title: Expression data of PTEN deficient PKO cells

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

summary:
Incurable metastatic castration-resistant prostate cancer (CRPC) eventually occurs after androgen deprivation treatment. It is important to understand how CRPC initiates/progress.
We generated a mouse androgen-independent prostate cancer cell line (PKO) from PTEN null and Hi-Myc transgenic mice in C57BL/6 background. Here we analyzed the expression profiles of PKO cells.

overall_design: The expression profile of PKO cells were analyzed and compared with Myc-Cap cells, an androgen-dependent mouse prostate cancer cell line.

first: Xueliang

last: Gao

first: Haizhen

last: Wang


title: Identification of tumor-related genes via RNA sequencing of tumor tissues in Xenopus tropicalis

status: Public on Aug 23 2023

city: Meguro-ku

first: Tatsuo

last: Michiue

address: 3-8-1, Komaba

country: Japan

institute: The University of Tokyo

type: Expression profiling by high throughput sequencing

summary: Cancer is often caused by mutations in many genes. Although genomic studies have identified many oncogenes and tumor suppressor genes, gene sets involved in tumorigenesis remain poorly understood. Xenopus, a genus of aquatic frogs, is a useful model to identify gene sets because it can be genetically and experimentally analyzed. So we analyzed gene expression in tumor tissues of three individuals in Xenopus tropicalis and compared with that in normal tissues.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor tumors and normal tissues of Xenopus tropicalis.

first: Kazuki

last: Kitamura


title: Transcriptional analysis of ZX-7101 treatment.

city: Beijing

first: Rui-Ting

last: Li

state: Beijing

address: No.20 Dongda Street, Fengtai District

department: State Key Laboratory of Pathogen and Biosecurity

country: China

institute: Beijing Institute of Microbiology and Epidemiology

summary: The potential mechanism of ZX-7101 against influenza viruses is unknown. In this study,  Transcriptome analysis demonstrated that ZX-7101 could directly inhibit viral replication and therefore affected the expression of genes involved in inflammation and the cell cycle.

overall_design: A549 cells were infected with pH1N1 for 1 hour. The cells were then treated with ZX-7101 (10 nM) for 48 hours. Total RNA was extracted at 48 hpi for RNA-seq

first: Dan

last: Luo

first: Qing

last: Ye

first: Hang-Yu

last: Zhou


title: RNA sequencing of rapidly paced canine atrium and its involvement in atrial fibrosis

city: Tianjin

first: Xue

last: Liang

address: Pingjiang Road

institute: Tianjin Institute of Cardiology, the Second Hospital of Tianjin Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: The findings of this study strengthen the role of circRNAs in AF-induced fibrosis and provide a perspective on disease mechanism and therapeutic target for AF.

overall_design: In this study, standardized reads number was used to screen differentially expressed circRNAs between two groups with multiple changes≥2.0 and P≤0.05 as the threshold of differential circRNAs.


title: Transcriptome reprogramming of Nannochloropsis oceanica in response to Nitrogen deprivation

city: Haikou

first: Li

last: WEI

state: Hainan

address: No. 99 Longkun South Road, Haikou City

institute: Hainan normal university

summary: Transcriptional regulation in response to nitrogen stress  for one ant two days, and epigenome-association with phenotypic plasticity of lipid metabolism are  uncovered in marine microalga Nannochloropsis oceanica IMET1.

overall_design: mRNA profiles of Nannochloropsis oceanica under nitrogen repletion and nitrogen deprivation.


title: Genome-wide analysis of INO80 knockdown

city: Tokyo

first: Imari

last: Mimura

address: 7-3-1 Hongo Bunkyo-ku

summary: We report the high-throughput profiling of INO80 knockdown by siRNA in human kidney-2 cells (HK-2).  We found that downstream target genes of INO80. This study provides novel insights into the chromatin remodeling factors regulated by INO80 in renal epithelial cells.

overall_design: We exposed HK-2 cells with control siRNA and INO80 siRNA for 48 hours. We collected mRNA of each samples and performed RNA-seq. Each condition is triplicate (N=3).The mRNA were analyzed by NGS.

first: Rika

last: Miura


title: Regulatory B cells expressing granzyme B (GZMB+Bregs)

city: Nantes

first: Nicolas

last: Sailliet

address: 30 Boulevard Jean Monnet

country: France

institute: Nantes université

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

overall_design: Refer to individual Series


title: Identification of adipose tissue metabolic memory of anorexia nervosa

city: La Jolla

first: Olivia

last: Osborn

state: CA

address: 9500 Gilman Drive

department: Medicine

country: USA

institute: UCSD

summary: Anorexia nervosa (AN) is a complex debilitating disease characterized by intense fear of weight gain and excessive exercise. It is the deadliest of any psychiatric disorder with a high rate of recidivism, yet its pathophysiology is unclear. The Activity-Based Anorexia (ABA) paradigm is a widely accepted mouse model of AN that recapitulates hypophagia and hyperactivity despite reduced body weight, however, not the chronicity. Here, we modified the prototypical ABA paradigm to increase the time to lose 25% of baseline body weight from less than 7 days to more than 2 weeks. We used this paradigm to identify persistently altered genes after weight restoration that represent a metabolic memory of under-nutrition and may contribute to AN relapse. We focused on adipose tissue as it was identified as a major location of metabolic memory of over-nutririon. We identified 300 persistently dysregulated genes, including Calm2 and Vps13d, which could be potential global regulators of metabolic memory in both chronic over- and under-nutrition. However, despite being on the opposite spectrum of weight perturbations, the majority of metabolic memory genes of under- and over-nutrition do not overlap, suggestive of the different mechanisms involved in these extreme nutritional statuses.

overall_design: Randomized controlled study

first: Rizaldy

middle: C

last: Zapata

first: Chanond

middle: A

last: Nasamran

first: Daisy

middle: R

last: Chillin-Fuentes

first: Stephanie

last: Dulawa


title: Gene expression profile of CD4+ CD25- T cells in coculture with regulatory B cells expressing granzyme B (GZMB+Bregs) or total B cells

summary: Regulatory B cells are considered as a very heterogenous population of different origin and functions. Here, we show that Notably, Bregs induced a strong inhibition of T cell genes associated to proliferation, activation, inflammation and apoptosis compared to total  B cells. We identified and validated 5 receptor/ligand interactions between Bregs and T cells.

overall_design: We used single cell RNA sequiencing (scRNA-seq) to analyze the impact of regulatory B cell expressing GZMB (GZMB+Bregs) or non-Bregs   on CD4+CD25- activated T cell transcriptome.

first: Hoa

last: Mai

first: Amandine

last: Dupuy

first: Gaëlle

last: Tilly

first: Cynthia

last: Fougeux

first: Martin

last: Braud

first: Magali

last: Giral

first: Jean-Michel

last: Robert

last: Degauque

first: Richard

last: Danger

first: Jeremie

last: Poschmann

first: Sophie

last: Brouard


title: Chronic PFOA Exposure in vitro Causes Acquisition of Multiple Tumor Cell Characteristics in Rat Liver Cells

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

summary: Perfluorooctanoic acid (PFOA) exposure is linked with tumorigenesis in rats, mice, and potentially tumorigenic in humans. Here, we studied long-term PFOA exposure with an in vitro transformation model using the rat liver epithelial cell, TRL 1215. Cells were cultured in 10 µM (T10), 50 µM (T50) and 100 µM (T100) PFOA for 38 weeks and compared to passage-matched control cells. T100 cells showed morphological changes, loss of cell contact inhibition, formation of multinucleated giant and spindle-shaped cells. T10, T50, and T100 cells increased LC50 values 20%, 29% to 35% above control with acute PFOA treatment, indicating a resistance to PFOA toxicity. PFOA-treated cells showed increases in Matrix metalloproteinase-9 secretion, cell migration, and developed more and larger colonies in soft agar.  Microarray data showed Myc pathway activation at T50 and T100, associating Myc upregulation with PFOA-induced morphological transformation. Western blot confirmed that PFOA produced significant increases in c-MYC protein expression in a time- and concentration-dependent manner. Tumor invasion indicators MMP-2 and MMP-9, cell cycle regulator cyclin D1, and oxidative stress protein GST were all significantly overexpressed in T100 cells. Taken together, chronic in vitro PFOA exposure produced multiple cell characteristics of malignant progression and differential gene expression changes suggestive of rat liver cell transformation.

overall_design: RNA from untreated TRL 1215 cells (Control) (x3 replicates); RNA from 10 µM PFOA treated TRL 1215 cells (T10) ) (x3 replicates); RNA from 50 µM PFOA treated TRL 1215 cells (T50) ) (x3 replicates);  RNA from 100 µM PFOA treated TRL 1215 cells (T100) (x3 replicates). Total are 12 samples.

first: Wei

last: Qu

first: Yitang

last: Yan

first: Kevin

last: Gerrish

first: Erica

last: Scappini

first: Charles

middle: J

last: Tucker

first: Darlene

last: Dixon

first: B

last: Merrick


title: Reactivation of low avidity, tumor-specific CD8+ T cells correlates with immunotherapeutic efficacy of anti-PD-1

city: Oxford

first: Doreen

last: Lau

address: Old Road Campus Research Building, Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

summary: To  investigate the phenotypic differences between high and low avidity tumor-specific CD8+ tumor-infiltrating lymphocytes (TILs) following anti-PD-1 therapy, we performed bulk RNA-seq on tetramer sorted GSW11-specific T cells from three regressing and three progressing CT26 tumors: giving three groups of total TethiCD8+CD44+ TILs from the progressing tumors (TetHighProg), TetloCD8+CD44+ TILs from the progressing tumors (TetLowProg) and TetloCD8+CD44+ TILs from the regressing tumors (TetLowReg), total 9 samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumor-specific CD8+ T cells of different TCR avidities found in regressing versus progressing tumors following anti-PD-1 therapy: TethiCD8+CD44+ TILs from the progressing tumors (TetHighProg), TetloCD8+CD44+ TILs from the progressing tumors (TetLowProg) and TetloCD8+CD44+ TILs from the regressing tumors (TetLowReg)

first: Tim

last: Elliott

first: Gessa

last: Sugiyarto

first: Samuel

middle: L

last: Hill


title: Chromatin structure signals of Nannochloropsis oceanica in response to nitrogen deprivation

first: Li

last: WEI

summary: Reorganization of 3D chromatin structure in response to nitrogen stress  for one ant two days, and epigenome-association with phenotypic plasticity of lipid metabolism are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1.

overall_design: chromatin structure of Nannochloropsis oceanica under nitrogen repletion and nitrogen deprivation


title: RNAseq analysis of Rhodosporidium toruloides BOT-A2 for nitrogen-starvation on glucose or xylose

city: LUND

first: Daniel

middle: P

last: Brink

address: Naturvetarvagen 14

department: Applied Microbiology

country: Sweden

institute: Lund University

summary: Oleaginous yeasts are capable of accumulating high levels of intracellular storage lipids from excess carbon during times when other key nutrients are limited. The basidiomycete yeast Rhodosporidium toruloides is an emerging host for microbial cell factory applications thanks to its naturally high lipid and carotenoid production. However, the engineering toolbox in this non-model host is limited and is currently a bottleneck for implementation of metabolic engineering strategies. In this study, we performed differential gene expression analysis with the goal to identify promoters that are strongly induced or repressed by nitrogen-limitation, a condition that is commonly used to induce lipid accumulation in oleaginous yeasts. The genome-wide transcriptional response of R. toruloides BOT-A2 was analysed using RNAseq during exponential growth and nitrogen-starvation, with either glucose or xylose as the sole carbon source. To validate the differential gene expression findings, reporter genes were constructed by placing the candidate promoters in control of a fluorescent protein, integrated in BOT-A2 and evaluated in vivo.

overall_design: The transcriptome response of the  basidiomycete yeast R. toruloides BOT-A2 was assesed during exponential growth and nitrogen-starvation. The yeast was grown on either glucose or xylose.

first: Friederike

last: Mierke

first: Joakim

last: Norbeck

first: Verena

last: Siewers

first: Thomas

last: Andlid


title: SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1

city: Boston

first: Zifeng

last: Wang

state: Massachusetts

address: 100 Morrissey Blvd, ISC/4610

department: CPCT

institute: UMASS Boston

type: Genome binding/occupancy profiling by high throughput sequencing


title: RNA-seq Mouse 2-cell 1,6-Hexanediol

city: Munich

first: Adam

last: Burton

address: Marchioninistr. 25

department: IES

country: Germany

institute: Helmholtz Munchen

summary: The majority of our genome is composed of repeated DNA sequences, which assemble into heterochromatin, a highly compacted structure that constrains their mutational potential. How heterochromatin forms during development and how its structure is maintained is not fully understood. Here, we show that mouse heterochromatin phase separates after fertilization, during the earliest stages of mammalian embryogenesis. Using high resolution, quantitative imaging and molecular biology approaches we show that pericentromeric heterochromatin displays liquid-like properties at the 2-cell stage, but it transitions into a more solid-like or gel-like state at the 4-cell stage, when chromocenters mature and heterochromatin becomes silent. Disrupting the condensates results in altered transcript levels of pericentromeric heterochromatin, suggesting a functional role for phase separation in heterochromatin function. Thus, our work shows that mouse heterochromatin forms membrane-less compartments with biophysical properties that change during development and provides new insights into the self-organization of chromatin domains during mammalian embryogenesis.

overall_design: Mouse 2-cell stage treated for 1 hour with 1.6-hexanediol and subjected to single-embryo Smart-seq2

first: Manuel

last: Gutthmann

first: Tamas

last: Schauer


title: Whole Blood RNA Expression in Pink1-/- and Wildtype Rats

city: Madison

first: Cynthia

last: Kelm-Nelson

state: WI

address: 1300 University Avenue, 416 Medical Sciences Center

department: Surgery

institute: University of Wisconsin- Madiso

summary: Early-onset pathology and reliable disease biomarkers for diagnostics are poorly understood for progressive degenerative disorders such as Parkinson disease (PD). PD is the second most common age-related degenerative disorder. The Pink1-/- rat is a mitochondrial dysfunction model of prodromal PD. In this study, we used RNA sequencing to examine gene expression within whole blood samples of young and old Pink1-/- rats as compared to age-matched wildtype controls.

overall_design: Comparative gene expression profiling analysis using data obtained from the RNA-sequencing between the two genotypes (Pink1-/- and WT) in both young and old rats.

first: Stephen

last: Gammie


title: Warburg effect enhanced by AKR1B10 promotes acquired resistance to pemetrexed in lung cancer-derived brain metastasis

city: Dalian

first: Wenzhe

last: Duan

address: Shahekou Zone, Zhongshan Road 467

institute: Second hospital of Dalian Medical University

summary: To investigate the function of AKR1B10 in the lung cancer brain metastasis cells, we established PC9-BrM3 cells in which AKR1B10 has been knocked down by shRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  PC9-BrM3 cells with or without AKR1B10 knockdown.

first: Wenwen

last: Liu

first: Shengkai

last: Xia

first: Qi


title: SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1 [ChIP-seq]

summary: We recently reported that in prostate cancer LSD1 can demethylate the lysine 270 of FOXA1 to stabilize FOXA1 chromatin binding and thus can enhance the activities of AR and other transcription factors that require FOXA1 as a pioneer factor. However, the methyltransferase that can methylate FOXA1 and negatively regulate the LSD1-FOXA1 oncogenic axis remains unknown. SETD7 is initially identified as a transcriptional activator through methylating histone 3 lysine 4 but can also function as a methyltransferase on other non-histone substrates. However, its function in PCa remains poorly understood. In this study, we found that SETD7 confers tumor suppressor activity in PCa cells and that loss of SETD7 expression is significantly associated with PCa progression and tumor aggressiveness. Mechanistically, we found that SETD7 primarily acts as a transcriptional repressor in CRPC cells by functioning as a methyltransferase of FOXA1-K270 to disrupt FOXA1-mediated transcription. Overall, our study provides novel mechanistic insights into the tumor-suppressive and transcriptional repression activities of SETD7 in mediating PCa progression and therapy resistance.

overall_design: ChIP-seq analysis of SETD7 in 22Rv1 cells. ChIP-seq analyses of FOXA1 in 22Rv1 cells stably expressing shNTC or shSETD7. ChIP-seq analysis of FOXA1 in LNCaP cells treated with with vehicle and GSK2879552 together with or without PFI-2.

first: Changmeng

last: Cai


title: SETD7 functions as a transcription repressor in prostate cancer via methylating FOXA1 [RNA-seq]

summary: To determine the transcriptional impact of SETD7,MLL1 silencing in CRPC cells, we performed an RNA-seq analysis in those 22Rv1 stable cell lines (under hormone-depleted conditions)

overall_design: Comparative gene expression profiling analysis of RNA-seq data in 22Rv1 cells transfected with siSETD7, siMLL versus siNTC (under hormone-depleted conditions)


title: Exploiting crosstalk between glucocorticoid and mineralocorticoid receptors enhances glucocorticoid-induced killing of multiple myeloma cells

city: Gent

first: Karolien

last: De Bosscher

address: Technologiepark-Zwijnaarde 75

country: Belgium

institute: VIB-UGent Center for Medical Biotechnology

summary: Long-term glucocorticoid treatment in multiple myeloma is hampered by deleterious side effects. Glucocorticoids bind to the glucocorticoid receptor (GR), which is a crucial drug target because its activation triggers myeloma cell death. The mineralocorticoid receptor (MR) is a closely related nuclear receptor but its impact on glucocorticoid responsiveness in myeloma is unknown. Here we reveal a functional crosstalk between GR and MR that culminates in improved myeloma cell killing. We show that the GR agonist Dexamethasone (Dex) downregulates MR levels in a GR-dependent way in myeloma cells. Co-treatment of Dex with the MR antagonist Spironolactone enhances Dex-induced cell killing in (primary) myeloma cells. The crosstalk is further evidenced by an endogenous interaction between GR and MR in myeloma cells that is ligand-inducible and by a distinctive gene expression profile. Our study demonstrates that GR-MR crosstalk is therapeutically relevant in myeloma and presents a glucocorticoid-based dose-reduction strategy that could diminish glucocorticoid-related side effects in patients.

overall_design: The transcriptomic signature underlying the GR-MR crosstalk in multiple myeloma MM1.S cells  using RNA-sequencing of the following conditions: EtOH, Dexamethasone (Dex), Spironolactone (Spi), Dex+Spi.

first: Dorien

last: Clarisse

first: Philip

last: Vlummens

first: Karlien

last: Van Wesemael

first: Jonathan

last: Thommis

first: Daria

last: Fijalkowska

first: Guillaume

last: Acke

first: lse

middle: M

last: Beck

first: Fritz

last: Offner


title: Genome-wide maps of histone modifications in response to nitrogen deprivation in Nannochloropsis oceanica.

first: Li

last: WEI

summary: Epigenetic regulation in response to nitrogen stress  for one ant two days, and epigenome-association with phenotypic plasticity of lipid metabolism are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that H3K27ac, Kcr, Kbu and H3K36me2 histone modifications were present in N. oceanica IMET1. Moreover, they regulated gene expression.

overall_design: Examination of four different histone modifications under nitrogen repletion and nitrogen deprivation in Nannochloropsis oceanica cells.


title: Quantification of microRNA expression in early-stage oral squamous cell carcinoma

status: Public on Aug 22 2023

city: Toon

first: Saika

last: Masato

state: Ehime

department: Department of Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

summary:
Microarray was used to find out the differentially expressed in tumor sites of early-stage oral squamous cell carcinoma compared with Normal parts. Furthermore, we compared cases of early-stage oral squamous cell carcinoma with lymph node metastasis with cases without lymph node metastasis.
The miRNAs obtained may not only serve as predictive biomarkers for lymph node metastasis, but may also be used further to understand disease.

overall_design: Human oral tissues samples were collected from 14 men and 16 women who were diagnosed with early OSCC (clinical Stage I-II) in the tongue at the Oral Surgery Department of Ehime University School of Medicine hospital for a total of 30 patients for 15 years from March 2006 to October 2020. Of these patients, 15 patients had cervical lymph node metastasis.

first: Masato

last: Saika

first: Koh-ichi

last: Nakashiro


title: Gene expression profiling of Scgb1a1+, CD24low cells isolated from the lungs of Scgb1a1-CreER; Rosa26-mTmG mouse.

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

institute: RIKEN

summary: We established a new method to find out subpopulation of lung epithelial stem cells, named scMORN, and uncovered the existence of Club cell subpopulations contributing to alveolar regeneration. We isolated entire Club cells by sorting Scgb1a1+, CD24low cells from the lungs of Scgb1a1-CreER; Rosa26-mTmG mouse. The gene expression profiling revealed that two genetically distinct types of Club cells.

sample_organism:
Mus musculus
metagenome

platform_organism:
Mus musculus
metagenome

overall_design: Scgb1a1+, CD24low cells were sorted from Epcam+CD45-CD31-CD24low fraction of Scgb1a1-CreER;Rosa26-mTmG mouse.

first: Takashi

last: Fujimura

first: Taisaku

last: Ogawa

first: Jianshi

last: Jin

first: Mitsuru

last: Morimoto


title: scRNA-seq analysis of Musashi2-CreER-MycT58A; R26-LSL-tdTomato Mouse pre-cancer derived Pancreas ASCP, PDAC, and ACC Tumors (post transplantation)

first: Nirakar

last: Rajbhandari

state: Ca

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

summary: Identifying the cells from which cancers arise, and the paths they take towards malignancy is critical for understanding the molecular basis of tumor initiation and progression. To determine whether stem and progenitor cells can serve as cells of origin for cancer, we created a new Msi2-CreERT2 knock-in strain. When crossed to a conditional CAG-LSL-MycT58A model, Msi2-CreERT2 mice developed multiple pancreatic cancer subtypes: pancreatic ductal adenocarcinoma (PDAC), adenosquamous carcinoma of the pancreas (ASCP), acinar cell carcinoma (ACC), and rare anaplastic tumors. Combining single-cell genomics with computational analysis of developmental states and lineage trajectories, we demonstrate that oncogenic MYC preferentially triggers the transformation of the most immature subset of Msi2+ cells, leading to the rise of a common pool of pre-cancer cells with multi-lineage properties. These pre-cancer cells subsequently diverge to distinct pancreatic cancer subtypes by activation of distinct transcriptional programs and large-scale genomic changes. Importantly, the enforced expression of specific molecular signals can redirect cells toward specific subtypes. This study shows that multiple pancreatic cancer subtypes can arise from a common pool of Msi2+ cells and provides a powerful framework to understand and control the programs that shape divergent fates in pancreatic cancer.

overall_design: To determine if a pool of trasncriptionally uncommitted cells can give rise to multiple subtypes of pancreatic cancer, precancerous cells from Msi2-Myc; R26-LSL-tdTomato were isolated (t=5) and orthotopically transplanted to recipient NSG mcie. At endpoint, tumors were harvested and sorted cancer cells were used for scRNA-seq.

first: Michael

last: Hamilton

first: Tannishtha

last: Reya


title: Effect of silencing of METTL1 oncastration-resistant prostate cancer cells

first: Mingpeng

last: zhang

state: tianjin

address: pingjiang road

institute: the Second Hospital of Tianjin Medical University

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

overall_design: Refer to individual Series


title: Dissection of Transcriptomic and Epigenetic Heterogeneity of Glioblastoma: Implications for Prognosis

city: Chicago

first: Wei

last: Zhang

state: IL

address: 680 N Lake Shore Drive, Suite 1400

department: Preventive Medicine

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

summary: Background: Glioblastoma (GBM) is the most aggressive and currently incurable brain tumor with a median survival of one year in adult patients. Elucidating novel transcriptomic and epigenetic contributors to the molecular heterogeneity underlying its aggressiveness may lead to improved clinical outcomes.   Methods: To identify GBM-associated 5-hydroxymethylcytosine (5hmC) and transcriptomic features as well as their cross-talks, genome-wide 5hmC and transcriptomic profiles of tissue samples from 61 patients with GBM and 9 normal controls were obtained for differential and co-regulation/co-modification analyses. Prognostic models on overall survival (OS) based on transcriptomic features and the 5hmC modifications summarized over genic regions (promoters, gene bodies) and brain-derived histone marks were developed using machine learning algorithms.   Results: Despite global reduction, the majority of differential 5hmC features showed higher modification levels in GBM tumors as compared to normal controls. In addition, the bi-directional correlations between 5hmC modifications over promoter regions or gene bodies and gene expression were greatly disturbed in GBM tumors regardless of IDH1 mutation status. Phenotype-associated co-regulated 5hmC-5hmC modules and 5hmC-mRNA modules not only are enriched with different molecular pathways that are indicative of the pathogenesis of GBM, but also are of prognostic significance comparable to IDH1 mutation status. Lastly, the best-performing 5hmC model can predict patient survival at a much higher accuracy (c-index = 74%) when compared to conventional prognostic factor IDH1 (c-index = 57%), capturing the molecular characteristics of tumors that are independent of IDH1 mutation status and gene expression-based molecular subtypes.  Conclusions: The 5hmC-based prognostic model offers a robust tool to predict survival in GBM patients, outperforming existing prognostic factors such as IDH1 mutations. The crosstalk between 5hmC and gene expression revealed another layer of complexity underlying the molecular heterogeneity in GBM, offering opportunities for identifying novel therapeutic targets.

overall_design:
To identify GBM-associated 5-hydroxymethylcytosine (5hmC) and transcriptomic features as well as their cross-talks, genome-wide 5hmC and transcriptomic profiles of tissue samples from 61 patients with GBM and 9 normal controls were obtained for differential and co-regulation/co-modification analyses. Prognostic models on overall survival (OS) based on transcriptomic features and the 5hmC modifications summarized over genic regions (promoters, gene bodies) and brain-derived histone marks were developed using machine learning algorithms.

** Submitter states that the raw data are not deposited due to patient privacy concerns **

first: Chang

last: Zeng

first: Xiao

last: Song

first: Zhou

first: Qinyun

last: Cai

first: Craig

last: Horbinski

first: Bo

last: Hu

first: Shi-Yuan

last: Cheng


title: Stress induces behavioral abnormalities by increasing expression of phagocytic receptor MERTK in astrocytes to promote synapse phagocytosis

city: Daejeon

first: Gyuri

last: Kim

address: Yuseong-gu Daehak-ro

country: South Korea

institute: Korea Advanced Institute of Science and Technology

summary: Early life stress such as childhood abues and childhood neglect has been frequently implicated in evoking mental disorders later in life. However, it is not well understood what is the underlying mechanism between early life stress and mental disorders. Our in vitro, in vivo and brain organoid experiments revealed that stress hormones increase Mertk expression in astrocytes through glucocorticoid receptor (GR). Furthermore, early life stress (ESD) exposure significantly incrased astrocyte-mediated synapse phagocytosis via GR/MERTK pathway in various brain regions including somatosensory cortex and orbitofrontal cortex. In those brain regions, the excitatory postsynaptic density was remarkably decreased with an increase in astrocytic phagocytosis of excitatory postsynapses. Importantly, ablating GR or MERTK in astrocytes prevented ESD-induced loss of excitatory snapses, abnormal neural activities and behavioral deficits. Taken together, this study revelas a new role of astrocytic GR/MERTK pathway in evoking stress-induced abnormal behaviors in mice, suggesting astrocytic GR/MERTK signaling could be a potential therapeutic target for stress-induced mental disorders.

overall_design:
To investigate the gene expression changes in astrocytes in control and astrocyte-specific GR knock-out mice (AGR cKO) after early life stress (ESD), we have designed four different groups (control Cre- mice: Cre- control, Cre- mice exposed to ESD: Cre- ESD, control AGR cKO mice: AGR cKO control, AGR cKO mice exposed to ESD: AGR cKO ESD). All four groups were injected 4-hydroxytamoxifen (4-OHT) from P5 to P7. The ESD group pups were separated from their dam for three hours a day from P1 to P14.
Astrocytes were prufied from the cortices from four different groups at postnatal day 14 (P14) by utilizing immunopanning methods and Miltenyi Biotec beads.

first: Youkyeong

middle: G

last: Byun


title: Transcriptional characterization of the Eif2b5[R191H] loss-of-function mouse model

city: South San Francisco

first: Thomas

last: Sandmann

email: genomics@dnli.com, sandmann@dnli.com

state: California

address: 161 Oyster Point Blvd

institute: Denali Therapeutics

summary: The integrated stress response (ISR) is a conserved pathway in eukaryotic cells that is activated in response to multiple sources of cellular stress. Although acute activation of this pathway restores cellular homeostasis, intense or prolonged ISR activation perturbs cell function and may contribute to neurodegeneration. We have characterized an eIF2B loss of function (LOF) mouse model, carrying the homozygous Eif2b5[R191H] mutation that is homologous to the Vanishing White Matter Disease (VWMD)-causing human R195H variant. Characterization of previously reported transcript markers in animals 3-4 weeks of age confirmed ISR activation in the brain, but not in heterozygous or wild-type littermates.The robust elevation of ISR markers was further confirmed in bulk brain RNA sequencing analysis of a separate cohort of homozygous mutants and wild-type littermates. Known ATF4 targets feature prominently among the most strongly up-regulated genes in the eIF2B mutant compared to WT littermates.

overall_design: We generated homozygous Eif2b5[R191H] knock-in mice to create a model of Vanishing White Matter Disease (VWMD). Bulk tissue from the anterior right hemisphere from mutant (n=9) and wildtype (n=12) animals at 3-4 months of age was collected and bulk RNA-seq data was collected with the QuantSeq 3' mRNA-Seq protocol.

first: Ernie

last: Yulyaningsih

first: Jung

middle: H

last: Suh

first: Melania

last: Fanok

first: Lesley

last: Kane

first: Pascal

middle: E

last: Sanchez


title: HSF2 Safeguards Against Genomic Instability and Radiation-Induced T-ALL Via Regulation of Pre-mRNA Splicing

city: Augusta

first: Nahid

middle: F

last: Mivechi

state: GA

department: Georgia Cancer Center

institute: Augusta University

summary: Prompt and accurate responses to DNA damage are crucial for maintaining normal cellular homeostasis and avoiding cell death.  These responses involve the activation of DNA repair pathways and changes in gene expression.  RNA polymerase II (RNAPII) is responsible for transcribing protein-coding genes and small nuclear RNAs (snRNAs).  Concurrent with transcription, pre-mRNA undergoes splicing by the spliceosome, a complex consisting of five ribonucleoproteins (snRNPs), snRNAs, and additional factors, which ensures proper pre-mRNA splicing and generation of mature mRNA, thereby promoting proteome diversity.    In this study, we provide new insights into the role of HSF2 in pre-mRNA splicing and maintenance of genomic stability.  We observed a significant reduction in RNAPIICTD pS7 following loss of HSF2 and this is accompanied by the inhibition of RNAPII recruitment to snRNA gene promoters and a significant reduction in snRNA transcription.  Moreover, the observed reduction in snRNAs expression in cells lacking HSF2 is associated with impaired pre-mRNA splicing and several other consequences.  These include a spontaneous increase in DNA damage, enhanced formation of R-loops, and elevated cellular sensitivity to ionizing radiation (IR).  These findings suggest that loss of HSF2 leads to multiple disruptions in cellular processes, ultimately resulting in compromised genome stability and increased susceptibility to DNA damage.    Furthermore, HSF2-deficient mice exhibit an accelerated IR-induced T cell acute lymphoblastic leukemia (T-ALL), as evidenced by the reduced snRNA levels and expression of IR-induced DNA repair genes.  Our findings reveal a previously unrecognized role for HSF2 in the process of snRNA transcription and its loss highlights its pathological consequences.   These features are also mirrored by the loss of the HSF2 target gene, HSP110, suggesting that HSP110 contributes, at least in part, to the phenotypes observed following HSF2 loss.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Total RNA was isolated from (1) Lin-cKit cells sorted (by FACS) from bone marrow of WT or hsf2-/- mice; (2) parental, sgHsf2, or sgHsp110 K562 cells. The RNA was used for RNA-seq. The gene expression profiles between different genotypes cells were compared and analyzed for differential expression and alternative splicing.

first: Xiiongjie

last: Jin

first: Junfeng

last: Pang


title: Effect of silencing of METTL1 on m7G modification within mRNA of castration-resistant prostate cancer cells LNCaP-AI via m7G AlkAniline-Seq analysis. [m7G]

city: Tianjin

first: Mingpeng

last: zhang

summary: Background: N7-methylguanosine (m7G) modification is, a more common epigenetic modification in addition to m6A modification, mainly found in mRNA capsids, mRNA interiors, transfer RNA (tRNA), pri-miRNA, and ribosomal RNA (rRNA). It has been found that m7G modifications play an important role in mRNA transcription, tRNA stability, rRNA processing maturation, and miRNA biosynthesis. However, the role of m7G modifications within mRNA and its “writer” methyltransferase 1(METTL1) in tumors, particularly prostate cancer (PCa), has not been revealed. Methods： The differential expression level of METTL1 between hormone-sensitive prostate cancer (HSPC) and castrate-resistant prostate cancer (CRPC) was evaluated via RNA-seq and in vitro experiments. The effects of METTL1 on CRPC progression were investigated through in vitro and in vivo assays. The upstream molecular mechanism of METTL1 expression upregulation and the downstream mechanism of its action were explored via Chromatin Immunoprecipitation quantitative reverse transcription polymerase chain reaction (CHIP-qPCR), Co-immunoprecipitation (Co-IP), luciferase reporter assay, transcriptome-sequencing, m7G AlkAniline-Seq, and mRNA degradation experiments, etc. Results and conclusion： Here, we found that METTL1 was elevated in CRPC and that patients with METTL1 elevation tended to have a poor prognosis. Functionally, the knockdown of METTL1 in CRPC cells significantly limited cell proliferation and invasive capacity. Mechanistically, we unveiled that P300 can form a complex with SP1 and bind to the promoter region of the METTL1 gene via SP1, thereby mediating METTL1 transcriptional upregulation in CRPC. Subsequently, our findings indicated that METTL1 leads to enhanced mRNA stability of CDK14 by adding m7G modifications inside its mRNA, ultimately promoting CRPC progression.

overall_design: To explore the potential molecular mechanisms underlying the effects of METTL1 on LNCaP-AI in castration-resistant prostate cancer cells, we used lentiviral constructs to silence METTL1 in LNCaP-AI cell lines stably. Control (three replicates) and knockdown (three replicates) LNCaP-AI cells were subjected to m7G AlkAniline-Seq analysis to reveal the regulation of m7G levels within mRNAs by METTL1.

first: Boya

last: Zhang

first: Zhiqun

last: Shang


title: Effect of silencing of METTL1 on gene expression of castration-resistant prostate cancer cells LNCaP-AI via RNA-seq technology.

overall_design: To explore the potential molecular mechanisms underlying the effects of METTL1 on LNCaP-AI in castration-resistant prostate cancer cells, we used lentiviral constructs to silence METTL1 in LNCaP-AI cell lines stably. Control (three replicates) and knockdown (three replicates) LNCaP-AI cells were subjected to 150bp bipartite sequencing using an Illumina Hiseq instrument, respectively.


title: Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects

city: Sevilla

first: Marta

last: Barrientos-Moreno

state: Sevilla

address: Avda. Americo Vespucio 24. Edif. CABIMER.Unidad de Genómica. Parque Científico y Tecnológico Cartuja

department: Department of Genome Biology

country: Spain

institute: Andalusian Molecular Biology and Regenerative Medicine (CABIMER), CSIC-University of Seville-University Pablo Olavide.

summary: Genome duplication occurs through the coordinated action of DNA replication and nucleosome assembly at replication forks. Defective nucleosome assembly causes DNA lesions by fork breakage that need to be repaired. In addition, it causes a loss of chromatin integrity. These chromatin alterations can be restored, even though the mechanisms are unknown. Here, we show that the process of chromatin restoration can deal with highly severe chromatin defects induced by the absence of the chaperones CAF1 and Rtt106 or a strong reduction in the pool of available histones, and that this process can be followed by analyzing the topoisomer distribution of the 2m plasmid. Using this assay, we demonstrate that chromatin restoration is slow and independent of checkpoint activation, whereas it requires the action of transcription and the FACT complex. Therefore, cells are able to “repair” not only DNA lesions but also chromatin alterations associated with defective nucleosome assembly.

overall_design: Chromatin analyses by MNase-seq were performed from two biological replicates for each yeast strain.

first: Douglas

last: Maya-Miles

first: Marina

last: Murillo-Pineda

first: Sara

last: Fontalva

first: M

last: Pérez-Alegre

first: Eloísa

last: Andujar

first: Félix

last: Prado


title: Fine mapping of a novel locus qIGL1 (INCREASE GRAIN LENGTH 1), a major QTL for modulating grain length in rice

city: nanjing

first: la

middle: yu

last: mei

address: xuanwu

institute: njau

summary: Grain length is a prominent determinant for the grain weight and appearance quality of rice. To elucidate the genetic basis of the control of grain length, we conducted quantitative trait locus (QTL) mapping to determine a genomic interval responsible for the a long-grain phenotype observed in a japonica cultivar HD385 by using an F2:3 population and recombinant inbred line (RIL) population, which is are derived from a cross between the long-grain japonica cultivar HD385 and short-grain japonica cultivar Nipponbare (NIP). This led to the identification of a novel QTL, which is located on chromosome 3, for grain length, named qIGL1 (for Increased Grain Length 1); the HD385-derived allele showed enhancement effects on grain length, and such an allele as well as NIP-derived allele are were thus designated qigl1 HD385 and qIGL1NIP, respectively. Genetic analysis revealed that qigl1HD385 displayed semi-dominant effects on grain length. To further narrow down the qIGL1 region, we developed a few advanced backcross populations to determine the precise location of qIGL1. Eventually, qIGL1 was delimited to a 70.8-kb region containing 9 open reading frames (ORFs). A comprehensive analysis indicated that ORF6 and ORF9, separately corresponding to LOC_Os03g30530 and LOC_Os03g30550, are were found to carry base substitutions and/or deletions, which resulted in changes or losses of amino acid residues. However, these alterations in coding sequences does did not significantly change the expression levels of both ORFs. To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP, and discovered that introduction of qigl1HD385 into the NIP background significantly lead resulted into the elevations of grain length and 1000-grain weight. Closer inspection of outer epidermal cells of grain surfaces of both lines revealed that the cell length and width in the longitudinal direction are were significantly longer in NIL-qigl1HD385 compared with in NIL-qIGL1NIP, which may might stem partly from the downregulation of several cell cycle-related genes. Hence, our study studies identify identified a new semi-dominant natural allele contributing to the increase of grain length, and further shed light on the regulatory mechanisms of grain length.

overall_design:
To further elucidate the mechanisms behind the increases of grain length conferred by qigl1HD385, we generated a pair of near-isogenic lines (NILs), termed NIL-qigl1HD385 and NIL-qIGL1NIP.
We performed gene expression profiling analysis using data obtained from RNA-seq of 8-10 cm young panicle of NIL-qigl1HD385 and NIL-qIGL1NIP.
Identify the differentially expressed genes (DEGs) between NIL-qigl1HD385 and NIL-qIGL1NIP by comparative gene expression profiling analysis of RNA-seq data for NIL-qigl1HD385 and NIL-qIGL1NIP.

first: Jiayu

last: Niu

first: Fei

last: Wang

first: Chengcheng

last: Yang

first: Qiwen

last: Ye

first: Jingxian

last: Huang

first: Yumei

last: La

first: Qianqian

first: Peijiang

first: Yu

last: Zou

first: Zhaoyu

last: Zhai

first: Jian

first: Dina

last: Abdulmajid

first: Huhui

last: Chen

first: Honggui


title: Chronic hypoxic response for human bronchial epithelial culture [bulkRNA-Seq batch2]

city: Chapel Hill

last: Mikami

address: 125 Mason Farm Rd

department: Marsico lung institute

institute: The University of North Carolina at Chapel Hill

summary:
Purpose: To identify the gene expression change under chronic hypoxia on HBE cells.
Methods: bulk RNA-seq was performed on primary human bronchial epithelial cells (HBE) that were cultured on air-liquid interface (ALI) condition and treated under normoxia or hypoxia (1% O2) for 5days.
Results: inflammatory cytokines, collagen degradation, and angiogenic genes were upregulated under chronic hypoxia.

overall_design: HBE cells from six different donors were cultured and mRNA was harvested for the analysis of mRNA profile.

first: Hong

last: Dang

first: Richard

last: Boucher


title: Cellular response to hypoxia on human bronchial epithelial culture [scRNA-Seq CAP]

summary:
Purpose: To identify the cell types change and gene expression change under hypoxia on HBE cells.
Methods: The primary human bronchial epithelial cells (HBE) were cultured on air-liquid interface (ALI) conditions. After 4 weeks, the cells were cultured under normoxic, symmetrical hypoxic (3.5% O2), or asymmetrical hypoxic (3.5% O2 basolateral with apical cap ~ 1% O2) conditions for 5 days. The cells were dissociated with Accutase solution and proceeded to scRNA-seq.
Results: Asymmetrical hypoxic cells showed more hypoxia-related responses than symmetrical hypoxic cells.

overall_design: single cell-based mRNA profiles of normoxia or hypoxia treated HBE cells

first: Kenichi

last: Okuda


title: Hypoxic response for human bronchial epithelial culture [bulkRNA-Seq batch1]

summary:
Purpose: To identify the gene expression change under hypoxia on HBE cells.
Methods: bulk RNA-seq was performed on primary human bronchial epithelial cells (HBE) that were cultured on air-liquid interface (ALI) condition and treated under normoxia or hypoxia (1% O2) for 6hr, 24hr, and 5days.
Results: hypoxia-related genes were significantly upregulated under hypoxia including EGLN3.


title: human bronchial epithelial culture


title: Exploring the cytotoxic effects of MZ1 on multiple molecular   subtypes of B-cell acute lymphoblastic leukemia cells

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

summary: Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy. B-cell acute myeloid leukemia (B-ALL) predominates in ALL, with current cure rates of ∼80%. However, the long-term survival rate of patients with early relapse or refractory B-ALL is very low. In recent years, Bromodomains and extra-terminal (BET) protein inhibitors have shown considerable prospect in hematological tumors. MZ1 is a novel BET inhibitor that degrades target proteins and inhibits tumor growth through proteolysis-targeting chimeras (PROTAC) technology. This study shows that MZ1 has cytotoxic effects on 697 (TCF3/PBX1) and RS4;11 (MLL-AF4) B-ALL cell lines representing different molecular subtypes of B-ALL. Furthermore, we observed that MZ1 could promote cell apoptosis, induce cells cycle arrest and inhibit B-ALL cell proliferation by depleting BET protein and downregulating the transcription of CCND3. Collectively, our results indicate that MZ1 might be exploited as a novel therapeutic strategy for the treatment of B-ALL.

overall_design: mRNA profiles of 697 cells treated with 1 μM MZ1 or same volume of DMSO for 24 h were generated by RNA sequencing, in double, using Illumina NovaSeq6000.

first: Li

last: Ma

first: Shaoyan

last: Hu


title: DNA methylome and gene expression profiling of paired primary cancer and liver metastasis from colorectal cancer patients

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

summary: We generated reduced representation bisulfite sequencing (RRBS) and RNA sequencing (RNA-Seq) data of 20 samples (paired primary and liver metastases from 10 CRC patients) to understand key molecular events involved in tumor progression and metastasis.

overall_design: Methylation profiling by high throughput sequencing  Expression profiling by high throughput sequencing

first: Euan

last: J Rodger

first: Gregory

last: Gimenez

first: Rachel

last: Purcell


title: Cellular response to hypoxia on human bronchial epithelial culture [scRNA-Seq]

summary:
Purpose: To identify the cell types change and gene expression change under hypoxia on HBE cells.
Methods: The primary human bronchial epithelial cells (HBE) were cultured on air-liquid interface (ALI) conditions. After 4 weeks, the cells were cultured under normoxic or hypoxic (1% O2) conditions for 6h or 5days. The cells were dissociated with Accutase solution and proceeded to scRNA-seq.
Results: Hypoxia did not induce any hypoxia-specific cell types, however, all cell types upregulated hypoxia-related, and senescence-related genes and downregulated cell proliferation genes.


title: Total transcriptome response for tyrosol exposure in Aspergillus nidulans

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Although tyrosol is a quorum-sensing molecule of Candida species, it has antifungal activity at supraphysiological concentrations. Here, we studied the effect of tyrosol on the physiology and genome-wide transcription of Aspergillus nidulans to gain insight into the background of the antifungal activity of this compound. Tyrosol efficiently reduced germination of conidia and the growth on various carbon sources at a concentration of 35 mM. The growth inhibition was fungistatic rather than fungicide on glucose and was accompanied with downregulation of 2199 genes related to e.g. mitotic cell cycle, glycolysis, nitrate and sulphate assimilation, chitin biosynthesis, and upregulation of 2250 genes involved in e.g. lipid catabolism, amino acid degradation and lactose utilization. Tyrosol treatment also upregulated genes encoding glutathione-S-transferases (GSTs), increased specific GST activities and the glutathione (GSH) content of the cells, suggesting that A. nidulans can detoxify tyrosol in a GSH-dependent manner even though this process was weak. Tyrosol did not induce oxidative stress in this species, but upregulated “response to nutrient levels”, “regulation of nitrogen utilization”, “carbon catabolite activation of transcription” and “autophagy” genes. Tyrosol may have disturbed the regulation and orchestration of cellular metabolism, leading to impaired use of nutrients, which resulted in growth reduction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of tyrosol treated and untreated  Aspergillus nidulans cultures.

first: Ágnes

first: Kinga

last: Csillag

first: Károly

last: Antal

first: Imre

last: Boczonádi

first: Renátó

last: Kovács

first: István

last: Pócsi

first: Tamás

last: Emri


title: Transcriptional profiling of Caenorhabditis elegans nematodes treated with L4440 (Empty Vector - EV) or grd-1 RNAi from L1 hatch, and collected at L3 of development.

city: Boston

first: Fasih

middle: Mubtasim

last: Ahsan

state: MA

address: 185 Cambridge Street CPZN 6500 Simches Research Building

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: Hedgehog morphogen GRD-1 regulates C. elegans growth and metabolism downstream of TOR complex 2. Both Hedgehog (Hh) signaling and target of rapamycin complex 2 (TORC2) are evolutionarily conserved pathways that regulate growth and metabolism. In C. elegans, loss of Hh morphogens often leads to developmental arrest, while loss of essential TORC2 component RICTOR (rict-1) causes delayed development, reduced brood, small size, increased fat, and shortened lifespan. Here we report that knockdown of Hh-related morphogen grd-1 causes developmental acceleration rather than arrest by speeding up molting transitions. Further, we show that RNAi to grd-1 not only suppresses the slow growth of rict-1 mutants, but also normalizes multiple abnormalities downstream of TORC2 including restoration of lifespan to near normal and partial rescue of low brood, small body size, and increased fat. Mechanistically, grd-1 slows growth downstream of TORC2 at least in part by increasing transcription of paraquat mediator 1 (PQM-1) target genes. Given the important role of TORC2 in governance of development, these data implicate grd-1 and pqm-1 as critical executors of organismal growth slowing in response to unfavorable growth conditions downstream of the nutrient sensor TORC2 in C. elegans.

overall_design: Three independent passages of wildtype N2 animals were bleach synchronized and grown from larval stage 1 (L1) of development to  larval stage 3 (L3) of development on three independently grown RNAi cultures of HT115 E. coli bacteria expressing L4440 (Empty Vector - EV Control) or grd-1 dsRNA to induce RNAi knockdown. Animals were collected via manual inspection at the L3 stage, and snap frozen for lysis, RNA extraction and downstream mRNA sequencing analysis. This experiment contains 3 control and 3 grd-1 knockdown replicates, for a total of 6 samples.

first: Sinclair

middle: W

last: Emans

first: Alexander

last: Soukas


title: The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [WES]

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

institute: Institute of Crop Sciences

summary: To reveal the origin of the wheat B sub-genome, we performed the whole genome sequencing of sitopsis species. Besides,  we also conducted the RNA seq of Ae.speltoides and hexaploid wheat Chinese Spring.

sample_organism:
Aegilops bicornis
Aegilops longissima
Aegilops searsii
Aegilops speltoides
Amblyopyrum muticum
Aegilops sharonensis
Triticum dicoccoides

overall_design: We conducted the whole genome sequencing of 5 species, whole exome sequencing of sitopsis.Besides, we also conducted the RNA-seq sequencing of 17 tissues of Ae.speltoides samples, 7 tissues of wheat.

first: Yuxin

last: Yang


title: Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [Chic-seq]

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

summary: Lymphoid tissue inducer (LTi) cells, known to be critical for the generation of secondary lymphoid tissues, are the founding member of innate lymphoid cells (ILCs). However, how the development and functions of this ILC subset are regulated is far from clear. In this study, we discovered a striking role of the transcription factor TCF-1 in the development of Peyer’s patches (PPs) but not lymph nodes (LNs). Despite TCF-1 is critical for ILC development at multiple stages, we found normal development of LTi cells in TCF-1-deficient mice indicating that dysfunction of these LTi cells led to the deficiency in Peyer’s patches formation. Through bulk and single cell RNA-Seq, we found differential gene expression patterns between LTi cells from the PPs, LNs and the small intestine laminal propria (siLP), and an important role of TCF-1 in regulating the expression of lymphotoxin (LT) specifically in PP LTi cells. Mechanistically, TCF-1 may regulate Lta indirectly through promoting the expression of GATA3, a critical transcription factor in regulating LTi functions. LTβR agonist injection during the embryonic stage partially rescued the formation of PPs in the TCF-1-deficient mice. Thus, a dose effect of LT expression in LTi cells regulated by TCF-1 contributes to a differential regulation of organogenesis of distinct secondary lymphoid structures.

overall_design: Live Lin-CD127+ KLRG1-NK1.1-NKp46-CCR6+ lymphoid tissue inducer (LTi) cells from Peyer's patches（Tcf7+/+） or small intestine lamina propria (siLP) （Tcf7fl/flVavCre） were used for ChIC-Seq analysis.

first: Mingzhu

last: Zheng

first: Chen

last: Yao

first: Gang

last: Ren

first: Kairui

last: Mao

first: Xi

last: Chen

first: Difeng

last: Fang

first: Dan

last: Li

first: Chao

last: Zhong

first: Hyunwoo

last: Chung

first: Xiaoxiao

first: Nikki

last: Cannon

first: Lei

last: Wang

first: Mingxu

last: Zhang

first: Bhandoola

last: Avinash

first: Keji

last: Zhao

first: John

last: O'Shea

first: Jinfang

last: Zhu


title: The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum [RNA-seq]

first: Zefu

last: Lu

sample_organism:
Triticum aestivum
Aegilops speltoides

platform_organism:
Triticum aestivum
Aegilops speltoides

first: Yuxin

last: Yang


title: Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [RNA-seq]

first: Gangqing

last: Hu

overall_design: Live Lin-CD127+ KLRG1-NK1.1-NKp46-CCR6+ lymphoid tissue inducer (LTi) cells from Peyer's patches or small intestine lamina propria (siLP) of Tcf7+/+ and Tcf7fl/flRorcCre mice were used for RNA-Seq analysis.

first: Mingzhu

last: Zheng

first: Chen

last: Yao

first: Gang


title: Acid- and lactic acid-treated spleen-derived MDSCs in a mouse model of lung cancer transplantation tumor

status: Public on Aug 21 2023

city: 镇江市

first: 文信

last: 笪

state: 江苏省

address: 镇江市京口区学府路301号江苏大学

institute: 江苏大学医学院

summary: Transcriptome sequencing after treatment of spleen-derived MDSCs in a mouse model of lung cancer transplantation tumors using lactic and ph6.7 acids

overall_design: Euthanasia of mice; magnetic bead sorting of spleen-derived MDSCs in mice; treatment of MDSCs with acid at ph 6.7 and lactic acid for 24 hours


title: CD271 activation prevents low to high-risk progression of cutaneous squamous cell carcinoma and improves therapy outcomes

city: Modena

first: Elisabetta

last: Palazzo

address: Via del Pozzo

country: Italy

institute: Unimore

summary:
Background: Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent form of skin cancer, showing a rapid increasing incidence worldwide. Although most cSCC can be cured by surgery, a sizeable number of cases are diagnosed at advanced stages, with local invasion and distant metastatic lesions. In the skin, neurotrophins (NTs) and their receptors (CD271 and Trk) form a complex network regulating epidermal homeostasis. Recently, several works suggested a significant implication of NT receptors in cancer. However, CD271 functions in epithelial tumors are controversial and its precise role in cSCC is still to be defined.

Methods: Spheroids from cSCC patients with low-risk (In situ or Well-Differentiated cSCC) or high-risk tumors (Moderately/Poorly Differentiated cSCC), were established to explore histological features, proliferation, invasion abilities, and molecular pathways modulated in response to CD271 overexpression or activation in vitro. The effect of CD271 activities on the response to therapeutics was also investigated. The impact on the metastatic process and inflammation was explored in vivo and in vitro, by using zebrafish xenograft and 2D/3D models.

Results: Our data proved that CD271 is upregulated in Well-Differentiated tumors as compared to the more aggressive Moderately/Poorly Differentiated cSCC, both in vivo and in vitro. We demonstrated that CD271 activities reduce proliferation and malignancy marker expression in patient-derived cSCC spheroids at each tumor grade, by increasing neoplastic cell differentiation. CD271 overexpression significantly increases cSCC spheroid mass density, while it reduces their weight and diameter, and promotes a major fold-enrichment in differentiation and keratinization genes. Moreover, both CD271 overexpression and activation decrease cSCC cell invasiveness in vitro. A significant inhibition of the metastatic process by CD271 was observed in a newly established zebrafish cSCC model. We found that the recruitment of leucocytes by CD271-overexpressing cells directly correlates with tumor killing and this finding was further highlighted by monocyte infiltration in a THP-1-SCC13 3D model. Finally, CD271 activity synergizes with Trk receptor inhibition, by reducing spheroid viability, and significantly improves the outcome of photodynamic therapy (PTD) or chemotherapy in spheroids and zebrafish.

Conclusion: Our study provides evidence that CD271 could prevent the switch between low to high-risk cSCC tumors. Because CD271 contributes to maintaining active differentiative paths and favors the response to therapies, it might be a promising target for future pharmaceutical development.

overall_design: SCC13 derived spheroids were transduced with Empty (MOCK) or CD271 overexpressing vectors. Total RNA samples were collected 48 hours later and used for RNA sequencing procedure.

first: Marika

last: Quadri

first: Stephen

last: Brooks

first: Maria

last: Morasso

first: Carlo

last: Pincelli


title: The genome sequencing of Sitopsis species provide insights into its contribution to the B subgenome in Triticum aestivum

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

sample_organism:
Aegilops bicornis
Aegilops longissima
Aegilops searsii
Triticum aestivum
Aegilops speltoides
Amblyopyrum muticum
Aegilops sharonensis
Triticum dicoccoides

overall_design: Refer to individual Series


title: MUC1 elevation promote the progress of cervical squamous cell carcinoma through ERK phosphorylation and ITGA2/ITGA3

first: Sai

last: Ma

address: 242 guangji road

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

summary: In contrast to the decreasing trends in developed countries, the incidence and mortality rates of cervical cancer in China have increased significantly. Screening and identification of reliable biomarkers and candidate drug targets of cervical cancer are urgent to improve the survival rate and quality of life of patients. In this study, we demonstrated that MUC1 displayed elevation in cervical squamous cell carcinoma (CSCC). The expression of MUC1 was higher in neoplastic compared with non-neoplastic tissues of the cervix, indicated its potential in early diagnosis of cervical squamous cell carcinoma. Next, we explored the regulatory mechanism of MUC1 in CSCC. MUC1 overexpression promoted the proliferation and metastasis abilities of cervical cancer cells. MUC1 could regulate ERK phosphorylation, then upregulated ITGA2 and ITGA3 expression. Further knockdown of ITGA2 and ITGA3 significantly inhibited tumorigenesis of cervical cancer cells. Moreover, we designed a combination drug regimen with MUC1-siRNA and ERK inhibitor in vivo, founding that the combination of drugs achieved better results in animals with xenograft compared with targeting MUC1 alone. Taken together, we discovered a novel regulatory MUC1/ERK/ITGA2/3 pathway in cervical cancer that may serve as potential biomarkers and therapeutic targets in the future.

overall_design: Small interfering RNA were used to knockdown MUC1 expression and compared the changes in RNA levels between the MUC1 knockout group and the control group by RNA-seq

first: Zhao

last: Aiqin

first: Yunzhi

last: Pan

first: Yingyin

last: Gao

first: Zheng

last: Zhi

first: Haiying

first: Bei

last: Dong

first: Xuan

first: Meiying

last: Wu

first: Fenxia

first: Sufang

last: Zhou


title: Transcription factor TCF-1 regulates the functions but not the development of lymphoid tissue inducer subsets in different tissues [DNase-seq]

first: Gangqing

last: Hu

overall_design: Live Lin-CD127+ KLRG1-NK1.1-NKp46-CCR6+ lymphoid tissue inducer (LTi) cells from Peyer's patches of Tcf7+/+and Tcf7fl/flRorcCre mice were used for Dnase-Seq analysis.

first: Mingzhu

first: Chen

first: Gang

last: Ren

first: Kairui

last: Mao

first: Xi

last: Chen

first: Difeng

last: Fang

first: Dan

last: Li

first: Chao

last: Zhong

first: Hyunwoo

last: Chung

first: Xiaoxiao

last: Lu

first: Nikki

last: Cannon

first: Lei

last: Wang

first: Mingxu

last: Zhang

first: Bhandoola

last: Avinash

first: Keji

last: Zhao

first: John

last: O'Shea

first: Jinfang

last: Zhu


title: RNA-Seq data of human glioma stem cells and fetal neural stem cells after knockdown of CASCADES

city: Toronto

first: Sunit

last: Das

state: Ontario

address: 30 Bond St

department: Division of Neurosurgery

country: Canada

institute: St. Michael's Hospital

summary: We report the effects of knockdown of Cancer Stem Cell Specific Distal Enhancer of Sox2 (CASCADES) in human glioma stem cells and fetal neural stem cells.

overall_design: RNA-seq performed after knockdown of CASCADES in GSCs and HFNS

first: Uswa

last: Shahzad

first: Chris


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA385363]

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

institute: Gyeongsang National University

summary: Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. In addition, we obtained existing transcriptome datasets in response to abiotic and biotic stressors, phytohormones, and various developmental stages. From 428 total samples comprising 841.49 Gb, we identified the AS landscape in C. annuum. We further uncovered 1,704,387 AS events through differential AS analysis and identified 6,280 differential alternative splicing (DAS) genes related to environmental stressors, developmental stages, and phytohormones. This information and approach will enable comparative analysis of differential AS from RNA-seq datasets. Additionally, our findings provide useful data for basic-research programs focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.

overall_design: Identify changes in transcriptome based on biotic stress, abiotic stress, signal molecule and tissue RNA-seq samples of chilli.

first: Nayoung

last: Kim

first: Junesung

last: Lee


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA223222]


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA987837]


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA634831]


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA525913]


title: CCDC50 promotes glioblastoma progression through regulating EGFR cell-surface recycle

city: Philadelphia

first: Tian

last: Tian

state: PA

address: 3615 Civic Center Blvd

department: Center of Applied Genomics

institute: Children's Hospital of Philadelphia

summary: Glioblastomas (GBM) are a kind of malignant tumor with high mortality. However, the mechanism of tumor progression remains poorly understood. Specifically, we find that the expression of autolysosome-associated protein CCDC50, is positively correlated with tumor malignancy, and poor survival of GBM patients. CCDC50 functions as a specific cargo adaptor to assist EGFR recycling back to the plasma membrane, leading to prolonged activation of the downstream signaling pathways. We reveal that targeting CCDC50 in GBM may be a promising therapeutic strategy, as CCDC50 deficiency significantly inhibited the proliferation and migration of tumor cells in vitro and in vivo. Moreover, targeting CCDC50 together with alkylating agent temozolomide (TMZ) induces synergistic function in regression of GBM tumors, representing an alternative strategy for malignant tumor therapy. We performed transcriptome profiling (RNA-seq) and quantitative reverse transcription polymerase chain reaction (qRT–PCR) in shCtrl and shCCDC50 cells to evaluate the GBM tumor growth and metastasis controlled by CCDC50.

overall_design: U87 cells were transduced with lentivirus carring shCtrl or shCCDC50 plasmids. The infected cells were selected with puromycin for 7 days. The deletion of CCDC50 was confirmed by qRT-PCR and immunobloting. The shCtrl and shCCDC50 cells were collected for mRNA profilling analysis.

first: Deyin

last: Guo

first: Panpan

last: Hou

first: Yuxin

last: Lin


title: The X-Linked Intellectual Disability gene, ZDHHC9, is important for oligodendrocyte maturation and myelin formation

city: Vancouver

first: Stephane

last: Flibotte

state: BC

address: 2370-6270 University Blvd.

department: Faculty of Science

institute: University of British Columbia

summary: Two percent of all patients with X-linked intellectual disability (XLID) exhibit loss-of-function mutations in the palmitoylating enzyme, ZDHHC9. One of the main anatomical deficits observed in these patients is a decrease in corpus callosum volume and a disruption of white matter integrity. We demonstrated that ablation of Zdhhc9 in mice substantially impairs the maturation of oligodendrocytes, resulting in fewer mature, myelinating oligodendrocytes, higher numbers of oligodendrocyte progenitor cells and a decrease in the density of myelinated axons. Ultrastructural analysis of the remaining myelinated axons in the corpus callosum revealed further disruptions in myelin integrity. RNA sequencing and proteomic analyses revealed a concomitant decrease in the expression of genes and proteins involved in lipid metabolism, cholesterol synthesis and myelin compaction. These results reveal a previously underappreciated and fundamental role for ZDHHC9 and protein palmitoylation in regulating oligodendrocyte differentiation and myelinogenesis and provide mechanistic insights into the deficits observed in white matter volume in patients with mutations in ZDHHC9.

overall_design: Wild-type and Zdhhc9 knockdown corpus callosum and optic nerve from mice were studied via RNA-seq using between 4 and 6 replicates for each tissue-genotype combination.

first: Rocio

middle: B

last: Hollman

first: Angela

last: Wild

first: Timothy

last: O'Leary

first: Andrew

last: Thompson

first: Tashana

middle: O

last: Poblete

first: Angie

last: Peng

first: Jason

last: Rogalski

first: Gurmaan

last: Gill

first: Shernaz

middle: X

last: Bamji


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

first: Seon-In

last: Yeom

overall_design: This submission includes read counts mapped to the pepper genome.


title: The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA973829]

first: Nayoung

last: Kim


title: A robust and practical myogenic cell system to explore cellular and genomic features of muscle differentiation

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo


title: Endothelial cell response in Kawasaki disease and Multisystem Inflammatory Syndrome in Children

city: La Jolla

first: Chisato

last: Shimizu

address: 9500 Gilman Dr.

institute: UCSD

summary: Abstract: Although Kawasaki disease (KD) and Multisystem inflammatory syndrome in children (MIS-C) share some clinical manifestations, their cardiovascular outcomes are different, and this may be reflected at the level of the endothelial cell (EC). We performed RNA-seq on cultured ECs incubated with pre-treatment sera from KD (n=5), MIS-C (n=7), and healthy controls (n=3). We conducted Weighted Gene Co-expression Network Analysis (WGCNA) using 935 transcripts differentially expressed between MIS-C and KD using soft filtering (un-adjusted p<0.05, >1.1 fold difference). We found seven gene modules annotated as increased TNFα/NFB pathway, decreased Endothelial-Mesenchymal Transition (EndoMT) and EC homeostasis, an-ti-inflammation and immune response, translation, and glucocorticoid responsive gene suppression in MIS-C. To further understand the difference in the EC response between KD and MIS-C, a hard filter was applied to identify 41 differentially expressed genes (DEGs) between KD and MIS-C (adjusted p<0.05, >2 fold-difference). Again, the majority was NFB pathway genes including nine upregulated pro-survival genes. Expression levels were higher in the genes influencing autophagy (UBD, EBI3, and SQSTM1). Other DEGs also supported the finding by WGCNA. Compared to KD, ECs in MIS-C had increased pro-survival transcripts, but reduced transcripts related to EndoMT and EC homeostasis. These differences in EC response may in-fluence the different cardiovascular outcomes in these two diseases.

overall_design: Analysis of RNA extracted from human Umbellical Vein Endothelial Cells (HUVECs) incubated with sera from KD and MIS-C patients and Healthy control (HC) or no sera (Blank)  sequences from the patients with Kawasaki disease using a computational toolbox of two gene signatures,

first: Jane

last: Burns


title: The lysine demethylase KDM7A regulates immediate early genes in neurons [CUT&Tag]

city: Shanghai

first: Yifan

last: Wang

address: 130 Dong An Road

institute: Fudan University

summary: There are multiple post-translational modifications on amino acid residues at the N-terminus of histones that affect the structure of chromatin and alter the transcription of genes, thereby regulating a variety of biological processes. Lysine demethylase 7A (KDM7A) mainly removes histone modifications such as H3K9me1/2 and H3K27me1/2. Current research on KDM7A has focused on tumors, metabolism and development, while research on the function of the mammalian nervous system is still lacking. The functions and mechanisms of KDM7A in the regulation of neuronal cell differentiation and cell activity in the nervous system were investigated. Our study found that KDM7A regulates H3K9me2 and H3K27me2 but also affects other inhibitory or active histones, such as H3K9me3 and H3K27ac, thereby disturbing the transcription of some immediate early genes (IEGs) and consequently affecting the differentiation and activity of neuronal cells. IEGs are important for neuron cell proliferation, differentiation, formation of dendrites and neural circuit-related proteins, which are involved in maintaining the normal function of the nervous system. Imbalances in IEG expression have been found in some neurological disorders, such as depression and schizophrenia. Moreover, the changes in various histone modifications in neurodegenerative diseases and brain injury have recently received increasing attention. Therefore, our study provides a basis for revealing the epigenetic regulatory mechanisms of neurological disorders.

overall_design: CUT &Tag for KDM7A in shCtrl or shKdm7a N2a cells.

first: Bo

last: Wen

first: Qin

last: Hong


title: A robust and practical myogenic cell system to explore cellular and genomic features of muscle differentiation [RNA-Seq]

summary: The ability to recapitulate muscle differentiation in vitro has proven invaluable to investigate mechanisms of myogenesis, muscle cell function and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases poses ethical and procedural challenges which limit investigations of molecular mechanisms of muscle pathophysiology. Alternative myogenic models have been developed, such as the derivation of myogenic cells from skin fibroblasts through activation of an endogenous myogenic program triggered by exogenous expression of murine Myod. In the context of this RNA-seq dataset, we compare the transcriptome of myo-converted human fibroblasts and isogenic in vitro differentiated myoblasts. We show that myogenic induction of fibroblasts elicits genome-wide transcriptomic changes indicative of strong myogenic commitment and differentiation, including marked upregulation of genes implicated in cell cycle exit and in several myogenic pathways. Yet, we find that myotubes are further along myogenic commitment than myo-converted fibroblasts under the conditions tested. Extension of myo-conversion to 7 days does not significantly enhance myogenic commitment, from a gene expression standpoint. This suggests that myo-converted fibroblasts and myotubes retain some cell type specificity of gene expression profiles. Although these myogenic cell types are not identical, our results nonetheless favor a view of myo-converted fibroblasts as a robust and practical model to investigate cellular and genomic properties of cells from patients with muscle pathologies.

overall_design:
We tested two myogenic differentiation cellular models. To this end, we differentiated immortalized myoblasts (MB) into  myotubes  for 5 days (MT) in 3 indpendent differentiation replicates, and compared the transcriptome of undifferentiated (untreated) myoblasts with that of myotubes.
We also elicited a myogenic conversion of immortalized fibroblasts ('NI') for 5 days ('DOX') or 7 days ('McF_D07') in 3 independent replicates (Rep1-3), and compared the transcriptome of unconverted (untreated) fibroblasts and myo-converted fibroblasts.
We also compared the transcriptome of day-5 or day-7 myo-converted fibroblasts with that of myotubes.

first: Louise

last: Benarroch

first: Julia

last: Østerbye

first: Mohamed

last: Abdelhalim

first: Anne

last: Bertrand

first: Gisele

last: Bonne


title: Mechanism of Forsythoside B in U251

city: Hangzhou

first: Chen

last: Zhichao

address: Shenyuan 11-407, NO.2318, Yuhangtang Rd, Yuhang District, 311121, Hangzhou, Zhejiang, P.R.China

institute: Hangzhou Normal University

summary: Forsythoside B can induce the changes of gene expression in U251 cells

overall_design: The cells were treated with 200μM Forsythoside B in the experimental group and compared with the control group.


title: Profiling nucleo/cytoplasmic distribution of mRNAs identifies a role for the Golgi-to-ER trafficking in C9orf72 toxicity

city: Rome

first: Savina

last: Apolloni

address: Via della Ricerca Scientifica, 1

department: Department of Biology

institute: University of Rome Tor Vergata

summary: Compelling evidence indicates that defects in nucleocytoplasmic transport contribute to the pathogenesis of amyotrophic lateral sclerosis (ALS). In particular, hexanucleotide (G4C2) repeat expansions in C9orf72, the most common cause of genetic ALS, have a widespread impact on the transport machinery that regulates the nucleocytoplasmic distribution of proteins and RNAs, thereby affecting their functions. We have previously reported that the expression of G4C2 hexanucleotide repeats in cultured human and mouse cells caused a marked accumulation of poly(A) mRNAs in cell nuclei, suggesting that mRNA trafficking is impaired by expanded C9orf72-ALS repeats. To further characterize the process, in this work we set out to systematically identify the specific mRNAs that are altered in their nucleocytoplasmic distribution in the presence of C9orf72-ALS repeats. Results from RNAseq profiling of nuclear and cytoplasmic RNA fractions obtained from cells expressing G4C231 repeats show a significant accumulation of mRNAs in the nuclei of G4C231 cells, further suggesting that nuclear retention of mRNAs is a major effect of C9orf72 expanded repeats expression. Interestingly, pathway analysis shows that mRNAs involved in ER-to-Golgi trafficking are particularly enriched among the identified mRNAs. Most importantly, functional studies in cultured cells and Drosophila indicate that the membrane trafficking route regulated by ARFGAP1, a GTPase-activating protein that associates with Golgi, is specifically affected by expanded C9orf72 repeats, as well as by C9orf72-related dipeptide repeat proteins (C9-DPRs), pointing to ER-to-Golgi vesicle-mediated transport as a target of C9orf72 toxicity.

overall_design: Gene expression profiling analysis of nuclear and cytoplasmic fractions from HeLa cells expressing a mock plasmid (control) or an expanded (G4C2)31 RNA repeat. A total of n=12 samples from n=3 independent experiment were analysed by RNA seq: n=3 nuclear and n=3 cytoplasmic control samples; n=3 nuclear and n=3 cytoplasmic G4C2 samples.

first: Simona

last: Rossi

first: Ivan

last: Arisi

first: Nadia

last: D'Ambrosi

first: Mauro

last: Cozzolino


title: Genome-wide profiling of endogenous single-stranded DNA using SSiNGLe-P1 method

city: Xiamen

first: Dongyang

last: Xu

state: Fujian

address: 668 Jimei Road

institute: Huaqiao University

summary: Endogenous single-stranded DNA (essDNA) can form in a mammalian genome as the result of a variety of molecular processes and can both play important roles inside the cell as well as have detrimental consequences to genome integrity — much of which remains to be fully understood. Here we established SSiNGLe-P1 approach based on limited digestion by P1 endonuclease for high-throughput genome-wide identification of essDNA regions in human cells. We applied this method to profile essDNA in both the mitochondrial and nuclear genomes. In the mitochondrial genome, the profiles of essDNA provide new evidence to support the strand-displacement model of mitochondrial DNA replication. In the nuclear genome, essDNAs were found to be enriched in certain types of functional genomic elements, particularly, origins of DNA replication, R-loops, and to a lesser degree, in promoters. Furthermore, many of the essDNA regions identified by SSiNGLe-P1 have not been annotated and thus represent yet unknown functional elements.

overall_design: Established a next-generation sequencing based approach for identification of endogenous single-stranded DNA

first: Philipp

last: Kapranov


title: Extra centrosomes induce PIDD1-mediated inflammation and Immunosurveillance

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

institute: CSIC-Instituto de Neurociencias de Alicante

summary: Unscheduled increases in cellular ploidy underlie defects in tissue function, premature aging, and malignancy. A concomitant event to polyploidization is the amplification of centrosomes, the main microtubule organization center in animal cells. Supernumerary centrosomes are frequent in tumors, correlating with higher aggressiveness and poor prognosis. However, extra centrosomes also exert an onco-protective effect by activating the p53 network and eliciting cell cycle arrest. Here, we report that extra centrosomes, arising during unscheduled polyploidization or aberrant centriole biogenesis, induce activation of NF-κB signaling and sterile inflammation. This signaling requires the NEMO-PIDDOsome, a multi-protein complex composed of PIDD1, RIPK1, and NEMO/IKKγ. Remarkably, the presence of supernumerary centrosomes suffices to induce a paracrine chemokine and cytokine profile, able to polarize macrophages into a pro-inflammatory phenotype. Furthermore, extra centrosomes, accumulating after cytokinesis failure, increase immunogenicity of cancer cells and render them more susceptible to NK-cell attack. Hence, extra centrosomes, the PIDDosome acts as a dual effector, able to engage not only the p53 network for cell cycle control but also NF-κB signaling to instruct innate immunity.

overall_design: Primary mouse embryonic fibroblasts (MEF) were treated with the Aurora kinase inhibitor ZM447439, 2mM for 72h, in WT or Pidd1-/- cells.

first: Irmina

last: Garcia-Carpio

first: Angel

last: Barco

first: Andreas

last: Villunger


title: Differential gene expression of RNA extracted from A549 cell line cultured with Amorphous Calcium Carboante (ACC) or without

city: Nes-Ziona

first: Yehudit

last: Natan

address: 11 Haharash

country: Israel

institute: Amorphical Ltd.

summary: Amorphous calcium carbonate (ACC) is a non-crystalline form of calcium carbonate, which is composed of aggregated nano-size primary particles. Here, we wanted to evaluate how ACC affects gene expression in a human lung cancer cell line (A549).

overall_design: A549 cell line was cultured with DMEM/F12 medium (control) or with DMEM/F12 calcium delpeted medium to which 2mM elemntal calcium as ACC was added. Cells were cultred for 8 consecutive passages. After which, total RNA extraction was perfomred and samples went for RNAseq. Experiment was done in triplicates for eacg group (ACC or control) (N=6).

first: Yigal

middle: D

last: Blum

first: Amir

last: Arav

first: Ylena

last: Poliansky

first: Sara

last: Neuwman

first: Orit

last: Ecker Cohen

first: Yossi

last: Ben


title: A robust and practical myogenic cell system to explore cellular and genomic features of muscle differentiation [ChIP-Seq]

first: Philippe

last: Collas

summary: The ability to recapitulate muscle differentiation in vitro has proven invaluable to investigate mechanisms of myogenesis, muscle cell function and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases poses ethical and procedural challenges which limit investigations of molecular mechanisms of muscle pathophysiology. Alternative myogenic models have been developed, such as the derivation of myogenic cells from skin fibroblasts through activation of an endogenous myogenic program triggered by exogenous expression of murine Myod. In the context of this ChIP-seq dataset, we compared the transcriptome and lamina-associated domains (LADs) as genome organizers in myo-converted human fibroblasts and in isogenic myotubes differentiated from myoblasts. We show that myogenic induction of fibroblasts elicits genome-wide transcriptomic changes indicative of myogenic commitment and differentiation. Yet, myotubes are further along myogenic commitment than myo-converted fibroblasts under the conditions tested. LADs with typical LAD properties (low gene density, containing mostly repressed genes, and H3K9me3-rich) are shared between the two cell types, but each cell type also displays nearly 700 unique LADs. Strikingly, myotube-specific LADs are smaller, more gene-rich and less heterochromatic than shared LADs or LADs unique to myo-converted fibroblasts. Thus, myo-converted fibroblasts and myotubes retain some cell type specificity of genome organization at this level. Although these myogenic cell types are not identical, our results favor a view of myo-converted fibroblasts as a robust and practical model to investigate cellular and genomic properties of cells from patients with muscle pathologies.

overall_design:
We investigated lamin A/C (LaA)-associated domains (LADs) and H3K9me3 profiles in two myogenic cell types. We differentiated immortalized myoblasts into  myotubes  for 5 days in 3 indpendent differentiation replicates, and mapped LADs in the differentiated myotubes in each replicate by ChIP-seq of lamin A/C .
We also elicited a myogenic conversion of immortalized fibroblasts for 5 days (here, 'Myoconv') in 3 independent replicates (Rep 1-3), and mapped lamin A/C ('LaA') LADs in the myo-converted fibroblasts.
We also mapped the histone modification H3K9me3  in day-5 myo-converted fibroblasts and day-5 myotubes by ChIP-seq of H3K9me3 in one replicate of each.

first: Louise

last: Benarroch

first: Julia

last: Østerbye

first: Mohamed

last: Abdelhalim

first: Anne

last: Bertrand

first: Gisele

last: Bonne


title: Vagus nerve inflammation in COVID-19

city: Hamburg

first: Marcel

middle: Seungsu

last: Woo

state: Hamburg

address: Falkenried 94

department: Neurology

institute: UKE

summary: To find inflammatory signatures in post mortem vagus nerves of COVID-19 patients in comparisin to non-infected controls.

overall_design: Post mortem vagus nerves of deceased COVID-19 patients and non-infected controls.

middle: S

first: Manuel

middle: A

last: Friese

first: Markus

last: Glatzel


title: Effects of overexpression of zebrafish bmp8a and mouse Bmp8a on gene expression during adipose differentiation in 3T3-L1 cells

city: Qingdao

first: shenjie

last: zhong

address: No. 5, Yushan Road

institute: ocean university of china

summary:
To investigate the  function  zebrafish bmp8a and mouse Bmp8a in the regulation of adipogenic differentiation,  we have established 3T3-L1 stably transfected target gene cell line using lentivirus.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 3T3-L1 cells and its Stable cell lines (LV-zsGreen, LV-bmp8a, and  mouse-LV-Bmp8a).

first: Shenjie

last: Zhong

first: Lihui

last: Chen


title: Use of transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates

city: Braunschweig

first: Matthias

last: Preusse

address: Inhoffenstr. 7

department: Molecular Bacteriology

institute: Helmholtz Center for Infection Research

summary: In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts non-overlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding diguanylate cyclases. We demonstrate that the selection of sub-groups of clinical isolates with high versus low expression of regulatory genes served the identification of their downstream regulons. Thus, analyzing transcriptional profiles of clinical isolates with variant expression of diguanylate cyclase genes might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates, we were unable to confirm diguanylate specific gene regulation. It is possible that the elevated c-di-GMP concentrations observed in the clinical P. aeruginosa isolates were due to a memory response, in which the bacteria maintain a certain level of c-di-GMP even after being removed from the conditions that induced the production of c-di-GMP. Further studies would be needed to determine the specific mechanisms underlying this memory response in P. aeruginosa.

sample_organism:
Pseudomonas aeruginosa
Pseudomonas aeruginosa UCBPP-PA14
Pseudomonas aeruginosa PAO1

overall_design: RNASeq of different Pseudomonas aeruginosa PA14/PAO1 and clinical isolates with a mutation in PA14_03790 or PA14_23130 - planctonic growth in LB medium.

first: Melisa

last: Gür

first: Jelena

last: Erdmann

first: Anke

last: Will

first: Susanne

last: Häußler


title: Inducible Rbpms-CreERT2 mouse line for functional studies of genes in retinal ganglion cell physiology and disease

city: Augusta

first: Lin

last: Gan

state: Geogia

address: 1120 15th Street

department: Department of Neuroscience & Regenerative Medicine

institute: Augusta University

summary: Retinal ganglion cells (RGCs) are the sole output neurons conveying visual stimuli from the retina to the brain and the dysfunction or loss of RGCs is the primary determinant of visual loss in traumatic and degenerative ocular conditions. Currently, there is a lack of RGC-specific Cre mouse lines that serve as invaluable tools for manipulating genes in RGCs and studying the genetic basis of RGC diseases. The RNA-binding protein with multiple splicing (RBPMS) is identified as the specific marker of all RGCs. Here, we report the generation and characterization of a knock-in mouse line in which a P2A-CreERT2 coding sequence is fused in-frame to the C-terminus of endogenous RBPMS, allowing the co-expression of RBPMS and CreERT2. The inducible Rbpms-CreERT2 mice exhibited a high recombination efficiency in activating the expression of tdTomato reporter gene in nearly all adult RGCs as well as in differentiated RGCs starting at E13.5. Additionally, heterozygous Rbpms-CreERT2 knock-in mice showed no detectable defect in the retinal structure, visual function and transcriptome. Altogether, our results demonstrated that the Rbpms-CreERT2/+ knock-in mouse can serve as a powerful and highly desired genetic tool for lineage tracing, genetic manipulation, retinal physiology study and ocular disease modeling in RGCs.

overall_design: Whole retinas are usd for the sequencing and each pair of retinas from one mouse is taken as 1 sample. Among same litters, genotype with +/+ mice are taken as wild type control samples, Rbpms-CreERT2/+ mice are taken as the heterzygous knockout samples, Rbpms-CreERT2/CreERT2 mice are taken as the homozygous knockout samples.

first: Luming

last: Guo

first: Shuchun

last: Li

first: Xiaoling

last: Xie


title: Ghrelin promotes cardiomyocyte differentiation of adipose tissue-derived mesenchymal stem cells by DDX17-mediated regulation of the SFRP4/Wnt/β-catenin axis

city: Mudanjiang

first: Ge

last: Sun

address: No. 15, Dongxiaoyun Street, Aimin District, Mudanjiang 157010, Heilongjiang, China.

institute: Department of Orthopedics, The Second Affiliated Hospital of Mudanjiang Medical University

summary: To  investigate the genes that regulated by ghrelin in the cardiomyocyte differentiation of ADMSCs, we cultured cells for RNA-Sequencing.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for induction medium treated ADMSCs with or without ghrelin addition.

first: Gui-Bo

last: Liu

first: Yong-Xia

last: Cheng

first: Hua-Min

first: Yong

first: Li-Xin

first: Qi

last: Wu

first: Shang-Fu

first: Ting-Ting

first: Chuan-Ling

last: Dong


title: Effects of CDK8/19 Mediator Kinase inhibition by BI1347 and depletion by SNX7886 on gene expression in HEK293 cells

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary: RNA-Seq analysis was carried out to investigate the effects of selective CDK8/19 inhibitor BI1347 and PROTAC degrader SNX7886 on gene expression in HEK293 cells (293-WT) or the CDK8/19 double-knockout (293-dKO) derivatives.

overall_design: 293-WT or 293-dKO cells were treated with 0.1% DMSO (vehicle control) or 200nM BI1347 or 200nM SNX7886 for 3 days (72 hours). Each treatment condition was done in biological triplicate or quadruplicate.

first: Mengqian

first: Hao

last: Ji

first: Igor

last: Roninson


title: The Lysine Demethylase KDM7A Regulates Immediate Early Genes in Neurons.

first: Yifan

last: Wang

summary: Lysine demethylase KDM7A removes histone modifications H3K9me1/2 and H3K27me1/2. KDM7A plays critical roles in gene expression and contribute to biological processes including tumorigenesis, metabolism, and embryonic development. However, the functions of KDM7A in mammalian nervous system are still poorly explored. In this study, functional roles of KDM7A are comprehensively investigated in neuronal cells by applying CUT&Tag-seq, RNA-seq and mice models. Knockdown of Kdm7a in N2A cells result in the alteration of histone modifications near transcription start sites (TSSs) and the expression changes of a large number of genes. In particular, the expression of immediate early genes (IEGs), a series of genes maintaining the function of the nervous system and associating with neurological disorders, are significantly decreased upon Kdm7a knockdown. Furthermore, in vivo knockdown of Kdm7a in dentate gyrus (DG) neuron of mice hippocampus, via Adeno-associated virus (AAV)-based stereotaxic microinjection, led to a significant decrease of the expression of c-Fos, a marker of neuron activity. Behavior assays in mice further revealed that Kdm7a knockdown in hippocampus repress neuron activity, which leading to impairment of emotion and memory. Collectively, the study reveals that KDM7A affects neuron functions by regulating IEGs, which may provide new clues for understanding epigenetic mechanisms in neurological disorders.

overall_design: Refer to individual Series


title: Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC

city: Randwick

first: Julie

last: Thoms

state: NSW

address: Level 2, C25 Lowy Cancer Research Centre, UNSW Sydney, High St

department: Adult Cancer Program

country: Australia

institute: UNSW Sydney

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


title: Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [ChIP-seq]

summary: Hematopoietic stem and progenitor cells (HSPCs) rely on a complex interplay of transcription factors (TFs) to regulate their differentiation into mature blood cells. A heptad of TFs - FLI1, ERG, GATA2, RUNX1, TAL1, LYL1, LMO2 - has been shown to bind to regulatory elements in bulk CD34+ HSPCs. However, whether specific combinations of these TFs have distinct roles in regulating hematopoietic differentiation remained unknown. In this study, we mapped the genome-wide binding profiles of these TFs and other chromatin-associated markers in distinct HSPC subsets (HSC, CMP, GMP, MEP). We found that the heptad occupancy and enhancer-promoter interactions varied significantly across cell types and were associated with cell-type specific gene expression. Moreover, we observed distinct regulatory elements that were enriched with specific combinations of TFs, such as stem-cell specific elements with ERG, and myeloid and megakaryocyte-erythroid specific elements with combinations of FLI1, RUNX1, GATA2, TAL1, LYL1, and LMO2. These findings suggest that specific combinations of TFs play critical roles in the regulation of hematopoietic differentiation, and provide a valuable resource for the development of targeted therapies to manipulate specific HSPC subsets.

overall_design: ChIP

first: Shruthi

last: Subramanian

first: John

last: Pimanda


title: Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiC]

overall_design: HiC


title: Genome-wide Transcription Factor binding maps reveal cell-specific changes in the regulatory architecture of human HSPC [HiChIP]

overall_design: HiChIP