

summary: Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells (HSC) point to shared core stemness properties. However, discordance between mRNA and protein signatures underscores an important role for post-transcriptional regulation by miRNAs in governing this critical nexus. Here, we identify miR-130a as a regulator of HSC self-renewal and differentiation. Integration of protein mass spectrometry and chimeric AGO2 eCLIP-seq identify TBL1XR1 as a primary miR-130a target. TBL1XR1 loss of function phenocopies miR-130a enforced expression impairing lymphoid differentiation and expanding long-term (LT)-HSC. This post-transcriptional regulation by miR-130a is usurped in t(8;21) acute myeloid leukemia (AML), whereby reduction of miR-130a results in differentiation of leukemic cells by altering chromatin binding and composition of the AML1-ETO complex. Our study establishes that comprehensive identification of the miRNA targetome within primary cells enables discovery of novel genes and molecular networks underpinning stemness properties of normal and leukemic cells.

overall_design: Identification of miR-130a targets using transcriptome-wide chimeric AGO2 eCLIP-seq and miR-130a targeted chimeric AGO2 eCLIP-seq in CD34+ hematopoietic stem and progenitor cells (HSPC) and Kasumi-1 AML cell line

first: Eric

last: Van Nostrand

first: Stefan

last: Aigner

last: Shiskin

first: Brian

last: Yee

first: Eugene

middle: R

last: Lechman


title: Catchet-MS identifies IKZF1-targeting Thalidomide analogues as novel HIV-1 latency reversal agents

status: Public on Feb 06 2022

city: Rotterdam

first: Tokameh

last: Mahmoudi

address: Dr Molewaterplein 40

institute: Erasmus Medical Center

summary: A major pharmacological strategy toward HIV cure aims to reverse latency in infected cells as a first step leading to their elimination. While the unbiased identification of molecular targets physically associated with the latent HIV-1 provirus would be highly valuable to unravel the molecular determinants of HIV-1 transcriptional repression and latency reversal, due to technical limitations, this has been challenging. Here we use a dCas9 targeted chromatin and histone enrichment strategy coupled to mass spectrometry (Catchet-MS) to probe the differential protein composition of the latent and activated HIV-1 5'LTR. Catchet-MS identified known and novel latent 5’LTR-associated host factors. Among these, IKZF1 is a novel HIV-1 transcriptional repressor, required for Polycomb Repressive Complex 2 recruitment to the LTR. We find the clinically advanced thalidomide analogue iberdomide, and the FDA approved analogues lenalidomide and pomalidomide, to be novel LRAs that, by targeting IKZF1 for degradation, reverse HIV-1 latency in CD4+T-cells isolated from virally suppressed people living with HIV-1.

overall_design: ChIP-sequencing was performed using the sequentially purified chromatin from  J-Lat 11.1 cells stably expressing HIV-LTR-HS2 guided HA-V5-FLAG-dCas9. Chromatin was first immunoprecipitated using V5 affinity beads to enrich for dCas9 bound sequences, eluted and re-immunoprecipitated using Histone H3-H2B affinity purification. One input and one immunoprecipitated sample were sequenced.

first: Enrico

last: Ne

first: Raquel

last: Crespo

first: Ray

last: Izquierdo-Lara

first: Shringar

last: Rao

first: Selin

last: Koçer

first: Alicja

last: Górska

first: Thomas

last: van Staveren

first: Tsung

last: Kan

first: Dick

last: Dekkers

first: Casper

last: Rokx

first: Panagiotis

last: Moulos

first: Pantelis

last: Hatzis

first: Robert-Jan

last: Palstra

first: Jeroen

last: Demmers


title: Co-condensation between transcription factor and coactivator p300 modulates transcriptional bursting kinetics

status: Public on Feb 28 2022

city: Beijing

first: Yihan

last: Lin

address: No.5 Yiheyuan Road, Haidian

institute: Peking University

summary: The coactivator p300/CBP regulates genes by facilitating the assembly of transcriptional machinery and by acetylating histones and other factors. However, it remains mostly unclear how both functions of p300 are dynamically coordinated during gene control. Here, we showed that p300 appears to orchestrate two functions through the formation of dynamic co-condensates with certain transcription factors (TFs), which is mediated by the interactions between the TF’s trans-activation domain (TAD) and the intrinsically disordered regions (IDRs) of p300. Co-condensation enables spatially defined, all-or-none activation of p300’s catalytic activity, priming the recruitment of other coactivators including Brd4. We further revealed that co-condensation modulates transcriptional initiation rate and burst duration of target genes, underlying nonlinear and cooperative gene regulatory functions. Intriguingly, such modulation is consistent with how p300 shapes transcriptional bursting kinetics globally. Together, complementary lines of evidence suggest a new p300-mediated gene control mechanism, where TF and p300 co-condensation contributes to transcriptional bursting regulation and cooperative gene control.

overall_design: Examination of RNA expression levels in mouse embryonic stem cells (mESC) WT cell line and in a p300 knock-in mESC cell line. The knock-in cell line (i.e., MLC460) was created by fusing monomeric enhanced green fluorescent protein (mEGFP) to the N-terminus of the endogenous p300 (mEGFP-p300) using CRISPR/Cas9. Two biological replicates were made for each cell line.

first: Liang

last: Ma


title: Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development

status: Public on Apr 19 2022

first: Zhuqing

last: Xiong

state: FOREIGN

address: Haidian District

institute: School of Life Science, Tsinghua Univers

summary:
In mammals, translational control plays critical roles during oocyte-to-embryo transition (OET) when transcription ceases. However, the underlying regulatory mechanisms remain challenging to study. Here, using low-input Ribo-seq (Ribo-lite), we investigated translational landscapes during OET using 30-150 mouse oocytes or embryos per stage. Ribo-lite can also accommodate single oocytes. Combining PAIso-seq to interrogate poly(A) tail lengths, we found a global switch of translatome that closely parallels changes of poly(A) tails upon meiotic resumption. Translation activation correlates with polyadenylation and is supported by polyadenylation signal proximal cytoplasmic polyadenylation elements (papCPEs) in 3' untranslated regions. By contrast, translation repression parallels global de-adenylation. The latter includes transcripts containing no CPEs or non-papCPEs, which encode many transcription regulators that are preferentially re-activated before zygotic genome activation. CCR4-NOT, the major de-adenylation complex, and its key adaptor protein BTG4 regulate translation downregulation often independent of RNA decay. BTG4 is not essential for global de-adenylation but is required for selective gene de-adenylation and production of very short-tailed transcripts. In sum, our data reveal intimate interplays among translation, RNA stability and poly(A) tail length regulation underlying mammalian OET.

Note: RNA-seq data for PN5 zygotes, early two-cell, late two-cell, four-cell and eight-cell stages and ICM were obtained from our previous publication (Zhang et al., Nature, 2016: Allelic reprogramming of the histone modification H3K4me3 in early mammalian development, GSE71434).

overall_design: By employing Ribo-seq and RNA-seq, we systematically examined the dynamics of translatome and transcriptome of WT oocytes, WT early embryos, Cnot6l/Btg4 KO oocytes and CHX/DRB treated early embryos.

first: Kai

last: Xu

first: Zili

first: Feng

last: Kong

first: Qiujun

last: Wang

first: Yujun

last: Quan

first: Lei

last: Li

first: Wei

last: Xie


title: Re-establishment of spermatogenesis after more than 20 years of cryopreservation of rat spermatogonial stem cells reveals an important impact in differentiation capacity

status: Public on Mar 15 2022

city: Philadelphia

first: Eoin

middle: Christopher

last: Whelan

state: PA

address: 3800 Spruce St

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

summary:
Treatment of cancer in children is increasingly successful but leaves many prepubertal boys suffering from infertility or subfertility later in life.  A current strategy to preserve fertility in these boys is to cryopreserve a testicular biopsy prior to treatment with the expectation of future technologies allowing for the reintroduction of stem cells and restoration of spermatogenesis.
Spermatogonial stem cells form the basis of male reproduction, differentiating into all germ cell types, including mature spermatozoa and can regenerate spermatogenesis following transplantation into an infertile testis.   Here we demonstrate for the first time that rat spermatogonial stem cells frozen for more than 20 years can be transplanted into recipient mice and produce all differentiating germ cell types.
However, compared with freshly-isolated cells or those frozen for a short period of time, long frozen cells do not colonize efficiently and showed reduced production of spermatids. Single cell RNA sequencing reveled similar profiles of gene expression changes between short and long frozen cells as compared with fresh immediately after thawing. Conversely, following transplantation, long frozen samples showed enhanced stem cell signaling in the undifferentiated spermatogonia compartment, consistent with self-renewal and a lack of differentiation.
In addition, long frozen samples showed fewer round spermatids with detectable protamine expression, suggesting a partial block of spermatogenesis after meiosis resulting in a lack of elongating spermatids. These findings strongly suggest that prolonged cryopreservation can impact the success of transplantation to produce spermatogenesis, which may not be revealed by analysis of the cells immediately after thawing.

overall_design: Single-cell RNA analysis of 56 samples across three treatments. Freezing state, 3 levels - fresh, short frozen, long frozen. Transplantation status, 2 levels - untransplanted and transplanted. Selection, 2 levels - unselected and EpCAM+ cells. Each treatment contains 3-5 biological replicates.

first: Fan

last: Yang

first: Mary

last: Avarbock

first: Megan

last: Sullivan

first: Daniel

last: Beiting

first: Ralph

middle: L

last: Brinster


title: Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [TBL1XR1 KD]

first: Alexander

last: Murison

overall_design:
Characterization of gene expression changes following TBL1XR1 knock-down in hematopoietic stem/progenitor cells.

>>>Submitter states: Raw data is being submitted separately to the EGA as we require controlled access for some data.<<<

first: Gabriela

last: Krivdova

first: Alex

first: John

last: Dick


title: Gene expression analysis of H1299 cells in response to the presence or absence of glutamine or glucose

status: Public on Apr 30 2022

city: Ann Arbor

first: Yue

last: Zhao

state: MI

address: 100 Washtenaw Avenue

department: Computational Medicine and Bioinformatics

institute: University of Michigan

summary: By a transcriptome analysis using RNA sequencing in H1299 cells, a non-small cell lung cancer cell line (NSCLC), we determined the response of lipogenic genes to absence vs. presence of glutamine (Gln) or glucose (Gluc). We found that neither glutamine nor glucose alone was able to activate the expression of genes regulating fatty acid and cholesterol synthesis, and uptake, including SREBF1, SREBF2, ACLY, ACACA, FASN, SCD1, HMGCR and LDLR, as compared to absence of both. And, activation of lipogenic genes required the presence of both glutamine and glucose, but SCAP gene expression was not affected by either glutamine or glucose. The RNA sequencing analysis in H1299 cells also confirmed that ammonia, similarly to glutamine, significantly activated the expression of genes controlling the fatty acid and cholesterol synthesis pathways as compared to glucose alone. This study detemines the intrinsic molecular connection between glutamine, glucose and lipid synthesis.

overall_design: H1299 cells were treated in fresh serum-free RPMI 1640 medium with or without glutamine (4 mM) or glucose (5 mM), or NH4Cl (4 mM) for 12 hr before analysis.

first: Deliang

last: Guo

first: Chunming

last: Cheng


title: Transcriptome changes upon androgen deprivation and DHT stimulation in LNCaP cells

status: Public on Jan 17 2022

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: The transcription factor and RNA-interacting Y-box binding protein-1 (YB-1 protein, YBX1 gene) has gained interest as a prognostic biomarker and therapeutic target in various malignancies including prostate cancer. Using a custom prostate-cancer-focussed microarray platform, we have established a transcriptome-wide profile of YB-1 target transcripts in the androgen sensitive prostate cancer cell line LNCaP.

overall_design: Gene expression changes in LNCaP prostate cancer cells in standard proliferative culture (FBS), in androgen ablated culture conditions (CSS - charcoal stripped serum) and after stimulation with 10 nM dihydrotestosterone (DHT) for 48 hrs.

first: Anja

last: Rockstroh

first: Morgan

last: Pokorny

first: Chelsea

last: Walker

first: Melanie

last: Lehman

first: Stephen

last: McPherson


title: CALGB 40603: Randomized Phase II 2 x 2 Factorial Trial of the Addition of Carboplatin +/- Bevacizumab to Neoadjuvant Weekly Paclitaxel Followed by Dose-Dense AC in Hormone Receptor-Poor/HER2-Negative Resectable Breast Cancer

status: Public on Jan 21 2022

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: This randomized phase II trial studies how well paclitaxel with or without carboplatin and/or bevacizumab followed by doxorubicin and cyclophosphamide works in treating patients with breast cancer that can be removed by surgery. Drugs used in chemotherapy, such as paclitaxel, carboplatin, doxorubicin, and cyclophosphamide, work in different ways to stop the growth of tumor cells, either by killing the cells or by stopping them from dividing. Bevacizumab may stop the growth of tumor cells by blocking blood flow to the tumor. Giving chemotherapy together with bevacizumab before surgery may make the tumor smaller and reduce the amount of normal tissue that needs to be removed.

overall_design:
Examination of pre-treatment breast carcinoma samples from patients that were afterwards randomized to neoadjuvant chemotherapy +/- bevacizumab and/or carboplatin.

The raw data have been deposited to dbGaP (phs001863) due to patient privacy concerns.

middle: M

first: Lisa

last: Carey

first: Ian

last: Krop

first: Deanna

last: Kroetz

first: David

last: Ollila

first: Baljit

last: Singh

first: Jennifer

last: Bellon

first: Patricia

last: Spears

first: Matthew

middle: G

last: Soloway


title: The effect of lithium and dexamethasone on fetal rat metatarsal bones transcriptome

status: Public on Jan 01 2022

city: Prague

first: Martin

last: Bezdicka

state: Czech Republic

address: V Uvalu 84

department: Department of Pediatrics

country: Czech Republic

institute: Second Faculty of Medicine and Motol University Hospital

summary: While dexamethasone impairs bone growth and adds to the development of osteoporosis, lithium enhances cell renewal. The aim of this project was to explore the genes and pathways affected by adding dexamethasone, lithium or both to the medium in which fetal rat metatarsal bones were cultivated. RNA sequencing and differential gene expression analysis were implemented to describe the transcriptome of the metatarsals. We identified significant opposite as well as independent effects of the substances on several cellular pathways. This may open up to identify the mechanisms of dexamethasone induced bone growth and structure impairment and possible preventive measures.

overall_design: Primary cultured fetal rat metatarsal bones were incubated in one of the four conditions: standard medium only (control sample, C), standard medium + dexamethason (Dex), standard medium + lithium (Li), standard medium + dexamethason and lithium (DL), at 37°C in 5% CO2 for 72 hours. All samples were prepared in triplicates.

first: Ondrej

last: Soucek

last: Cinek


title: MicroRNA156 conditions auxin sensitivity to enable growth plasticity in response to environmental changes in Arabidopsis (miRNA-Seq)

status: Public on Feb 11 2023

city: Riverside

first: Meng

last: Chen

state: CA

address: 2150 Batchelor Hall, 900 University Ave.

institute: University of California, Riverside

summary: MicroRNAs (miRNAs) play diverse roles in plant development, but whether and how miRNAs participate in thermomorphogenesis remains ambiguous. Here we show that HYPONASTIC LEAVES1 (HYL1) – a key component of microRNA biogenesis – acts downstream of the thermal regulator PHYTOCHROME INTERACTING FACTOR 4 in temperature-dependent plasticity of hypocotyl growth in Arabidopsis. A hyl1-2 suppressor screen identified a dominant dicer-like1 (dcl1) allele, dcl1-24, which rescues hyl1-2’s defects in miRNA biosynthesis and warm temperature-induced hypocotyl elongation. Genome-wide miRNA and transcriptome analysis reveal microRNA156 (miR156) and its target SQUAMOSA PROMOTER-BINDING-LIKE 9 (SPL9) as critical regulators of thermomorphogenesis. Surprisingly, perturbation of the miR156/SPL9 module disengages seedling responsiveness to warm temperatures by impeding auxin sensitivity. Moreover, the miR156-dependent auxin sensitivity also operates in the shade avoidance response at lower temperatures. Thus, these results unveil the miRNA156/SPL9 module as a previously-uncharacterized genetic circuitry that enables plant growth plasticity in response to environmental temperature and light changes.

overall_design: We compared global miRNA levels in 4-d-old Col-0, hyl1-2 and dcl1-24/hyl1-2 seedlings grown in 50 umol m-2 s-1 red light at either 21  C or 27  C.

first: Xuemei


title: Single Cell RNA Sequencing reveals heterogenous tumor associated immune cell compartment in lean vs obese mice using an MC38 tumor model

status: Public on Oct 06 2021

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

institute: Vanderbilt University Medical Center

summary: Immunotherapy is life saving for some cancer patients and while obesity can promote cancer, it may also increase immunotherapy efficacy.  Mechanisms of this effect have been unclear, although obesity can promote an inflammatory state that may modify tumor infiltrating lymphocytes and tumor associated macrophage (TAM) populations in tumors.  To identify mechanisms by which obesity affects anti-tumor immunity, diet-induced obese and lean C57BL/6 mice received subcutaneous murine MC38-CEA1 colon cancer tumors. Obesity increased tumor growth rate and tumor burden. Fewer immune cells were present in tumors from obese mice, and the T cells had an activated and exhausted phenotype. Macrophages in obese animals had decreased expression of iNOS2 and MHCII, supporting a weaker “M1” anti-tumor phenotype compared to lean mice. When treated with anti-PD-1 antibodies, however, obese mice had a greater absolute decrease in tumor burden than lean mice. PD-1 blockade repolarized the macrophages to an M1-phentoype in obese mice, but this did not occur in the lean mice. Mechanistically, leptin is a pro-inflammatory adipokine that is increased in obesity and may mediate enhanced anti-tumor immunity in obesity.  To test the effect of leptin on tumor growth and anti-tumor immunity, lean mice were treated with leptin and tumors were observed over time. Leptin had single-agent preventative and therapeutic anti-tumor efficacy similar to PD-1 checkpoint therapy.  These data demonstrate that obesity has dual effects in cancer through promotion of tumor cell initiation while also enhancing anti-tumor immunity through elevated levels of leptin that can reprogram inflammatory macrophages.

overall_design: 8-week-old C57BL/6 male mice were fed ad libitum a 10% kcal from fat (low fat) diet or a 45% kcal fat (high fat) diet (Research Diets D12450H and D12451, respectively). Following 28 weeks of diet treatment mice were injected subcutaneously with 2x10^5 MC38 cells. Tumors were collected on Day 20 post injection and mechanically and enzymatically digested using miltenyi mouse tumor digestion kit following manufacturer’s instructions. CD45+ cells were separated from tumor suspensions using CD45+ microbeads (miltenyi) and enriched for live cells using a dead cell removal kit (miltenyi). Three samples from each diet treatment group were resuspended in PBS + 0.4% FBS and pooled together in equal number of live cells prior to submitting to single cell sequencing.

first: Jackie

last: Bader

first: Xiang

last: Ye


title: Transcriptomic profile of YB-1 regulated downstream targets in LNCaP prostate cancer cells

first: Colleen

last: Nelson

summary:
The transcription factor and RNA-interacting Y-box binding protein-1 (YB-1 protein, YBX1 gene) has gained interest as a prognostic biomarker and therapeutic target in various malignancies including prostate cancer. Using a custom prostate-cancer-focussed microarray platform, we have established a transcriptome-wide profile of YB-1 target transcripts in the androgen sensitive prostate cancer cell line LNCaP, including RNAs regulated by YB-1 at the transcriptional and post-transcriptional level; under standard culture conditions (FBS), in androgen deprived culture conditions (CSS) and following stimulation with dihydrotestosterone (DHT).

This SuperSeries is composed of the SubSeries listed below.

overall_design:
The project consists of 3 data sets / SubSeries that were processed and analysed separately. Each data set was derived from 3-4 independent biological repeats for each sample group.

Refer to individual Series

first: Anja

last: Rockstroh

first: Morgan

last: Pokorny

first: Chelsea

last: Walker

first: Melanie

last: Lehman

first: Stephen

last: McPherson

middle: C


title: Identification of the Global miR-130a Targetome Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML

first: Alexander

last: Murison

overall_design: Refer to individual Series


title: Global Identification of the miR-130a targetome in  human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]

summary: Gene expression profiling and proteome analysis of normal and malignant hematopoietic stem cells have firmly established the existence of shared core stemness properties. However, the discordance between mRNA and protein signatures underscores an important role for post-transcriptional regulation by miRNAs in governing this critical nexus. Here, we identify miR-130a as a regulator of hematopoietic stem cell (HSC) self-renewal and lineage differentiation. Integration of mass spectrometry and chimeric AGO2 eCLIP-seq identify TBL1XR1 as a primary miR-130a target. TBL1XR1 loss of function impairs lymphoid differentiation and expands long-term (LT)-HSC. This post-transcriptional regulation by miR-130a is usurped in t(8,21) acute myeloid leukemia (AML). Reduction of miR-130a levels in t(8,21) AML cells results in altered chromatin binding and composition of the AML1-ETO complex, demonstrating that miR-130a is critical for maintaining the oncogenic molecular program mediated by AML1-ETO. Our study establishes that comprehensive identification of the miRNA targetome within primary tissue enables the discovery of novel genes and molecular networks underpinning stemness properties of normal and leukemic cells.

overall_design:
Examination of binding occupancy of AML1-ETO following miR-130a knock-down in Kasumi-1 cell line.

>>>Submitter states: Raw data is being submitted separately to the EGA as we require controlled access for some data.<<<

first: Gabriela

last: Krivdova

first: Sajid

middle: A

last: Marhon

first: John

last: Dick


title: scRNA-seq of BMP-treated micropatterned hPSCs after 42h

status: Public on Aug 14 2021

first: Idse

last: Heemskerk

address: 109 Zina Pitcher Pl

summary: We performed 10x scRNA-seq of BMP4-treated micropatterned hPSCs (700um diameter) after 42h

first: Kyoung

last: Jo


title: YB-1 knock.down - siRNA driven YBX1 knock.down in LNCaP cells in std FBS culture

overall_design: Gene expression changes in LNCaP prostate cancer cells in standard FBS culture condition after siRNA driven knock down of YBX1 (YBX1-SI) for 48 hrs compared to a non-targeting control siRNA (SC).


title: Interaction between maternal immune activation and peripubertal stress in rats: impact on cocaine addiction-like behaviour, morphofunctional brain parameters and striatal transcriptome

status: Public on Oct 04 2021

city: Madrid

first: Alejandro

last: Higuera-Matas

state: Madrid

address: Calle Juan del Rosal 10

department: Psychobiology

country: Spain

institute: Universidad Nacional de Educación a Distancia (UNED)

summary: Substance use disorders are more prevalent in schizophrenia, but the causal links between both conditions remain unclear. Maternal immune activation (MIA) is associated with schizophrenia which may be triggered by stressful experiences during adolescence. Therefore, we used a double-hit rat model, combining MIA and peripubertal stress (PUS), to study cocaine addiction and the underlying neurobehavioural alterations. We injected lipopolysaccharide or saline on gestational days 15 and 16 to Sprague-Dawley dams. Their male offspring underwent five episodes of unpredictable stress every other day from postnatal day 28 to 38. When animals reached adulthood, we studied cocaine addiction-like behaviour, impulsivity, Pavlovian and instrumental conditioning, and several aspects of brain structure and function by MRI, PET and RNAseq. MIA facilitated the acquisition of cocaine self-administration and increased the motivation for the drug; however, PUS reduced cocaine intake, an effect that was reversed in MIA + PUS rats. We found concomitant brain alterations: MIA + PUS altered the structure and function of the dorsal striatum, increasing its volume and interfering with glutamatergic dynamics (PUS decreased the levels of NAA + NAAG but only in LPS animals) and modulated specific genes that could account for the restoration of cocaine intake such as the pentraxin family. On its own, PUS reduced hippocampal volume and hyperactivated the dorsal subiculum, also having a profound effect on the dorsal striatal transcriptome. However, these effects were obliterated when PUS occurred in animals with MIA experience. Our results describe an unprecedented interplay between MIA and stress on neurodevelopment and the susceptibility to cocaine addiction.

overall_design: Gene expression profiles of the nucleus accumbens and dorsolateral striatum of male Sprague-Dawley rats after prenatal immune activation induced by LPS administration and peripubertal unpredictable stress. We analysed 24 samples (3 per group) corresponding to  experimental groups (including saline-exposed and/or non-stressed controls).

first: Roberto

last: Capellán


title: a6A-seq: N6-allyladenosine-based cellular messenger RNA metabolic labelling and sequencing

status: Public on Dec 31 2021

first: Xiao

last: Shu

state: Zhejiang Province

address: Zheda Road 38

department: Department of Polymer Science and Engineering

institute: Zhejiang university

type: Methylation profiling by high throughput sequencing

summary: In this work, we applied a6A to label and sequence cellular mRNA in an immunoprecipitation-free and mutation-based manner, termed a6A-seq.  a6A-seq was utilized to study the change of cellular gene expression profile under a methionine-free stressed condition. Compared with regular RNA-seq, a6A-seq could more sensitively detect the level change of newly synthesized mRNAs.

overall_design: Profiles of a6A-labeled mRNA in HeLa cells (methionine-deficient and methionine-sufficient treatment) were generated by high-throughput sequencing, in duplicate, using HiSeq X Ten.


title: A two-color haploid genetic screen identifies novel host factors involved in HIV-1 latency

status: Public on Nov 22 2021

first: Tokameh

last: Mahmoudi

summary: To identify novel host factors as putative targets to reverse HIV-1 latency, we performed an insertional mutagenesis genetic screen in a latently HIV-1-infected pseudohaploid KBM7 cell line (Hap-Lat). Following mutagenesis, insertions were mapped to the genome, and bioinformatic analysis resulted in the identification of 69 candidate host genes involved in maintaining HIV-1 latency.

overall_design: A latently HIV-1-infected pseudohaploid KBM7 cell line was generated according to a previously described strategy used in Jurkat cells (Jordan et al., 2003). Subsequently, haploid latent (Hap-Lat) cells harboring a latent integrated HIV-1-derived virus containing a green fluorescent protein (GFP) reporter were subjected to insertional mutagenesis using a gene-trap virus carrying an mCherry reporter. Instead of using a lethality-selecting scheme, our system relies on fluorescence-activated cell sorting (FACS) to select for reactivated cells, marked by elevated GFP expression resulting from insertional mutagenesis of genes essential for maintenance of HIV-1 latency. Cells expressing both GFP and mCherry were FACS sorted and expanded for multiple rounds, after which GT insertion sites were mapped and identified by inverse PCR and high-throughput sequencing.

first: Michael

last: Röling

first: Panagiotis

last: Moulos

first: Robert-Jan

last: Palstra

first: Vaggelis

last: Harokopos

first: Pantelis

last: Hatzis


title: Bioactive RNA in Maternal Breastmilk

status: Public on Jan 11 2022

city: Hershey

first: Steven

last: Hicks

state: Pennsylvania

address: 500 University Drive

department: Pediatrics

institute: Penn State College of Medicine

summary: Describe the changing landscape of milk microRNA levels over time, and their relationships to maternal and infant health

overall_design: Longitudinal cohort study of 221 breastfeeding mother-infant dyads from birth through twelve months of age

middle: D


title: Single-cell analysis of the epigenomic and transcriptional landscape of innate immunity to seasonal and adjuvanted pandemic influenza vaccination in humans (TIV_scRNA-seq)

status: Public on Jun 25 2021

city: Palo Alto

first: Florian

last: Wimmers

address: 1651 Page Mill Road

department: School of Medicine

institute: Stanford University

summary: Human subjects were vaccinated with seasonal influenza vaccine (TIV, 2014-2015). We then used scRNA-seq to constructed the single-cell landscape of the innate immune response to TIV at the transcriptional level. PBMCs from vaccinated individuals were isolated at day 0, 1, and 30, then enriched for DC subsets using flow cytometry and analyzed using droplet-based single-cell gene expression profiling.

overall_design: A total of 9 samples from 3 healthy individuals at 3 time points was analyzed: day 0 before vaccination, and day 1 and day 30 after vaccination. Individual abx-02 lacks d30 sample.

first: Tal

last: Ashuach

first: Sanne

last: deJong


title: Roles of Stra8 and Tcerg1l in retinoic acid induced spermatogonial differentiation in mouse.

status: Public on May 05 2021

first: Eoin

last: Whelan

summary:
Retinoic acid (RA) induces spermatogonial differentiation, but the mechanism by which it operates remains largely unknown. We developed a germ cell culture assay system to study genes involved in spermatogonial differentiation triggered by RA. Stimulated by Retinoic Acid 8 (Stra8), an RA-inducible gene, is indispensable for meiosis initiation, and its deletion results in a complete block of spermatogenesis at the pre-leptotene/zygotene stage due to failure to complete pre-meiotic DNA replication.
To interrogate the role of Stra8 in RA mediated differentiation of spermatogonia, we derived germ cell cultures from the neonatal testis of both wild type and Stra8 knock-out mice. We provide the first evidence that Stra8 plays a crucial role in modulating the responsiveness of undifferentiated spermatogonia to RA and facilitates transition to a differentiated state. Stra8-mediated differentiation is achieved through downregulation of a large portfolio of genes and pathways, most notably including genes involved in the spermatogonial stem cell self-renewal process.
We also report here for the first time the role of Transcription Elongation Regulator-1 Like (Tcerg1l) as a downstream effector of RA-induced spermatogonial differentiation.

overall_design: Cultured germ cells of WT and Stra8-KO genotype were treated with DMSO (control) or retinoic acid (RA) for 4, 8 or 24 hours along with 0h untreated samples. mRNA was extracted from three replicates of each treatment/time point and sequenced.

first: Nilam

last: Sinha

middle: W

last: Tobias

first: Mary

last: Avarbock

first: Darko

last: Stefanovski

first: Ralph

last: Brinster


title: ZFP36L2-mRNA Interaction: Drawing general rules based on transcriptomic analysis

status: Public on Oct 01 2021

first: Alain

last: Laederach

institute: UNC-Chapel Hill

summary: In this study we focus on identifying potential physiological targets of ZFP36L2 (Zinc finger protein like 2 or L2), one of the three primate members of the ZFP36 protein family. Most studies on ARE specificity of this small family were conducted using the prototypical family member, ZFP36 or TTP; however, less is known about the other family member’s specificity. Previous studies of ZFP36L2 target mRNAs identified a high proportion of transcription factors in two different systems, cells from the erythrocyte lineage and oocytes. However, there is minimal overlap between the genes identified in these studies and those identified here using mouse spleens lacking ZFP36L2 (L2-cKO). This observation suggests that ZFP36L2 targeting is occurring in a highly tissue specific manner. Aiming to understand what factors govern this potential tissue specificity, we characterized the differentially expressed genes in our L2-cKO mouse model in the spleen, an organ that expresses L2 at high levels in humans and mice. We performed transcriptome-wide analysis in RNA spleen samples from mice lacking ZFP36L2 (L2-cKO) and normally expressing (WT). Differential gene expression (DEG) of WT vs. L2-cKO spleens revealed 549 up regulated and 603 down regulated genes. Nine genes were validated in qPCR assays.

overall_design:
Adenine-uridine rich element-RNA-binding proteins (ARE-RBP) generally either stabilize or destabilize the target transcripts they bind. A remaining challenge in the field is understanding the specificity of targeting by ARE-RBPs and how this dictates function.
We performed transcriptome-wide analysis in RNA spleen samples from mice lacking ZFP36L2 (L2-cKO) and normally expressing (WT).

first: Ian

last: Redmon

first: Matthew

last: Ardizzone

first: Silvia

middle: B

last: Ramos


title: Single cell transcriptomics reveal the heterogeneity of the human cornea to identify novel markers of the limbus and stroma

status: Public on Oct 25 2021

city: Maastricht

first: Vanessa

last: LaPointe

address: Universiteitssingel 40

institute: MERLN Institute

summary: The cornea is the clear window that lets light into the eye. It is composed of five layers: epithelium, Bowman’s layer, stroma, Descemet’s membrane and endothelium. The maintenance of its structure and transparency are determined by the functions of the different cell types populating each layer. Attempts to regenerate corneal tissue and understand disease conditions requires knowledge of how cell profiles vary across this heterogeneous tissue. We performed a single cell transcriptomic profiling of 19,472 cells isolated from eight healthy donor corneas. Our analysis delineates the heterogeneity of the corneal layers by identifying cell populations and revealing cell states that contribute in preserving corneal homeostasis. We identified that the expression of CAV1, CXCL14, HOMER3 and CPVL were exclusive to the corneal epithelial limbal stem cell niche, CKS2, STMN1 and UBE2C were exclusively expressed in highly proliferative transit amplifying cells, and NNMT was exclusively expressed by stromal keratocytes. Overall, this research provides a basis to improve current primary cell expansion protocols, for future profiling of corneal disease states, to help guide pluripotent stem cells into different corneal lineages, and to understand how engineered substrates affect corneal cells to improve regenerative therapies.

overall_design: In this study, we provide a high-quality single-cell ribonucleic acid sequencing (scRNAseq) dataset from 19,472 corneal cells isolated from four female and four male donors. Six full donor corneas and the limbi of two donor corneas were manually dissected by layer and dissociated into single cells for single-cell RNA sequencing. Prior to loading the cells on the 10x Chromium controller, cells were rehydrated in rehydration buffer. Cells were then counted to assess cell integrity and concentration. Approximately 9,000 cells (comprising 3,000 cells from each of the three layers) from corneas 01, 02, 03 and 04 were separately loaded by layer and cornea. Furthermore, 3,000 cells (1,000 cells from each of the three layers) from corneas 05 and 06, and 3,000 cells from corneas 07 and 08 (from the limbal samples) were separately loaded. The resulting sequencing libraries were prepared following a standard 10x Genomics protocol. After filtering low quality cells, the transcriptome profiles of 19,472 cells were further analyzed

first: Pere

last: Catala Quilis


title: Pod size regulator in soybean (Glycine max L. Merr.): heat shock protein 70 is associated with duration of cell proliferation in early pod development

status: Public on Apr 01 2021

city: Fukuoka

first: Yushi

last: Ishibashi

state: Fukuoka

address: 744 Motooka, Nishi-ku

department: Department of Bioresource Sciences

institute: Kyushu University, Faculty of Agriculture

summary: Pod size varies among soybean cultivars, but the mechanism is largely unknown. We investigated pod size differences between two cultivars. The larger pod of ‘Tachinagaha’ was due to longer cell proliferation activity than in the shorter pod of ‘Iyodaizu’. Pod size of soybean 9  (GmPSS9), a member of the heat shock protein 70 family, was detected in a major QTL (qPSS on Chr. 2) as a candidate gene for determining pod length by QTL and expression QTL analysis. Expression of GmPSS9 in pods was higher in ‘Tachinagaha’ than in ‘Iyodaizu’ and was highest in early pod development. The difference in expression resulted from an indel polymorphism, Tachinagaha-specific-1, which has a 5′-UTR Py-rich stretch motif that boosts transcription. Treatment with an HSP70 inhibitor reduced plant height, pod length, and pod cell number. Our results identify GmPSS9 as a target gene for pod length which regulates cell number during early pod development.

overall_design: Differentially expressed genes in pod at 9 days after flowering between Tachinagaha and Iyodaizu cultivars in soybean.

first: Seiya

last: Tanaka

first: Andressa

last: Nakagawa

first: Yuri

last: Ariyoshi

first: Takatoshii

last: Taniguchi

first: Norimitsu

last: Hamaoka

first: Mari

last: Iwaya-Inoue


title: DREAM, a Possible Answer to the Estrogen Paradox of the Women’s Health Initiative Trial

status: Public on Dec 27 2021

city: Edmonton

first: Judith

last: Hugh

state: Alberta

address: 87 ave and 114 st

department: Laboratory Medicine and Pathology

institute: University of Alberta

summary: Estrogen is thought to cause proliferation of all estrogen receptor positive (ER+) breast cancers. Paradoxically, in the Women’s Health Initiative Trial, estrogen-only hormone replacement therapy reduced the incidence and mortality of low grade, ER+, HER2- breast cancer. We gave estradiol to 19 post-menopausal women with newly diagnosed low-grade, ER+, HER2- breast cancer in a prospective window of opportunity clinical trial and examined the changes in proliferation and gene expression before and after estradiol treatment. Ki67 decreased in 13/19 (68%) patients and 8/13 (62%) showed a decrease in Risk of Recurrence Score. We chose three prototypical estrogen responders (greatest decrease in ROR) and non-responders (no/minimal change in ROR) and applied a differential gene expression analysis to develop pre-treatment (PRESTO-30core) and post-treatment (PRESTO-45surg) gene expression profiles. The PRESTO-30core predicted adjuvant benefit in a published series of tamoxifen, the partial estrogen agonist. Of the 45 genes in the PRESTO-45surg, thirty contain the Cell cycle genes Homology Region (CHR) motif that binds the class B multi-vulva complex (MuvB) a member of the DREAM (Dimerization partner, retinoblastoma-like proteins, E2F, MuvB) complex responsible for reversible cell cycle arrest or quiescence. There was also near uniform suppression (89%) of the remaining DREAM genes consistent with estrogen induced activation of the DREAM complex to mediate cell cycle block after a short course of estrogens. To our knowledge, this is the first report to show hormonal modulation of DREAM genes and suggest involvement of DREAM pathway associated quiescence in endocrine responsive post-menopausal ER+ breast cancers.

overall_design: Paired RNA profiles from ER+ postmenopausal breast cancer tissues obtained at the initial needle-core biopsy (Bx) and following < 2 weeks of 6 mg daily estradiol (Sx) were generated using the Illumina NextSeq500 platform.

first: Lacey

middle: J

last: Haddon

first: John

last: Githaka