title: Hepatic transcriptomic changes following equivalent weight loss by calorie restriction or vertical sleeve gastrectomy in mice with hepatic steatosis

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

summary: Sleeve gastrectomy (VSG) leads to improvement in hepatic steatosis, associated with weight loss. The aims of this study were to investigate whether VSG leads to weight-loss independent improvements in liver steatosis in mice with diet-induced obesity (DIO); and to transcriptomically profile hepatic changes in mice undergoing VSG. Methods: Mice with DIO were treated with VSG, sham surgery with subsequent food restriction to weight-match to the VSG group (Sham-WM), or sham surgery with return to unrestricted diet (Sham-Ad lib). Hepatic transcriptomics were investigated at the end of the study period and treatment groups were compared with mice undergoing sham surgery only (Sham-Ad lib). Results: VSG led to much greater improvement in liver steatosis than Sham-WM (liver triglyceride mg/mg 2.5 ± 0.1, 2.1 ± 0.2, 1.6 ± 0.1 for Sham-AL, Sham-WM and VSG respectively; p=0.003). Homeostatic model assessment of insulin resistance was improved following VSG only (51.2 ± 8.8, 36.3 ± 5.3, 22.3 ± 6.1 for Sham-AL, Sham-WM and VSG respectively; p=0.03). The glucagon-alanine index, a measure of glucagon resistance, fell with VSG but was significantly increased in Sham-WM (9.8 ± 1.7, 25.8 ± 4.6 and 5.2 ± 1.2 in Sham Ad-lib, Sham-WM and VSG respectively; p=0.0003). Genes downstream of glucagon receptor signalling which govern fatty acid synthesis (Acaca, Acacb, Me1, Acyl, Fasn and Elovl6) were downregulated following VSG but upregulated in Sham-WM. Conclusion: Changes in glucagon sensitivity may contribute to weight-loss independent improvements in hepatic steatosis following VSG.

overall_design: Mice with Diet Induced Obesity were treated with VSG, sham surgery with subsequent food restriction to weight-match to the VSG group (Sham-WM), or sham surgery with return to unrestricted diet (Sham-Ad lib). Four samples from each treatment group were selected for NGS sequencing, followed by Gene Set Enrichment Analysis.

first: Emma

last: McGlone

first: Tricia

last: Tan


title: Temporal single-cell transcriptomic profiling of cardiac differentiation in pulmonary atresia with intact ventricular septum (PA-IVS) derived induced pluripotent stem cells

status: Public on Mar 13 2024

city: Columbus

first: Cankun

last: Wang

state: OH

address: 281 W Lane Ave, Columbus, OH 43210

country: USA

institute: The Ohio State University Wexner Medical Center

type: Expression profiling by high throughput sequencing

summary: Pulmonary atresia with the intact ventricular septum (PA-IVS) is a rare congenital cardiac disease characterized by atresia of the pulmonary valve, resulting in the absence of a connection between the right ventricular outflow tract and pulmonary arteries. PA-IVS is characterized by varying degrees of right ventricular hypoplasia: from single ventricle palliation (1v) to 1½-ventricle palliation (1.5v) and bi-ventricle repair (2v). To understand how cardiac development is impaired in PA-IVS-1v, we generated PA-IVS-1v patient-specific induced pluripotent stem cells (iPSCs). We then ran single-cell RNA-seq to temporally profile transcriptomic changes during cardiac differentiation in healthy control (Control) and PA-IVS-1v iPSCs. We collected differentiating cells at multiple time points corresponding to different development stages, ie. Day 5 (cardiac mesoderm), Day 10 (cardiac progenitor), Day 14 (early cardiomyocyte), and Day 30 (fetal cardiomyocyte).  Single-cell transcriptomic analysis indicates that cell lineage commitment of cardiac progenitors is skewed towards epicardial and first heart field progenitors in the differentiating iPSCs from PA-IVS-1v.

overall_design: Single-cell transcriptomic analysis of differentiating cells collected at different time points (Day 5, Day 10, Day14, Day 30) during cardiac differentiation of healthy control and PA-IVS-1v iPSCs.

first: Ming-Tao

last: Zhao

first: Yang

last: Yu


title: Gene expression of HCC827 and HCC827-TET2-KO cell line [HCC827_TET2_KO_RNA]

city: Chengdu

first: Jian

last: Zhang

state: Sichuan

address: Guoxuexiang Road

department: Westchina Hospital

country: China

institute: Sichuan University

summary: To investigate the influence of TET2 knock-down in lung cancer cell line, We performed gene expression profiling analysis using data obtained from RNA-seq of HCC827 cell line and HCC827-TET2-KO cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCC827 cells and HCC827-TET2-KO cells.


title: Gene expression of HCC827 and HCC827-OR cell line [HCC827OR_RNA]

summary: To investigate the abnormal gene expression in Osimertinib Resistance lung cancer cell line, We performed gene expression profiling analysis using data obtained from RNA-seq of HCC827 cell line and HCC827OR cell line.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HCC827 cells and HCC827-OR cells.


title: Mutational analysis of PC9 and PC9-OR cell lines. [JXQ_WES]

summary: To investigate if there are new genetic mutations occurred within the PC-9 osimertinib resistant cells compared with the parental cells.

overall_design: Comparative gene mutational profiling analysis of WES-seq data for PC9 and PC9-OR cell lines.


title: RNA-seq of hESCs and hiPSCs treated with 5-OXO-ETE and Calcitriol, respectively

city: Guangzhou

first: Juli

last: Liu

state: Guangdong

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

summary: To know gene expression patterns affected by 5-OXO-ETE and Calcitriol

overall_design: RNA-seq pair 1: hESCs treated with Ethanol (Control) and hESCs treated with 5-OXO-ETE; RNA-seq pair 2: hiPSCs treated with DMSO (Control) and hiPSCs treated with Calcitriol. All were 3 biological replicates.

first: Shaoxian

last: Cheng


title: RNA-seq of cardiac differentiation of N and P hiPSCs on day 7

summary: To know gene expression patterns between N and P hiPSCs derived cardiac cells.

overall_design: RNA-seq pair 1: P hiPSC-derived cardiac cells vs. N hiPSC-derived cardiac cells. All were 3 biological replicates.


title: ATAC-seq of N and P hiPSCs

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To know the chromatin accessibilities alterations between N and P hiPSCs.

overall_design: ATAC-seq pair 1: P hiPSC vs. N hiPSC. All were 2 biological replicates.


title: Cell fusion between tumor cells and macrophages promotes the metastasis of OSCC patient through the activation of the chemokine signaling pathway

city: Nanjing

first: Chengwan

last: Xia

state: Jiangsu

address: No.30 Central Rd., Xuanwu District

institute: Department of Oral and Maxillofacial Surgery, Nanjing Stomatological Hospital, Medical School of Nanjing University

summary: Tumor metastasis is responsible for the high mortality rate of patients with oral squamous cell carcinoma (OSCC). Although many hypotheses have been proposed to elucidate the mechanism of tumor metastasis, the origin of the metastatic tumor cells remains unclear. In this study, we explored the role of cell fusion in the formation of OSCC metastatic tumor cells. Murine OSCC tumor cells and macrophages were fused in vitro, and the cell proliferation, migration, and phagocytosis abilities of hybrid cells and parental cells were compared. Subsequently, we compared the transcriptome differences between hybrid and parental cells. Finally, we observed an association between the hybrid cells and the prognosis of patients with OSCC. Murine OSCC tumor cells and macrophages were successfully fused in vitro. The cytological and molecular experimental results revealed that OSCC tumor cells obtained a migration-related phenotype after fusion with macrophages, and the migration ability of hybrid cells was related to the activation of the “chemokine signal pathway”. Moreover, we proved that the existence of hybrid cells in OSCC tumor tissues is closely related to lymph node metastasis and poor prognosis. After fusion with macrophages, the chemokine signaling pathway in OSCC tumor cells was activated, leading to metastasis.

overall_design: SCC7 cells and Raw 264.7 cells were fused in vitro to generate fusion cells.Total RNA was extracted fromSCC7 cells, Raw 264.7 cells and fusion cells.

first: C

first: Q

first: Y

last: Pu

last: Hu


title: RNA-seq of hiPSCs derived mosaic Down syndrome (undi)

summary: To know gene expression patterns affected by 3 copies of chromosome 21

overall_design: isogenic pair: Normal hiPSCs and Timsomy 21 hiPSCs


title: Arresting the Bad Seed: HDAC3 Regulates Proliferation of Different Microglia after Ischemic Stroke [ATAC-seq]

city: Shanghai

first: Yue

state: Shanghai

address: 131, Dong'an Road, Xuhui

department: Institute of Brain Science

institute: Fudan University

summary: The rapid accumulation of self-renewed polarized microglia in the penumbra is the critical neuroinflammatory process after the onset of ischemic stroke, leading to secondary demyelination and neuronal loss. HDAC3 has been reported to regulate cell proliferation of tumour cells and modulate neuroinflammation. However, the mechanism by which HDAC3 regulates microgliosis and microglial polarization remains ambiguous. Herein, we demonstrated that microglia-specific ablation of HDAC3 (HDAC3-miKO) ameliorated poststroke long-term functional and histological outcomes. Starting with unbiased RNA seq of microglia, we identified mitosis as the most significant process reversed by loss of HDAC3. Notably, HDAC3-miKO specifically inhibited the proliferation of M1-like microglia but not M2-like microglia, resulting in microglial transition to an M1-like state. Moreover, ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) revealed that HDAC3 deletion induced drastic closing of accessible regions enriched with motifs for PU.1. Taken together, we uncovered for the first time that HDAC3/PU.1-mediated differential proliferation-related reprogramming in different microglia populations drives poststroke inflammatory state transition of microglia and thereby contributes to the pathophysiology of ischemic stroke.

overall_design: Chromatin accessibility of ATAC-seq data for  WT-Sham, miKO-Sham, WT-tFCI, miKO-Tfci.

first: Jiaying

last: Li

first: Yichen

last: Huang

first: Ziyu

last: Shi

first: Hailian

first: Hui

last: Cao

first: Chenran

first: Yana

first: Di

last: Chen

first: Shuning

first: Yongfang

first: Yangfan

first: Yueyan

last: Zhu

first: Yan

last: Jiang

first: Ye

last: Gong

first: Yanqin

last: Gao


title: Keratinocyte-derived circulating exosomal miRNAs as a novel biomarker of disease severity in psoriasis

city: Suwon

first: Eun-So

last: Lee

address: 164, Worldup-ro, Yeongtong-gu

department: Dermatology

country: South Korea

institute: Ajou University

type: Non-coding RNA profiling by high throughput sequencing

summary:
To reveal the relationship between circulating exosomal miRNAs and the disease severity of psoriasis, we performed next-generation sequencing from plasma exosomes of patients with high psoriasis area and severity index (PASI) score (>10) and low PASI score (<5).
We identified 19 differentially expressed exosomal miRNAs that were significantly different between the groups. We validated the top three up-and down-regulated exosomal miRNAs using quantitative real-time PCR.

overall_design:
We performed next-generation sequencing from plasma exosomes of patients with high psoriasis area and severity index (PASI) score (>10) and low PASI score (<5)

Please note that the processed data columns are assocaited with the samples as below:
X2_OYJ Mild 1
X2_NYH Mild 2
X2_KJH Mild 3
X1_KSJ Severe 1
X1_KST Severe 2
X1_YJM Severe 3
X1_JBM Severe 4
X1_JKS Severe 5

first: Young

middle: J

last: Park

first: Dong

middle: C

last: Kim

first: Ji

middle: Y

first: Su

first: Jae

last: Cheong


title: N7-methylguanosine tRNA modification promotes tumorigenesis and chemoresistance through WNT/β-Catenin pathway in nasopharyngeal carcinoma

first: Shuibin

last: Lin

state: China

address: Zhongshan 2nd road, Guangzhou

department: Clincial for Translational Medicine

institute: The First Affliliated Hospital, Sun Yat-sen University

summary: Treatment selections are very limited for patients with advanced nasopharyngeal carcinoma (NPC) experiencing disease progression. Uncovering the potential mechanism underlying NPC progression is crucial for identify novel treatments. Here we show that N7-methylguanosine (m7G) tRNA modification enzyme METTL1 and its partner WDR4 are significantly elevated in NPC and associated with poor prognosis. Loss-of-function and gain-of-function assays demonstrated that METTL1/WDR4 mediated m7G tRNA modification promotes NPC growth and metastasis in vitro and in vivo. Mechanistically, m7G tRNA modification selectively regulates the translation of transcripts with higher percentage of m7G tRNA decoded codons. Moreover, further analysis revealed that METTL1-mediated m7G tRNA modification activates WNT/β-Catenin signaling pathway to promote NPC cell epithelial-mesenchymal transition (EMT) and chemoresistance to cisplatin and docetaxel in vitro and in vivo. Our work uncovers a novel layer of mRNA translation regulation mechanism at codon recognition step mediated by tRNA modification and reveals the critical function of tRNA modification in cancer progression.

overall_design: TRAC-Seq were developed to identify the tRNA m7G methylome in nasopharyngeal carcinoma cell line. Polyribosome-bound-RNA-seq and Ribo-seq was used to study the differential translated genes in the Mettl1 knockout and control cells.

first: Hao

last: Peng


title: CUT&Tag seq of control, FK866-, FK866 plus succinate-treated ILC2s in vitro

status: Public on Mar 12 2024

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

summary: To investigate the effect of NAD+ metabolism on ILC2s, sorted ILC2s from the gut were treated with FK866 or FK866 plus succinate for CUT-Tag sequcecing.

overall_design: Sorted ILC2s from the gut were cultured with IL-2, IL-7, IL-25 and IL-33, and treated with with FK866 or FK866 plus succinate.

first: Zhen

first: Xiaoyu

last: Liu

first: Shiyang


title: Selenomethionine Modulates Insulin Secretion in the MIN6-K8 Mouse Insulinoma Cell Line

city: Chicago

first: Robert

last: Sargis

state: IL

address: 835 S Wolcott st

institute: University of Illinois at Chicago

summary: Selenium is an essential trace element that has gained interest for its potential role in glucose homeostasis. The purpose of the present study was to investigate the impact of selenium supplementation as selenomethionine (SeMet) on insulin secretion in MIN6-K8 cells, a model of pancreatic -cells. We found that 40 μM and 80 μM SeMet significantly enhanced percent insulin secretion at low (2.8 mM), intermediate (11.7 mM), and high (16.7 mM) glucose stimulation. SeMet also increased tolbutamide- or KCl-induced percent insulin secretion at 40 μM and 80 μM. Ca2+ influx was only reduced with 80 μM SeMet. RNA-sequencing showed that 40 μM SeMet supplementation upregulated expression of selenoprotein H (SelH) and thioredoxin reductase 1 (Txnrd 1) and downregulated expression of glutathione peroxidase 3 (Gpx3), selenoprotein O (SelO), and selenoprotein P (SelP). Gpx3 knockdown increased both percent and total insulin release with high glucose stimulation. SelP knockdown increased insulin release at high glucose. In conclusion, high SeMet supplementation augments insulin secretion, while reductions in Gpx3 and SelP expression, from SeMet supplementation or via silencing, augment -cell function in the MIN6-K8 cell line. These studies support a putative role for selenium and selenoproteins in the regulation of glucose homeostasis and diabetes risk.

overall_design: Four experimental replicates were analyzed for 2 conditions (control and 40 uM SeMet)

first: Lidan

last: Zhao


title: Single-cell profiling of environmental enteropathy reveals epithelial and immune dynamics

city: Cambridge

first: Conner

middle: Samuel

last: Kummerlowe

state: MA

address: 77 Massachusetts Avenue

institute: MIT

summary: Here, we use the single-cell RNA-sequencing platform Seq-Well to generate a cellular atlas of environmental enteropathy in the proximal small intestine

overall_design: Single-cell RNA sequencing of proximal intestine samples from 11 patients with environmental enteropathy (EE) and 3 patients with eosinophilic esophagitis (EoE) and 2 patients with dysphagia from South Africa (SA)

first: Thomas

last: Wallach

first: Simutanyi

last: Mwakamui

first: Travis

last: Hughes

first: Nolawit

last: Mulugeta

first: Victor

last: Mudenda

first: Ellen

last: Besa

first: Kanekwa

last: Zyambo

first: Ira

last: Fleming

first: Marko

last: Vukovvic

first: Ben

last: Doran

first: Toby

last: Aicher

first: Marc

last: Wadsworth

first: Juliet

last: Bramante

first: Amiko

last: Uchida

first: Rabiah

last: Fardoos

first: Osaretin

last: Asowata

first: Nicholas

last: Herbert

first: Henrik

last: Kloverpris

first: John

last: Garber

first: Jose

last: Ordovas-Montanes

first: Zev

last: Gartner

first: Alex

last: Shalek

first: Paul

last: Kelly


title: RNA‐sequencing reveals genes linked with oocyte developmental potential in bovine cumulus cells

city: Madrid

first: Leopoldo

last: González-Brusi

state: Madrid

address: Avda Puerta de Hierro, 12

department: Animal Reproduction

country: Spain

institute: Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria

summary: Cumulus cells provide an interesting biological material to perform analyses to understand the molecular clues determining oocyte competence. The objective of this study was to analyze the transcriptional differences between cumulus cells from oocytes exhibiting different developmental potentials following individual in vitro embryo production by RNA‐seq. Cumulus cells were allocated into three groups according to the developmental potential of the oocyte following fertilization: (1) oocytes developing to blastocysts (Bl+), (2) oocytes cleaving but arresting development before the blastocyst stage (Bl-), and (3) oocytes not cleaving (Cl-).

overall_design: RNAseq analysis was performed on 4 (Cl-) or 5 samples (Bl+ and Bl-) of cumulus cells pooled from 10 cumulus‐oocyte complexes per group

first: A

last: Martínez-Moro

first: L

first: I

last: Lamas-Toranzo

first: E

last: O'Callaghan

last: Esteve-Codina

first: P

last: Lonergan

last: Bermejo-Álvarez


title: Distribution of genomic 5hmC marks in HCC827 and HCC827-TET2-KO cell line [HCC827_TET2_KO_5hmC]

first: Jian

last: Zhang

type: Methylation profiling by high throughput sequencing

summary: To investigate the influence of TET2 knock-down in lung cancer cell line, We performed 5hmC landscape analysis using data obtained from 5hmC-seq of HCC827 cell line and HCC827-TET2-KO cell line.

overall_design: Comparative analysis of genomic 5hmC distribution difference between HCC827 cells and HCC827-TET2-KO cells.


title: Analysis of transcriptomic  consequences of Tyrobp deletion in a freshly isolated microglia from Huntington's disease mouse model

city: New York

first: Michelle

middle: E

last: Ehrlich

state: NY

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary: We report the gene expression alterations observed in freshly isolated microglia from the striatum 10-month-old Q175 mice with and without Tyrobp

overall_design: Examination of gene expression alterations in the striatum of Q175 with and without Tyrobp

first: Jordi

last: Creus-Muncunill

first: Daniele

last: Mattei

first: Angie

last: Ramirez


title: Transcriptomic profiling of HBG gene expression in HEK293T cell line

city: Xianmen

first: Yuchen

last: Liu

address: Xiangan South Road

institute: Xianmen University

summary: Efficiency of HBG gene activation by the Cas12f/cgRNA system. In a doxycycline-inducible dCas12f-VPR knock-in (KI) HEK293T cell line, transiently transfected plasmids encoding U6, linear, and circular gRNAs targeting HBG1, and cgRNAs targeting mNeonGreen (negative control, NC) to activate HBG gene expression. RNA-seq analysis showed that cgRNAs exhibited increased efficiency in the target gene HBG1 and slight lower specificity when compared with U6 and linear gRNAs.

overall_design: To define whether Cas12f/cgRNA system could enhance dCas12f-based endogenous gene activation, we transiently transfected different plasmids encoding gRNAs to activate HBG gene expression in the doxycycline-inducible dCas12f-VPR knock-in (KI) HEK293T cell line. Then we performed RNA-sequencing and compared our date with HBG gene expression from publicly available databases.

first: Xin

last: zhang

first: Ying

last: Lin

first: Zhili

last: Rong


title: Gigaxonin as a prognistic marker of human cancer

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

summary: Gigaxonin, the GAN gene product, is a E3 ubiquitin ligase adaptor and is involved in neural cell and fibroblast intermediate filament processing. We have previously shown that gigaxonin in association with p16 ubiquitinates NF-κB in head and neck cancer. The cancer genomic database search has shown higher frequency of GAN gene exon 8 single nucleotide polymorphism (SNP, rs2608555), c.1293 C>T, p.Y431Y, in the normal Caucasian population (44.25% vs <20% in other populations). To determine whether this SNP is related to tumor development, we analyzed normal and tumor DNAs of cervical and head and neck cancer subjects and have found higher frequency of the SNP (Tumor 47% vs 25% normal, p=0.0017) in tumor samples. Although there was no relationship to HPV status, an inverse relationship to tumor recurrence and metastasis was observed. Two cervical cancer cell lines, ME180 and HT3, containing the SNP (T/T alleles) showed higher gigaxonin expression, reduced in vitro tumor cell growth and enhanced cisplatin sensitivity in comparison to 5 other cervical and 5 head and neck cancer cell lines containing the C allele (C/C or C/T alleles). CRISPR-Cas9 mediated conversion of T/T to C/C alleles of the ME180 cell line led to decreased gigaxonin expression, enhanced expression of snail, and twist (Epithelial to Mesenchymal transition - EMT markers) and increased in vitro tumor cell growth including invasion through Matrigel. Re-expression of gigaxonin in CRISPR-Cas9 cells using a lentiviral system resulted in increased expression of gigaxonin and reduced expression of snail accompanied by decreased in vitro cell growth. Mouse tail vein injection studies showed lung metastasis of CRISP-Cas9 cells which was inhibited in gigaxonin overexpressing cells. Our results strongly suggest that GAN gene exon 8 SNP correlates with gigaxonin expression, and inhibition of EMT phenotype in human tumors.

overall_design: 4 samples were analyzed. Respective libraries were made and sequenced for the analysis

first: Eri

middle: S

last: Srivatsan

first: Matteo

last: pellegrini

first: Karolina

middle: K

last: Urbanowicz

first: Ali

last: Ibraheem

first: Weihong

last: Yan


title: Complement C3 released from neurotoxic reactive astrocytes impairs learning and memory in the mouse model of postoperative neurodegenerative disorders

city: Hong Kong

last: Chen

address: No.21 Sassoon Road

country: Hong Kong

institute: the University of Hong Kong

summary: Perioperative neurocognitive disorder (PNDs) can commonly occur after major surgery in at risk patients and its occurrence increases medical healthcare burdens and even mortality. Accumulating evidence points to neuroinflammation being pivotal to the pathogenesis of these conditions. The complement cascade contributes to neuroinflammatory responses in the central nervous system (CNS) and complement C3 has been implicated in the manifestation of cognitive deficits in several neurological conditions. Neurotoxic reactive astrocytes function differently to their non-activated counterparts and release complement components in response to pathological triggers. We observed previously that surgery induces a rapid rise and then fall in cytokines but a more sustained glial activation response that coincided with postoperative cognitive impairment. In this study, we explored the relationship between the expression of complement C3, glial activation, and cognitive deficits.   Using a murine model of surgery, we characterized the transcriptional profiles of hippocampal astrocytes after surgery and examined the effects of C3 suppression on the neuroinflammatory response and cognitive performance. There was a delayed but sustained rise in hippocampal C3 of astrocytic in origin after surgery which corresponded with the onset of cognitive decline. Furthermore, the A1 or the neurotoxic phenotype predominated in this postoperative astrocytic activation, and these cells have a distinct transcriptional profile including C3 upregulation. Suppression of C3 inhibited synaptic phagocytosis by microglia and attenuated postoperative cognitive impairment. Therefore, C3 from reactive astrocytes appear central to the development of cognitive dysfunction associated with postoperative neuroinflammation.

overall_design: The mRNA profiles of purified hippocampal astrocytes from control mice and laparotomy mice

first: John

last: Man-Tak Chu


title: Single cell RNA sequencing of dorsal root ganglia (DRG) in Cdx2-Cre; Piezo2 conditional mutants and control littermates, age P21-P24

first: Nikhil

last: Sharma

institute: Columbia University

summary: We report scRNA-seq of adolescent mouse (P21).  We use these data to identify cell type specific genes for transcriptionally defined DRG sensory neurons.  The cell type specific markers are used to generate recombinase knock in mice under the control of cell type specific genes.

overall_design: Dorsal root ganglia from all segmental levels were dissected and dissociated to obtain neurons for single cell RNA sequencing analysis.

first: Lijun

last: Qi

first: David

middle: D

last: Ginty


title: RNA sequencing of slgols2 tomato fruits

city: Shenyang

first: Huidong

last: Zhang

address: No.120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, P.R.C.

institute: Shenyang Agricultural University

summary: To explore the molecular mechanism via which the galactinol synthase 2 (slgols2) affects Chl accumulation and chloroplast development, the RNA-seq experiment was conducted using slgols2 mutant and WT tomato fruits.

overall_design: We used CRISPR-Cas9 gene editing technology to create the slgols2 mutation. RNA sequencing of WT tomato (Solanum lycopersicum cv. Ailsa Craig) and slgols2 tomato pericarps of the shoulder at 30 DPA.

first: Kunpeng

first: Xueya

last: Zhao

first: Mengxi

last: Bi

first: Yudong

first: Shuo

last: Wang

first: Yi

last: He

first: Kui

last: Ma

first: Mingfang


title: LncRNA LUCAT1 Promotes Glioblastoma Progression by Enhancing HIF1⍺ Activity [ChIP-seq]

city: CLEVELAND

first: Haidong

last: Huang

address: 9500 EUCLID AVE RK-15

department: Cancer Biology

institute: Cleveland Clinic Foundation

summary: Glioblastoma (GBM) is characterized by a high degree of hypoxia. Hypoxia-inducible factors (HIFs) modulate glioma stem-like cell (GSC) responses to hypoxia and promote GBM progression, therapeutic resistance, and recurrence.  Here we identify a new transcript of the long non-coding RNA LUCAT1 and show that it reinforces HIF1⍺ signaling in GSCs under hypoxia. LUCAT1 expression is highly induced under hypoxia in GBM and GSCs in a HIF1⍺-dependent manner. High LUCAT1 expression in human GBM correlates with increased aggression and poor survival. Mechanistically, LUCAT1 associates with chromatin and modulates interaction between HIF1⍺ and coactivator CBP to hypoxia response elements (HREs) to drive HIF1⍺-target gene expression under hypoxia. Thus, LUCAT1 acts as a positive feedback factor to augment HIF1⍺ signaling under hypoxic stress in GSCs. Loss of LUCAT1 reduces tumor growth and prolongs mouse survival in xenograft models of GBM. Our findings provide new insights into how GSCs regulate gene expression under hypoxia and identify LUCAT1 as therapeutic target in GBM.

overall_design: GSCs were transduced with tet-RfxCas13d and LUCAT1 sgRNAs and treated with (KD) or without (control) doxycyclie. HIF1a or CBP ChIP-seq experiments were performed.

first: Jennifer

last: Yu


title: Identification of gene regulatory networks affected across drug-resistant epilepsies

city: Brussels

first: Liesbeth

last: François

state: Brussels

address: Allée de la Recherche 60

country: Belgium

institute: UCB Pharma SA

summary: Epilepsy is a chronic and heterogenous disease characterized by recurrent unprovoked seizures, that are commonly resistant to antiseizure medications. This study applies a transcriptome network-based approach across epilepsies aiming to improve understanding of molecular disease pathobiology, recognize affected biological mechanisms and apply causal reasoning to identify therapeutic hypotheses. This study included the most common drug-resistant epilepsies (DREs), such as temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), and mTOR pathway-related malformations of cortical development (mTORopathies). This systematic comparison characterized the global molecular signature of epilepsies, elucidating the key underlying mechanisms of disease pathology including neurotransmission and synaptic plasticity, brain extracellular matrix and energy metabolism. In addition, specific dysregulations in neuroinflammation and oligodendrocyte function were observed in TLE-HS and mTORopathies, respectively. The aforementioned mechanisms are proposed as molecular hallmarks of DRE with the identified upstream regulators offering opportunities for drug-target discovery and development.

overall_design: Bulk RNA-seq of four epilepsy pathologies (TLE-HS, FCD IIa, FCD Iib, TSC) and matching control cortex and hippocampal samples

first: Alessia

last: Romagnolo

first: Eleonora

last: Aronica

first: Stefanie

last: Dedeurwaerdere


title: LncRNA LUCAT1 Promotes Glioblastoma Progression by Enhancing HIF1⍺ Activity [RNA-seq]

overall_design: GSCw were transduced with shNT or shLUCAT1 and incubated in normoxia or hypoxia for 24 hours.


title: Neural and Metabolic Dysregulation in PMM2 deficient human in vitro neural models

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

summary: PMM2-CDG is a rare inborn error of metabolism caused by deficiency of the phosphomannomutase-2 (PMM2) enzyme, which leads to impaired protein glycosylation. While the disorder presents with primarily neurological symptoms, there is limited knowledge about the specific brain-related changes that result from PMM2 deficiency. We found aberrant neural activity in 2D neuronal networks from individuals with PMM2-CDG. Utilizing multi-omics datasets from 3D brain organoids derived from individuals with PMM2-CDG, we found widespread decreases in protein glycosylation, highlighting impaired glycosylation as a key pathological feature of PMM2-CDG. Furthermore, we identified impaired mitochondrial structure and abnormal glucose metabolism in PMM2-CDG brain organoids, indicating disturbances in energy metabolism. Correlation between PMM2 enzymatic activity in brain organoids and symptom severity suggests that the level of PMM2 enzyme function directly influences neurological manifestations. These findings enhance our understanding of specific brain-related perturbations associated with PMM2-CDG, offering insights into the underlying mechanisms and potential directions for therapeutic interventions.

overall_design: Human cortical organoids derived from control and PMM2 mutant hiPSC lines. Organoids collected at various stages from d95 to d169. Whole organoids were used for sequencing.

first: Silvia

last: Radenkovic

first: Rohit

last: Budhraja

first: Teun

last: Klein-Gunnewiek

first: Alexia

middle: T

last: King

first: Tarun

last: Bhatia

first: Anna

last: Ligezka

first: Karen

last: Driesen

first: Rameen

last: Shah

first: Bart

last: Ghesquière

first: Akhilesh

last: Pandey

first: Nael

middle: N

last: Kasri

middle: A

first: Eva

last: Morava

first: Tamas

last: Kozicz


title: Epithelial relay of microbial signals coordinates intestinal macrophage supported barrier repair [E. coli strains]

first: Ming-Ting

middle: Kessler

last: Tsai

address: 408 E 69th Street Z1619

department: Immunology

institute: Memorial Sloan Kettering Cancer Center

summary: The gastrointestinal tract is colonized by trillions of microorganisms collectively known as the gut microbiota. These microbes provide essential signals to support healthy gut function. The microbiota is separated from internal tissue by a single layer of intestinal epithelial cells that not only provides a physical barrier but also relays luminal signals to underlying gut immune cells. Altered microbiota composition including loss of anti-inflammatory microbes or outgrowth of mucosa-associated bacteria such as adherent-invasive E. coli (AIEC) are hallmarks of inflammatory disease including inflammatory bowel disease (IBD). In contrast to their hypothesized role in pathology, we recently identified select AIEC isolates that improve outcomes in mouse colitis models. These AIEC induce macrophage production of the anti-inflammatory cytokine IL-10 which limits gut inflammation and supports barrier repair. These benefits were lost if the AIEC was unable to attach to epithelial cells. However, the epithelial signaling underlying this protection remained unclear. To understand if intestinal epithelial cells signaled to immune cells after microbial attachment, we utilized human colonic organoid monolayers and found co-culture with a subset of AIEC isolates upregulated immune regulatory genes including CCL2, a macrophage recruiting chemokine. This effect was only observed in undifferenced epithelial cells, indicating epithelial stem cell recognition of microbes leads to macrophage recruitment. In vivo, antibody blockade of CCR2 abrogated the protective effect of AIEC colonization. Using bacterial transcriptome analysis, we identified high flagellin expression in AIEC isolates that activated epithelial signaling, with lost signaling in organoids deficient for TLR5, the receptor for flagellin. Together our findings suggest intestinal epithelial cells recognize microbial signals to coordinate macrophage recruitment that support intestinal repair, protecting from colitis.

overall_design: We screened a panel of E. coli strains, which were isolated from mucosal biopsy as part of the human microbiome projec, using Caco2 cells to indentify strains that induces epithelial responses. Of the strains tested, about half induced upregulation of the epithelial immune response genes as 541-15. We grouped them as "activators" while we classified the rest as "non-activators". To identify the signature genes that specifically expressed by the activators or non-activators, we performed bacterial transctiptome profiling.

first: Tsai

last: Ming-Ting

first: Diehl

last: Gretchen


title: Reduced heart failure effects through novel integrin targeting approach

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

summary: Heart failure remains one of the largest clinical burdens globally, with little to no improvement in the development of disease-eradicating therapeutics. Integrin targeting has been used in the treatment of ocular disease and cancer, but little is known about its utility in the treatment of heart failure. Here we sought to determine whether the second generation orally available, αvβ3-specific RGD-mimetic, 29P, was cardioprotective. Male mice were subjected to transverse aortic constriction (TAC) and treated with 50μg/kg 29P or volume-matched saline as Vehicle control. At 3 weeks post-TAC, echocardiography showed that 29P treatment significantly restored cardiac function and structure indicating the protective effect of 29P treatment in this model of heart failure. Importantly, 29P treatment improved cardiac function giving improved fractional shortening, ejection fraction, heart weight and lung weight to tibia length fractions, together with partial restoration of Ace and Mme levels, as markers of the TAC insult. At a tissue level, 29P reduced cardiomyocyte hypertrophy and interstitial fibrosis, both of which are major clinical features of heart failure.  RNA sequencing identified that, mechanistically, this occurred with concomitant alterations to genes involved molecular pathways associated with these processes such as metabolism, hypertrophy and basement membrane formation. Overall, targeting αvβ3 with 29P provides a novel strategy to attenuate pressure-overload induced cardiac hypertrophy and fibrosis, providing a possible new approach to heart failure treatment.

overall_design: Left ventricle apex tissue from male C57Bl6/J mice following 3 weeks transverse aortic constriction treated with 50μg/kg of the RGD mimetic 29P or volume-matched saline as Vehicle control.

first: Alex

last: Njegic

first: Lina

last: Laid

first: Min

last: Zi

first: Laura

last: Wisniewski

first: Jenna

last: Hunter

first: Sukhpal

last: Prehar

first: Nicholas

last: Stafford

first: Chaim

last: Gilon

first: Amnon

last: Hoffman

first: Michael

last: Weinmüller

first: Horst

last: Kessler

first: Elizabeth

last: Cartwright

first: Jun

last: Wang

first: Kairbaan

last: Hodivala-Dilke


title: Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

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

overall_design: Refer to individual Series


title: Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (RNA-Seq)

summary: There are two major types of Epstein-Barr Virus (EBV): type 1 (EBV-1) and type 2 (EBV-2). EBV functions by manipulating gene expression in host B cells, using virus-encoded gene regulatory proteins including Epstein Barr Nuclear Antigen 2 (EBNA2). While type 1 EBNA2 is known to interact with human transcription factors (hTFs) like RBPJ, EBF1, and SPI1, type 2 EBNA2 shares only ~50% amino acid identity and may have distinct effects on the genome. In this study, we examined EBNA2 binding in EBV-1 and EBV-2 transformed human B cells to identify shared and unique EBNA2 interactions with the human genome, revealing thousands of type-specific EBNA2 ChIP-seq peaks. Our analyses revealed that both types 1 and 2 EBNA2 strongly bind to SPI1 and AP-1 motifs (BATF and JUNB). However, type 1 EBNA2 showed preferential co-occupancy with EBF1, and type 2 EBNA2 with RBPJ. These differences in b hTF co-occupancy revealed type-specific gene expression of known EBNA2 targets. Both type 1 and 2 EBNA2 binding events were highly enriched at systemic lupus erythematosus (SLE) and showed type-specific enrichment at the risk loci of multiple sclerosis (type 1) and primary biliary cholangitis (type 2). Collectively, this study reveals extensive type-specific EBNA2 interactions with the human genome, genotype-dependent binding, and distinct associations with autoimmune disorders. Our results highlight the importance of considering EBV type in disease-related investigations.

overall_design: We performed RNA-seq in AG876, Jiyoye, GM12878, Mutu, and Akata cell lines. Experiments were performed in three replicates per cell line.

first: Leah

last: Kottyan


title: ALKBH5 regulates paclitaxel resistance in NSCLC via inhibiting CEMIP-mediated EMT

first: Lingyue

last: Gao

address: Wenhua Road

institute: Shenyang Pharmaceutical University

summary: N6-methyladenosine (m6A) is the most printed and prevalent mRNA modification, which was verified to be closely correlated with cancer occurrence and progression. As m6A demethlyase, the dysregulation of ALKBH5 was observed in various cancer. However, the role and underlying machinery of ALKBH5 in NSCLC pathogenesis, especially the chemo-resistance was poorly elucidated. The current study indicated that ALKBH5 was decreased during paclitaxel (PTX) resistant process and its down-regulation usually implied poor prognosis of NSCLC patients. Over-expression of ALKBH5 in PTX-resistant cells could suppressed cell proliferation and enhanced chemo-sensitivity. Whereas, knockdown of ALKBH5 exerted opposite effect, which further supported the tumor suppressive role of ALKBH5. Over-expression of ALKBH5 also could reverse the EMT process in PTX-resistant cancer cells. Mechanistically, data of RNA-seq, Real-time PCR and western blotting indicted that CEMIP, also known as KIAA1199, may be the downstream target of ALKBH5. And ALKBH5 could negatively regulated the CEMIP level by decreasing its mRNA stability. Collectively, current data demonstrated that ALKBH5/CEMIP axis modulates the EMT process in NSCLC, which in turn regulates chemo-sensitivity of cancer cells to PTX.

overall_design:
To identify the function and downstream target of ALKBH5, H460/PTX cells were infected with Control or ALKBH5 lentivirus to overexpress ALKBH5
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells with 3 replicates.
Comparative gene expression profiling analysis of RNA-seq data for H460/PTX cells and its OE derivative (OE-ALKBH5).

first: Lihui

first: Li

last: Qiao

first: Yingying

last: Li


title: SETD3-mediated histidine methylation of MCM7 regulates DNA replication by facilitating chromatin loading of MCM

city: Wuhan

first: Shuang

address: Hubei province

institute: Wuhan University

summary: The minichromosome maintenance complex (MCM) DNA helicase is an important replicative factor during DNA replication. The proper chromatin loading of MCM is a key step to ensure replication initiation during G1/S phase. Because replication initiation is regulated by multiple biological cues, additional changes to MCM may provide deeper understanding towards this event. Here, we uncover that the histidine methyltransferase SETD3 promotes DNA replication in an enzymatic activity dependent manner. Nascent-strand sequencing (NS-seq) shows that SETD3 regulates replication initiation, as depletion of SETD3 attenuates early replication origins firing. Mechanistically, biochemical experiments reveal that SETD3 binds MCM mainly during G1/S phase, which is required for CDT1-mediated chromatin loading of MCM. The MCM loading relies on the histidine-459 methylation (H459me) on MCM7 that is catalyzed by SETD3. Impairment of H459 methylation attenuates DNA synthesis and chromatin loading of MCM. Furthermore, we show that CDK2 phosphorylates SETD3 at Serine-21 during the G1/S phase, which is required for DNA replication and cell cycle progression. These findings demonstrate a novel mechanism by which SETD3 methylates MCM to regulate replication initiation.

overall_design: Nascent Strand DNA sequencing (NS-seq) for the nascent DNA in WT and shSETD3 HeLa S3 cells

first: Hongguo

last: Duan


title: Discovery of a Novel Class of Bioactive Molecules Suppressing Pathogenic Fibroblast Activation through Hyou1 Targeting

city: Vari

first: George

last: Kollias

state: Attica

address: 34 Fleming Street

department: Institute for Bioinnovation/ Department of Physiology, School of Medicine

country: Greece

institute: BSRC "Alexander Fleming"/ National and Kapodistrian University of Athens

summary: Fibroblasts play an important role in fibrosis, chronic inflammatory diseases (CIDs) and cancer. Targeting their pathogenicity is crucial, considering the limitations and side effects of existing biologic therapies that focus on inflammatory mediators (TNFα/IL-6). Herein, a multidisciplinary approach utilizing activated primary fibroblasts (PFs) and macrophages (MFs), which are key regulators in inflammation and fibrosis, is presented. The research encompasses medicinal chemistry, molecular phenotyping, mechanism of action studies, RNA-sequencing analysis and ADMET/PK/in vivo evaluation. A novel anti-inflammatory pharmacophore acting through Hypoxia up-regulated protein 1 (Hyou1) was discovered, thus emerging the potential of Hyou1 down-regulation/inhibition in fibroblast-related disorders. The study highlights the need for further investigation into the effects of Hyou1 activity on fibroblasts while providing the first reported Hyou1 small molecule inhibitor leads for drug discovery.

overall_design: To investigate the deregulated genes on activated fibroblasts upon compound 33 treatment, we performed 3prime UTR sequencing comparing compound treated hTNFtg synovial fibroblasts versus the vehicle (dmso) treated controls

first: Dimitra

last: Papadopoulou

first: Vasiliki

last: Mavrikaki

first: Filippos

last: Charalampous

first: Christos

last: Tzaferis

first: Martina

last: Samiotaki

first: Konstantinos

last: Papavasileiou

first: Antreas

last: Afantitis

first: Niki

last: Karagianni

first: Maria

last: Denis

first: Julie

last: Sanchez

first: Robert

last: Lane

first: Zacharias

middle: F

last: Brotzakis

first: Georgios

last: Skretas

first: Dimitris

last: Georgiadis

first: Alexios

last: Matralis


title: Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (ATAC-Seq)

first: Matthew

last: Weirauch

overall_design: We performed ATAC-seq in AG876, Jiyoye, GM12878, and MutuIII cell lines. Experiments were performed in two replicates per cell line.

first: Leah

last: Kottyan


title: RNA-sequence analysis of JMJD1A target genes in subcutanous white adipose tissue.

city: Tokyo

first: Juro

last: Sakai

address: 4-6-1, Komaba, Meguro-ku

department: Division of Metabolic Medicine

country: Japan

institute: Research Center for Advanced Science and Technology, The University of Tokyo

summary: Mitochondria play a vital role in non-shivering thermogenesis in both brown and subcutaneous white adipose tissues (BAT and scWAT, respectively). However, specific regulatory mechanisms driving mitochondrial function in these tissues have been unclear. Here we demonstrate that prolonged activation of β-adrenergic signaling induces epigenetic modifications in scWAT, specifically targeting the enhancers for the mitochondria master regulator genes Pgc1a/b. This is mediated at least partially through JMJD1A, a histone demethylase that in response to β-adrenergic signals, facilitates H3K9 demethylation of the Pgc1a/b enhancers, promoting mitochondrial biogenesis and the formation of beige adipocytes. Disruption of demethylation activity of JMJD1A in mice impairs activation of Pgc1a/b driven mitochondrial biogenesis and limits scWAT beiging, contributing to reduced energy expenditure, obesity, insulin resistance, and metabolic disorders. Notably, JMJD1A demethylase activity is not required for Pgc1a/b dependent thermogenic capacity of BAT especially during acute cold stress, emphasizing the importance of scWAT thermogenesis in overall energy metabolism.

overall_design: Mice were individually caged in a thermostatic chamber and allowed to acclimate to thermal neutrality (30°C) for 1 week prior to the cold exposure experiments. Then, the mice were placed in a chamber maintained at either 30°C or 8°C with ad libitum access to food and water for 1 week. The mice were sacrificed and subcutanous adipose tissues were harvested and snap frozen in liquid nitrogen. The tissues were subjected to RNA extraction and RNA-sequence analysis using Illumina HiSeq 2500.

first: Yoshihiro

last: Matsumura

first: Ryo

last: Ito


title: Transcriptomic analysis (RNA-seq) of early iPSC-CMs between PA-IVS and healthy control.

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

summary: Transcriptomic analysis by RNA-seq revealed that pathways associated with cell cycle and mitosis were downregulated in day 13 PA-IVS-1v iPSC derived cardiomyocytes.

overall_design: Gene expression profiling of post-differentiation day 13 iPSC-CMs derived from PA-IVS-1v patients and healthy controls

first: Ming-Tao

last: Zhao

first: Shiqiao

last: Ye

first: Yang

last: Yu


title: ATAC-sequence analysis of immortalized subcutanous white adipose tissue cells.

overall_design: Immortalized white adipose tissue (im-scWAT) cells were established from WT or Jmjd1a HY/HY mice. scWAT cells before or after differentiation into beige adipocytes (day 0 or day 8) were subjected to ATAC-sequence analysis using Illumina Novaseq 6000.


title: CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors

city: Beijing

first: Yuting

last: Liu

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

institute: Peking University

summary: CCCTC-binding factor (CTCF), a ubiquitously expressed architectural protein, has emerged as a key regulator of cell identity gene transcription. However, the precise molecular mechanism underlying specialized functions of CTCF remains elusive. Here, we investigate the mechanism through integrative analyses of primary hepatocytes, myocytes, and B cells from mouse and human. We demonstrate that CTCF cooperates with lineage-specific pioneer transcription factors (TFs), including MyoD, FOXA, and PU.1, to control cell identity at 1D and 3D levels. At the 1D level, pioneer TFs facilitate lineage-specific CTCF occupancy via opening chromatin. At the 3D level, CTCF and pioneer TFs form regulatory hubs to govern the expression of cell identity genes. This mechanism is validated using MyoD-null mice, CTCF knockout mice, and CRISPR editing during myogenic differentiation. Collectively, these findings uncover a general mechanism whereby CTCF acts as a cell identity cofactor to control cell identity genes via orchestrating regulatory hubs with pioneer TFs.

overall_design: RNA-seq for C2C12 cell lines with and without CTCF knockdown. ATAC-seq for myoblast and myocyte from wild type and MyoD-null mice.

first: Xin

last: Wan

first: Hu

last: Li


title: Effect of CLDN1 mAb on primary patient derived liver organoids

city: Strasbourg

first: Frank

last: Jühling

address: 3 Rue Koeberlé

country: France

institute: Université de Strasbourg, Inserm, Institut de Recherche sur Les Maladies Virales et Hépatiques UMR_S1110

summary: Organoids were established from non-tumorous cirrhotic liver tissue and treated with CLDN1 mAb or Control mAb for 4 days. Organoids were harvested and mRNA was extracted.  RNAsequencing was performed for comparative gene expression profiling.

overall_design: Transcriptomic profiling analysis of primary liver organoids treated with CLDN1 mAb or Control mAb.

first: Natascha

last: Roehlen

first: Maike

last: Hofmann

first: Thomas

last: Baumert


title: Genome-wide RNAseq of liver tissue derived from humanized mice fed by CDA-HFD and treated with CLDN1 mAb or vehicle Control

summary: Six-week old Fah−/−/Rag2−/−/Il2rg −/− (FRG) –NOD breeding mice were intravenously injected with 1.5 x 10^9 plaque forming units (pfu) of an adenoviral vector encoding the secreted form of the human urokinase-like plasminogen activator (Ad-uPA). Forty-eight hours later, 10^6 PHH were injected intrasplenically. Successfully transplanted mice were fed with CDA-HFD for 16 weeks and then treated with humanized CLDN1 specific mAb 500 µg or vehicle for additional 8 weeks. RNA was extracted from non-tumorous liver tissue of 4 NASH fibrosis mice treated with CLDN1 mAb, 3 vehicle Control treated NASH fibrosis mice as well as 3 humanized mice fed by regular diet. Libraries were sequenced on the Illumina HiSeq 4000 as Single-Read 50 base reads.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: mRNA profiles of humanized mice fed a regular diet, humanized NASH fibrosis mice treated with vehicle control and humanized NASH fibrosis mice treated with CLDN1 mAb

first: Hussein

last: El Saghire

first: Antonio

last: Saviano

last: Röhlen


title: Genome-wide RNAseq of liver tissue derived from DEN-CDA-HFD mice treated with CLDN1 mAb or vehicle Control

summary: Seven-week old male C57BL/6J mice received a single i.p. injection of DEN (100 mg/kg) and were subsequently fed with CDA-HFD after 3 weeks. After 6 weeks of diet, the mice were randomized in 2 groups, receiving weekly i.p. injections of 500 µg of either CLDN1 specific mAb or vehicle control for 16 weeks. RNA was extracted from non-tumorous liver tissue of 6 DEN-CDA-HFD mice treated with CLDN1 mAb, 6 DEN-CDA-HFD mice treated with vehicle Control as well as 5 C57BL/6J Control mice fed by regular diet. Libraries were sequenced on the Illumina HiSeq 4000 as Single-Read 50 base reads.

overall_design: mRNA profiles of C57BL/6J mice fed a regular diet and DEN-CDA-HFD mice treated with vehicle control or CLDN1 mAb


title: Alternative polyadenylation is a minor feature of primary human muscle differentiation

city: Melbourne

first: Akriti

last: Varshney

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

summary: Alternative polyadenylation has been explored in multiple native and disease transitions. The prevailing hypothesis being that differentiated cells use longer 3’UTRs with more scope for regulation, whereas undifferentiated cells use shorter, less regulated 3’UTRs. Here we describe gene-expression and alternative polyadenylation of human primary myocytes over a time course differentiation. Contrary to expectation, only minor changes to 3’-end choice were detected. To reconcile this finding with published differentiation data in the immortalized C2C12 myocyte cell line, a systematic comparison was undertaken. Less than half the genes differentially expressed in the immortalized model were recapitulated in primary cells, and of these, important metabolic states were either absent, underrepresented or regulated in the opposite direction. A new bioinformatic approach, developed to quantitate the degree of alternative polyadenylation between unrelated experiments demonstrated that alternative polyadenylation was reduced by ~50% with less than 1/10 of the genes that underwent alternative polyadenylation in C2C12 differentiation showing alternative processing in primary muscle differentiation. A possible explanation for this difference was a less pronounced down regulation of the cleavage and polyadenylation factors in the differentiation primary cell. In sum, the data promote the use of primary human myocytes to model muscle biogenesis over immortalized models that may not fully recapitulate human muscle development.

overall_design: Two primary human skeletal muscle cell lines were cultivated in Hams F-10 with 20% Fetal Bovine Serum and basic Fibroblast Growth Factor (bFGF) at 37˚C until 80% confluent. Samples T1 was collected 24h post seeding and T2 was collected at 80% confluence. Cells were differentiating in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 2% horse serum. Samples T3, T4, T5 and T6, were collected 1, 3, 5 and 7 days post differentiation respectively. Samples were analyzed via Quant-seq 3'UTR focused deep-sequencing in replicate using the Illumina Hiseq 3000 platform.

first: Traude

last: Beilharz


title: Shared and distinct interactions of Epstein-Barr Nuclear Antigen 2 type 1 and type 2 with the human genome (ChIP-Seq)

first: Matthew

last: Weirauch

overall_design: We performed ChIP-seq in AG876, Jiyoye, GM12878, and Akata cell lines. Experiments were performed in three replicates per cell line.

first: Leah

last: Kottyan


title: MLL1 regulates cytokine-driven cell migration and metastasis

city: Baltimore

first: Denis

last: Wirtz

state: MD

address: 130 Croft Hall, Johns Hopkins University, 3400 N Charles Street

institute: Johns Hopkins University

summary: The interaction between MLL1 And Menin controls cancer cell proliferation, migration, and tumor progression. MLL1 depletion reduced 3D cell migration in vitro and led to lesser metastatic burden and prolonged survival in vivo. Mechanistically, MLL1-Menin interaction controls actin filament assembly and protrusion generation through IL-6-pSTAT3-Arp3 axis. MLL1-Menin interaction also controls TGF-β1-mediated acto-myosin contractility via Gli2-ROCK1/2-pMLC2 axis. Additionally, MLL1-menin inhibition decreased cell proliferation via a multitude of cell-cycle related pathways. Mice bearing MLL1-depleted tumors exhibited decreased significant lung metastatic burden when sacrificed at a set tumor size, indicating that MLL1 played a role in the invasion of tumor cells in vivo. Finally, MLL1-Menin inhibition was additive with standard chemotherapeutics, both in vitro and in vivo.

overall_design: Samples were divided into two groups. First group consisted of wild type MDA-MB-231 cells, cells transduced with MLL1 shRNA, and cells transduced with non-targeting scrambled shRNA control. Second group consisted of cells treated with MI-2-2 at two doses, cells treated with MI-503 at 3 doses, and cells treated with DMSO as a negative control. All conditions were performed as triplicates.

first: Praful

last: Nair


title: RNA-seq analysis of jmj28-3 and genome-wide occupancy of JMJ28 in Arabidopsis

city: shanghai

first: li

last: peng

institute: PSC


title: Genome-wide occupancy of JMJ28 in Arabidopsis

summary: ChIP-seq was performed to detect genome-wide binding sites of JMJ28

overall_design: Arabidopsis wild-type Col-0 and JMJ28-4Myc plants were subject to ChIP-seq analysis using the Myc antibody.

first: Si-Si

last: Xie

first: Li

last: Peng

first: Cheng-Guo

last: Duan


title: RNA-seq analysis of WT, jmj28-3 in Arabidopsis

summary: RNA-seq was performed to detect transcripts level of WT and mutants

overall_design: Total RNAs were extracted from 12-day-old seedlings grown during long days using a RNeasy Plant Mini kit (Qiagen)


title: DNA-sensing AIM2 inflammasome promotes the overgrowth of ileal mucosal Lachnospiraceae to potentiate antitumor immunity

city: Shanghai

first: Min

last: Huang

address: 555, Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: The spatial organization of gut microbiome is essential for their interactions with the host. Recently, microbiota alteration in ileum is getting the increasing recognition due to the close interplay with inflammatory diseases and the tumor immunosurveillance. However, how ileal microbiome is spatially regulated remains unclear. Here, we show that DNA-damaging chemotherapy specifically remodels microbiota in ileal mucosa, resulting in the overgrowth of local family Lachnospiraceae that promotes antitumor immunity and synergizes with immune checkpoint blockage. Mechanistically, the prominent proliferative state of transit amplifying cells (TACs) in the ileal crypt presents a vulnerability to chemotherapy-caused genomic stress, resulting in the accumulation of cytosolic dsDNA that subsequently activates AIM2 inflammasome. AIM2-dependent production of IL18 boosts Th1 immunity in ileal lamina propria, which further impairs the antimicrobial host defense of proximal Paneth cells via activating IFN-γ-JAK-STAT signaling. Our findings demonstrate that AIM2 inflammasome shapes ileal microbiome via governing the compartmentalized cellular interplay in ileal crypt, providing mechanistic insights into the regulation of gut biogeography and implicating therapeutic strategies of spatial microbiome intervention using chemotherapy.

overall_design: RNA-seq analysis of ileal crypt cells from CPT-11 or vehicle treated mice

first: Jun

last: Xu

first: Congying

last: Pu

first: Yixian

last: Fu


title: Genome-wide methylation profile of uterine cervical carcinoma in Indian patients

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

summary: Cancer of the uterine cervix (CACX) is the third most commonly diagnosed cancer and the fourth leading cause of cancer deaths in women worldwide. In India, CACX accounts for approximately 1,22,844 new cases and 67,477 deaths annually. Previously, we catalogued global copy-number aberrations [GSE76911] and performed gene expression profiling [GSE122697] in CACX. Interestingly, differential change in the expression between normal and tumor tissues of several genes did not correlate with the chromosomal copy-number alteration. This encouraged us to perform genome-wide DNA methylation analysis. Hence, in the current study, we discover the global methylation in cervical tumors at different clinical stages and HPV-negative normal ectocervix along with HPV16-positive cervical squamous cell carcinoma cell line, SiHa.

overall_design: Bisulphite converted DNA from the 16 samples (5 normal,  and 10 tumor) were hybridised to the Illumina Infinium HumanMethylation850 BeadChip

first: Anirban

last: Roychowdhury

first: Priyanka

last: Dutta

first: Sudip

last: Sammadar

first: Arindam

last: Maitra

first: Chinmay

last: Kumar Panda


title: Analysis of gene expression signatures for Litchi knockout during motor neuron differentiation

status: Public on Mar 11 2024

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

summary: We identified Litchi (Gm2990) as a novel regulator for orchestrating motor neuron (MN) maturation. To study the function of Lithci during MN differentiation, we knocked out Litchi in mouse ESCs and differentiated into MN.

overall_design: Total RNA were extracted from both WT and Litchi knockout ES derived motor neurons on Day7 and Day9. Subsequently, ES~MNs transcriptome was analyzed by Agilent SurePrint G3 Mouse GE 8x60K Microarray (Agilent-G4858A-028005).

first: Ho-Chiang

last: Hsu


title: Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

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

overall_design: Refer to individual Series


title: Comparison of CcrM-dependent methylation in Caulobacter crescentus and Brucella abortus by nanopore sequencing

city: Amherst

first: Maxwell

middle: B

last: Campbell

address: 240 Thatcher Way

department: Molecular and Cellular Biology

institute: UMass Amherst

summary: Bacteria rely on DNA methylation for restriction modification systems and for epigenetic control of gene expression. In Alphaproteobacteria, the CcrM orphan methyltransferase is particularly noteworthy in a range of transcriptional regulation. The wider adoption of nanopore sequencing and updated processing pipelines has made epigenome measurements in bacteria more convenient than before. Here, we validate this approach in Alphaproteobacteria by measuring CcrM-dependent DNA methylation in Caulobacter crescentus and show excellent correlation with other approaches. Continuing in Caulobacter, we directly measure the impact of Lon-mediated CcrM degradation on the epigenome and show that the AlkB demethylase has no global impact on DNA methylation during normal growth. We report on the global DNA methylation in Brucella abortus for the first time and find that CcrM-dependent methylation is reliant on Lon in an unexpected species- and chromosome-specific manner. Finally, we measure the impact of the MucR transcription factor on the Brucella methylome. Given the ease and reduced costs, our work demonstrates the utility of nanopore-based sequencing for epigenome monitoring in Alphaproteobacteria.

sample_organism:
Brucella abortus 2308
Caulobacter vibrioides NA1000

overall_design:
Caulobacter crescentus NA1000, along with its derivative strains, were initially cultured on Peptone Yeast Extract (PYE) agar plates. These plates contain a specific nutrient mix: 2 g/L of peptone, 1 g/L of yeast extract, 0.5 mM of MgSO4, 0.5 mM of CaCl2, and 1.5% agar (produced by Difco), and were incubated overnight at 30°C. Following incubation, isolated colonies were picked and further cultured in PYE liquid media overnight at 30°C within shaken flasks. The cultures were then diluted to achieve a starting optical density (OD600) of 0.1, and allowed to grow to a mid-exponential phase (OD600 of ~0.6) prior to the isolation of chromosomal DNA.
Brucella abortus 2308 and derivative strains were grown on Schaedler agar (Becton, Dickinson, and Co., Sparks, MD, USA) supplemented with 5% defibrinated bovine blood (SBA) incubated at 37°C under 5% CO2 or in brucella broth (Becton, Dickinson, and Co., Sparks, MD, USA) incubated at 37°C with shaking. Growth media were supplemented with kanamycin (45 ug/mL) or chloramphenicol (10 ug/mL) when appropriate. For isolation of chromosomal DNA, Brucella abortus 2308 and derivative strains were grown overnight in brucella broth, subcultured to an OD 600 of 0.1 and then grown to  mid-exponential phase (OD 600 of ~0.6) before isolation of chromosomal DNA by guanidine thiocyanate.
Caulobacter strains were sequenced using nanopore R.9.5 pores, and Brucella strains were sequenced using nanopore R.10.4.1 pores.
Raw nanopore sequencing outputs (Fast5 format) for Caulobacter strains were quality-controlled and trimmed using Guppy. High-quality reads were aligned to the reference genome NC_011916.1 with Minimap2, using default parameters. Fast5 files were converted to slow5 files and aligned to the mapped reads using the 'eventalign' function within Nanopolish. Methylated bases were quantified using mCaller, employing the precompiled 'r95_twobase_model_NN_6_m6A.pkl' model for assessing modified adenines. The methylation results were then annotated using Bedtools.
Raw nanopore sequencing outputs (Fast5 format) from nanopore sequencing for Brucella strains, were converted into pod5 files for optimization. Dorado’s standard basecalling command was employed, utilizing the model ‘dna_r10.4.1_e8.2_400bps_sup@ v4.2.0’. In addition, modified base calling was executed using the specialized model ‘dna_r10.4.1_e8.2_400bps_sup @v4.2.0_6mA@v2’. The produced bed files were then aligned to NCBI reference genomes NC_007618.1 and NC_007624.1 with the mapped reads using the align and sort functions of samtools . The resulting modified bam files were run with modbam2bed with default settings.

first: Ian

last: S Barton

first: R

middle: M

last: Roop

first: Peter

last: Chien


title: The Cdc14 phosphatase, Clp1, does not affect genome expression

first: Shaimaa

last: Hassan

address: Gower Street, Darwin Building London

department: Bioscience

institute: UCL

summary: Schizosaccharomyces pombe Clp1 is a Cdc14-family phosphatase that reverses mitotic Cdk1 phosphorylation. Despite evolutionary conservation, Clp1’s mammalian orthologs do not share this function. Rather, higher eukaryotic Cdc14 enzymes act in DNA repair, ciliogenesis, and gene regulation. To examine if Clp1 regulates gene expression, we compared the transcriptional profiles of cells lacking Clp1 function to that of wildtype. Because clp1∆ cells are sensitive to the actin depolymerizing drug, LatrunculinA, we also investigated whether a transcriptional response was involved. Our results indicate that Clp1 does not detectably affect gene expression and highlight the organism-specific functions of this conserved phosphatase family.

overall_design: Two independent biological experiments were performed each for clp1Δ and for clp1-C286S experiments as well as for LatrunculinA-treatment wildtype and clp1Δ experiments, including one dye swap in each case

first: Luis

middle: L

last: Maury

first: Liping

last: Ren

first: Jürg

last: Bähler

first: Kathleen

last: Gould


title: Gene expression profile of human mono-derived DCs stimulated with the bacterial lysate OM-85

city: Bellinzona

first: Greta

last: Guarda

address: Via Francesco Chiesa 5

institute: Institute for Research in Biomedicine (IRB)

summary: OM-85 is a bacterial lysate used in clinical practice to reduce duration and frequency of recurrent respiratory tract infections. Whereas knowledge on its regulatory effects in vivo has substantially advanced, the mechanisms of OM-85 sensing remain inadequately addressed.The purpose of this study was to investigate the transptomic profile of human mo-DCs after ex vivo stimulation with OM-85 at determine to what extent OM-85-induced gene signature in different myeloid cell subsets is dependent on TLR2/TLR4 expression. We also aimed to compare the OM-85-triggered gene signature with the signatures induced by specific TLR2 or TLR4 agonists.

overall_design: To this aimes, mo-DCs were treated with the bacterial lysate OM-85 (100-300-900 ug/ml) for 2-8hr. To investigate the contribution of TLRs in response to OM-85, mo-DCs were pre-treated with isotype control antibody or blocking antibodies agaisnt TLR2 or TLR4 or both for 90 min followed by stimulation with 300 ug/ml OM-85 for 2hr. Cells in parallel were stimulated with  0.1 ng/ml LPS or 10ng/ml Pam3CSK4 for 2hr to compare the TLR2/TLR4 specific gene expression profiles with the one of OM-85.


title: Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations [MethylationEPIC]

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

institute: KRIBB

type: Methylation profiling by genome tiling array

summary: Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, and is even more in women. EGFR mutations and ALK fusions are major alterations observed in NSLA. We have focused on NSLA without EGFR and ALK alteration (NENA) rather than NSLA with EGFR and ALK (EA). First, we selected 141 NSLA tissues, and performed proteogenomic analyses including the whole-genome sequencing (WGS), transcriptome, methylation EPIC array, total proteome and phosphoproteome. We then excluded 40 patients with EA and 7 patients with NENA microsatellite instability. Genome analysis revealed that TP53 (25%), KRAS (22%), ROS1 fusion (14%), and SETD2 (11%) were the most frequently mutated  genes  in  NENA  patients.  Proteogenomic  impact  analysis revealed that STK11 and ERBB2 somatic mutations had broader effects on cancer-associated genes in NENA. Through DNA copy-number alteration analysis, we identified 22 prognostic proteins, inﬂuencing transcriptomic and proteomic changes. Gene set enrichment analysis revealed that the estrogen signaling emerged as the key pathway activated in NENA. A lot of proteogenomic evidence supported the increased estrogen signaling, such as copy-number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was suggested as a potential drug for targeting activated estrogen signaling in NENA, and was experimentally validated in vitro using cell line model. In this study, we enhanced our understanding of the etiology of NENA NSLA through the proteogenomic landscape, based on which we proposed saracatinib as an effective drug

overall_design: The Infinium MethylationEPIC BeadChip (Illumina) was employed for methylation array experiments following the manufacturer’s instructions. Briefly, 500 ng of gDNA from lung tissues was treated with 20 µL of sodium bisulfite solution using an EZ DNA Methylation-Gold µKit (Zymo Research). Bisulfite-converted DNA (4 µL) was amplified using the Infinium Methylation Assay Kit (Illumina). The amplified DNA was hybridized to the Infinium MethylationEPIC BeadChip and scanned using an Illumina iSCAN system. CpG methylation values were calculated as average-values using Minfi (v3.11), with the following equation: average = M/(M + U + 100), where M and U are the methylated and unmethylated signal intensities, respectively. Measurements with a p-value <0.05 were considered significant above the background. Additionally, redundant probes, including multi-hit probes and SNPs, which could affect the analysis results, were filtered using the ChAMP package filter function.


title: Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations [RNA-seq]

overall_design: Expression profiling by high throughput sequencing


title: Antisense transcription can induce expression memory via stable promoter repression

city: Berlin

first: Till

last: Schwämmle

state: Berlin

address: Ihnestrasse 63

department: Otto-Warburg-Laboratory

country: Germany

institute: Max Planck Institute for Molecular Genetics

summary: The capacity of cells to retain a memory of previous signals enables them to adopt unique cell fates and adjust to their surrounding environment. The underlying gene expression memory can arise from mutual repression of two genes, forming a toggle switch. Such mutual repression may occur at antisense loci, where two convergently oriented genes repress each other in cis. Under which conditions antisense transcription can generate expression memory remains poorly understood. To address this question, we combine mathematical modeling, genomics and a synthetic biology approach. Through simulations we show that stable memory can emerge, if both genes in an antisense pair transcribe through the convergent promoter and induce a stable repressive chromatin state. Genome-wide analysis of nascent transcription further supports antisense-mediated promoter repression with promoter-overlapping antisense gene pairs exhibiting mutually exclusive expression. Through constructing a synthetic antisense locus in mouse embryonic stem cells (mESCs) we then show that such a locus architecture can indeed maintain a memory of a transient stimulus. Mutual repression and the capacity for memory formation are elevated, when mESCs differentiate, showing that epigenetic memory is a cell type-specific property. Our finding that stem cells adapt their ability to remember stimuli as they differentiate might help to elucidate how stemness is maintained.

overall_design: We performed Whole-genome bisulfite-sequencing (WGBS) in differentiating female mouse embryonic stem cells (TX1072dXIC XX cell line). Samples were collected at days 0, 2 and 4 of 2i/LIF-withdrawal.

first: Verena

last: Mutzel

first: Svearike

last: Oeverdieck

first: Lucia

last: Librenjak

first: Benedikt

last: Boesen

first: Melissa

last: Bothe

first: Rutger

last: Gjaltema

first: Ilona

last: Dunkel

first: Gemma

last: Noviello

first: Edda

middle: G

last: Schulz


title: Epithelial relay of microbial signals coordinates intestinal macrophage supported barrier repair

city: New York

first: Ming-Ting

last: Tsai

address: 408 E 69th Street Z1619

institute: Memorial Sloan Kettering Cancer Center

summary: The gastrointestinal tract is colonized by trillions of microorganisms collectively known as the gut microbiota. These microbes provide essential signals to support healthy gut function. The microbiota is separated from internal tissue by a single layer of intestinal epithelial cells that not only provides a physical barrier but also relays luminal signals to underlying gut immune cells. Altered microbiota composition including loss of anti-inflammatory microbes or outgrowth of mucosa-associated bacteria such as adherent-invasive E. coli (AIEC) are hallmarks of inflammatory disease including inflammatory bowel disease (IBD). In contrast to their hypothesized role in pathology, we recently identified select AIEC isolates that improve outcomes in mouse colitis models. These AIEC induce macrophage production of the anti-inflammatory cytokine IL-10 which limits gut inflammation and supports barrier repair. These benefits were lost if the AIEC was unable to attach to epithelial cells. However, the epithelial signaling underlying this protection remained unclear. To understand if intestinal epithelial cells signaled to immune cells after microbial attachment, we utilized human colonic organoid monolayers and found co-culture with a subset of AIEC isolates upregulated immune regulatory genes including CCL2, a macrophage recruiting chemokine. This effect was only observed in undifferenced epithelial cells, indicating epithelial stem cell recognition of microbes leads to macrophage recruitment. In vivo, antibody blockade of CCR2 abrogated the protective effect of AIEC colonization. Using bacterial transcriptome analysis, we identified high flagellin expression in AIEC isolates that activated epithelial signaling, with lost signaling in organoids deficient for TLR5, the receptor for flagellin. Together our findings suggest intestinal epithelial cells recognize microbial signals to coordinate macrophage recruitment that support intestinal repair, protecting from colitis.

overall_design: To understand epithelial responses to adherent microbes, we utilized human colonoid-derived monolayers as a model to study epithelial responses to different E. coli strains. Three human colonoid lines were used in this study: ASC103, MSK161N and MSK162N. Human colonoid monolayers cultured in transwell inserts were either maintained as undifferentiated (UD) monolayers or differentiated for 5 days as differentiated (DF) monolayers. Both UD and DF monolayers were left untreated (NT) or colonized with AIEC 541-15 or non-AIEC T75. Cells were harvested at 4 hours post colonization using Qiagen RNeasy kits. Each treatment (NT, T75, 541-15) were technically duplicated or triplicated.

first: Tsai

last: Ming-Ting

first: Diehl

last: Gretchen


title: Mannose is crucial for mesoderm specification and symmetry breaking in gastruloids

city: Cambridge

first: Chaitanya

middle: Dnyanehwar

last: Dingare

address: Downing Site

department: Dept of Genetics

institute: University of Cambridge

summary: Patterning and growth are fundamental features of embryonic development that must be tightly coordinated during morphogenesis. As metabolism can control cell growth while also providing mechanistic links to developmental signalling pathways, it is ideally placed to enable this coordination. To understand how metabolism impacts early mesoderm specification, we used mouse embryonic stem (ES) cell-derived gastruloids, as these enable temporal control over metabolic manipulations and can be generated in large quantities. Gastruloids show mosaic expression of two glucose transporters,Slc2a1andSlc2a3both of which co-express with the expression of both the mesodermal markerT/Braand the neural markerSox2. To understand the significance of cellular glucose uptake in development, we used the glucose metabolism inhibitor 2-deoxy-D-glucose (2-DG). 2-DG specifically blocks the expression ofT/Brawithout affecting the expression ofSox2and abolishes axial elongation in gastruloids. Surprisingly, removing glucose completely from the medium did not phenocopy 2-DG treatment despite a significant decline in glycolytic intermediates occurring under both conditions. As 2-DG can also act as a competitive inhibitor of mannose, we added mannose together with 2-DG and found that it could rescue the mesoderm specification. Together, our results show that while mannose is crucial for mesoderm specification, the glycolytic pathway is dispensable at early stages ofT/Braexpression in gastruloids.

overall_design: We treated gastruloids with 5mM of a glucose metabolism inhibitor 2-Deoxy-D-Glucose (2-DG), 0mM and 63.75 mM (3X) of glucose between day 3-4 of gastruloid development and compared the transcriptome of these treatments with that of the control i.e.gastruloids  treated with 21.25mM (1X) Glucose.

first: Dingare

last: Chaitanya

first: Yang

last: Jenny

first: Steventon

last: Ben


title: Improving coriander yield and quality with a beneficial bacterium

first: Huiming

last: Zhang

address: No. 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences

summary: Plant growth-promoting rhizobacteria (PGPR) are soil microbes that can promote plant growth and/or increase plant resistance to one or multiple stress conditions. These natural resources are environmentally friendly tools for reducing the use of chemical fertilizers and pesticides and for improving the nutritional quality of plants, including pharmacological metabolites. Coriander (Coriandrum sativumL.), commonly known as cilantro or Chinese parsley, is a worldwide culinary and medicinal plant with both nutritional and medicinal properties. Little is known about how PGPR may promote plant growth or affect metabolite profiles in coriander. Here, by usingAeromonassp. H1 that is a PGPR strain, we investigate how coriander yield and quality could be affected by PGPR with transcriptome insights.

overall_design: To gain mechanistic insights into the H1-induced growth promotion, we profiled the coriander transcriptome by mRNA sequencing at 8-DAT when the growth promotion was about to become apparent. In detail, the aerial parts of the coriander plants were harvested at 8 DAT (days after H1 treatment) and total RNA was extracted using the Eastep Super Total RNA Extraction Kit (Promega). The aerial parts from 4 plants were harvested as 1 biological replicate and each sample contains 3 biological replicates.


title: Specificity protein 6 governs human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements

city: Hohhot

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University


title: Perilipin 5 deletion protects against nonalcoholic fatty liver disease and hepatocellular carcinoma by modulating lipid metabolism and inflammatory responses

city: Zagreb

first: Paula

last: Štancl

state: Grad Zagreb

address: Horvatovac 102a

department: Department of Biology

country: Croatia

institute: Faculty of Science

summary: The molecular mechanisms underlying nonalcoholic fatty liver disease (NAFLD) transition to hepatocellular carcinoma (HCC) are incompletely understood. During NAFLD development, Perilipin 5 (PLIN5) can regulate lipid metabolism by suppressing lipolysis and preventing lipotoxicity. Other reports suggest that lack of PLIN5 decreases hepatic injury, indicating a protective role in NAFLD pathology. To better understand the role of PLIN5 in liver disease, we established mouse models of NAFLD and NAFLD-induced HCC, in which wild type and Plin5 null mice were exposed to a single dose of acetone or 7,12-dimethylbenz[a]anthracene (DMBA) in acetone, followed by a 30-week high-fat diet supplemented with glucose/fructose. In the NAFLD model, RNA-seq revealed significant changes in genes related to lipid metabolism and immune response. At the protein level, signaling pathways such as AMP-activated protein kinase (AMPK), signal transducer and activator of transcription 3 (STAT3), Janus kinase (JNK) and protein kinase B (AKT) were blunted in Plin5 deficient (Plin5-/-) mice compared to wild type mice (WT). In the NAFLD-HCC model, only WT mice developed hepatic tumors, while Plin5-/- mice were resistant to tumorigenesis. Furthermore,  only 32 differentially expressed genes were identified that were associated with NAFLD progession in Plin5 null mice. Markers of mitochondrial function and immune response such as the peroxisome proliferator‐activated receptor-γ, coactivator 1‐α (PGC-1a) and pSTAT3 were decreased. Lipidomics analysis revealed differential levels of some sphingomyelins between WT and Plin5-/- mice. Interestingly, these changes were not detected in the HCC model, indicating a possible shift in the metabolism of sphingomelins during carcinogenesis.

overall_design: To investigate the roles of Plin5 depletion in a NAFLD and NAFLD-HCC model, we induced both pathologies in WT and Plin5 KO mice and performed RNA-seq analysis to check their transcriptional profiles.

first: Paola

last: Mass-Sanchez

first: Marinela

last: Krizanac

last: Stancl

first: Marvin

last: Leopold

first: Kathrin

last: Engel

first: Eva

last: Buhl

first: Josef

last: van Helden

first: Nikolaus

last: Gassler

first: Jürgen

last: Schiller

first: Rosa

last: Karlic

first: Diana

last: Möckel

first: Twan

last: Lammers

first: Steffen

last: Meurer

first: Ralf

last: Weiskirchen

first: Anastasia

last: Asimakopoulos


title: Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice [MTA array, Affymetrix]

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

summary: Chronic stress episodes increase metabolic disease risk even after recovery. We propose that persistent stress detrimentally impacts hepatic metabolic reprogramming, particularly mitochondrial function. In male C57BL/6 mice chronic variable stress (Cvs) reduced energy expenditure (EE) and body mass despite increased energy intake versus controls. This coincided with decreased glucose metabolism and increased lipid β-oxidation, correlating with EE. After Cvs, mitochondrial function revealed increased thermodynamic efficiency (ƞ-opt) of complex CI, positively correlating with blood glucose and NEFA and inversely with EE. After Cvs recovery, the metabolic flexibility of hepatocytes was lost. Reduced CI-driving NAD+/NADH ratio, and diminished methylation-related one-carbon cycle components hinted at epigenetic regulation. Although initial DNA methylation differences were minimal after Cvs, they diverged during the recovery phase. Here, the altered enrichment of mitochondrial DNA methylation and linked transcriptional networks were observed. In conclusion, Cvs rapidly initiates the reprogramming of hepatic energy metabolism, supported by lasting epigenetic modifications.

overall_design: C57/Bl6 male mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012), or left untreated (Ctrl). Transcriptome analyses (MTA array, Affymetrix) was performed in Ctrl and Cvs liver biopsies of each condition. Mice were phenotyped for body composition, serum analyses, methylome,  mitochondrial proteome and mitochondrial function and thermodymamic efficency immediately after stress to determine CVS dependant molecular alterations im metabolic regulation.

first: Aleksandra

last: Nikolic

first: Pia

last: Fahlbusch

first: Joerg

last: Kotzka


title: Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor

city: Memphis

first: Hongjian

last: Jin

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

summary: Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, or JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a “molecular glue” that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is coupled with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.

overall_design: To determine the gene expression profile To determine the gene expression and splicing profile with and without GAC and KGA expression in of neuroblastoma cells, BE2C and SKNAS were transduced with Lenti virus control, GAC and KGA to overexpression GCA and KGA.of neuroblastoma cell with,  line BE2C, SKNAS

first: Waise

last: Quarni

first: Jie

last: Fang

first: Jun

last: Yang


title: Specificity protein 6 governs human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements [ChIP-seq]

first: Chen

last: Yanglin

summary: The commitment and differentiation of human placental progenitor cytotrophoblast (CT) cells are crucial for a successful pregnancy, but the underlying regulatory mechanism remains poorly understood. Here we identified the transcription factor (TF), Specificity protein 6 (SP6), as a human species-specific trophoblast lineage TF expressed in human placental CT cells. Using pluripotent stem cells as a model, we demonstrated that SP6 governs CT generation and the establishment of trophoblast stem cells (TSCs) and discovered msh homeobox 2 (MSX2) as the downstream effector in these events. Mechanistically, we showed that SP6 interacts with histone acetyltransferase P300 to modulate the landscape of H3K27ac at targeted regulatory elements, thereby favoring transcriptional activation and facilitating CT cell fate decisions and TSC maintenance. Our results established SP6 as a novel regulator of the human trophoblast lineage and implied its regulatory role in placental development and the pathogenies of placental diseases.

overall_design: To investigate the function of SP6 in the regulation of trophoblast cell generation, we established GATA3-mCherry knock in (G3M), SP6 knock out (SP6 KO) and inducible exogenous SP6 overexpression (DOX/noDOX) EPSCs cell lines. These cells were differentiated to cytotrophoblast-like cells respectively. Chromatin Immunoprecipitation DNA-seq for SP6-HA, H3K4me3, H3K27ac, H3K27me3 and P300 were performed.

first: Yanglin

last: Chen


title: Kidins220 and Aiolos promote thymic iNKT cell development by reducing TCR signals

city: Freiburg

first: Sagar

address: Hugstetter Straße 55

department: Department of Internal Medicine II

institute: University Medical Center Freiburg

summary: Development of T cells is controlled by the signal strength of the TCR. The scaffold protein Kinase D-interacting substrate of 220 kDa (Kidins220) binds to the TCR; however, its role in T cell development was unknown. Here, we show that T cell-specific Kidins220 knock-out (T-KO) mice have strongly reduced invariant natural killer T (iNKT) cell numbers and modest decreases in conventional T cells. Enhanced apoptosis due to increased TCR signaling in T-KO iNKT thymocytes of developmental stage 2 and 3 shows that Kidins220 downregulates TCR signaling at these stages. scRNAseq indicated that the transcription factor Aiolos is downregulated in Kidins220-deficient iNKT cells. Analysis of an Aiolos KO demonstrated that Aiolos is a downstream effector of Kidins220 during iNKT cell development. In the periphery, T-KO iNKT cells show reduced TCR signaling upon stimulation with α-galactosylceramide, suggesting that Kidins220 promotes TCR signaling in peripheral iNKT cells. Thus, Kidins220 reduces or promotes signaling dependent on the iNKT cell developmental stage.

overall_design: To perform the single-cell RNA sequencing experiments, cells of 4 thymi of Ctrl mice were pooled and the same was done with 4 thymi of T-KO mice. Cells were stained with CD1d tetramers, anti-TCRβ, anti-NK1.1, anti-CD44 and anti-CD24 antibodies on ice. Cells were sorted by flow cytometry for TCRβ+, CD1dt+, CD24+, NK1.1- cells to obtain stage 0 iNKT cells, and for TCRβ+, CD1dt+, NK1.1+, CD24-, CD44+ cells to obtain stage 3 iNKT cells. This was done twice in parallel, to have two replicas each. After sorting, each cell population was barcoded by hash-tagged antibodies (TotalSeqC format, anti-mouse Hashtag 1 to 8; clone M1/42, 30-F11, BioLegend). The antibody concentrations used were 1 ug per million cells. After staining, cells were washed three times in PBS containing 2% BSA and 0.01% Tween 20, followed by centrifugation (300 x g 5 min at 4 °C) and supernatant exchange. Then all 8 populations were pooled (2x stage 0 Ctrl, 2x stage 0 T-KO, 2x stage 3 Ctrl, 2x stage 3 T-KO) for single-cell RNA sequencing.

first: S

last: Sagar


title: Targeting postsynaptic glutamate receptor scaffolding proteins PSD-95 and PICK1 for obesity treatment

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

summary: Abstract: Human genome-wide association studies (GWAS) suggest a functional role for central glutamate receptor signaling and plasticity in body weight regulation. Here, we utilize UK Biobank GWAS summary statistics of body mass index (BMI) and body fat percentage (BF%) to identify genes encoding for proteins known to interact with postsynaptic AMPA and NMDA receptors. Loci in/near Discs Large MAGUK Scaffold Protein 4 (DLG4) and protein interacting with C kinase 1 (PICK1) reached genome-wide significance (P<5x10-8) for BF% and/or BMI. To further evaluate the functional role of PSD-95 (gene name: DLG4) and PICK1 in energy homeostasis, we used dimeric PDZ-domain-targeting peptides of PSD-95 and PICK1 to demonstrate that pharmacological inhibition of PSD-95 and PICK1 induces prolonged weight-lowering effects in obese mice. Collectively, these data demonstrate that the glutamate receptor scaffolding proteins, PICK1 and PSD-95, are genetically linked to obesity and that pharmacological targeting of their PDZ domains represents a promising new therapeutic avenue for sustained weight loss.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from mouse prefrontal cortex (PFC) and hippocampus, treated with saline or inhibtors of PSD-95 or PICK1.

first: Nicole

last: Fadahunsi

first: Sophia

last: Metz

first: Jonas

last: Petersen

first: Rita

middle: C

last: Andersen

first: Cecilie

middle: V

last: Mathiesen

first: Anders

last: Bach

first: Tuomas

middle: O

last: Kilpeläinen

first: Kristian

last: Strømgaard

first: Kenneth

last: Madsen

first: Christoffer

last: Clemmensen


title: Epigenetic control over IFN Type-I response antagonizes self-renewal in acute myeloid leukemia

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster


title: Epigenetic Control over IFN Type-I Response antagonizes self-renewal in acute myeloid leukemia (RNA-seq)

summary: To investigate the impact of PHF8 demethylase activity and PHF8 phosphorylation changes in blocking AML cells progression. We established THP1-wt, THP1-PHF8 and THP1-F279S cell lines for demethylase activity studies and THP1-PHF8AA and THP1-PHF8DD for phosphorylation studies.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for THP-1 cells and its derivatives (THP1-PHF8 and THP1-F279S or THP1-PHF8AA and THP1-PHF8DD).

first: Mari-Francis

last: Arteaga

first: Jan-Henrik

last: Mikesch


title: Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice [MeDIP-seq]

first: Birgit

last: Knebel

first: Aleksandra

last: Nikolic

first: Pia

last: Fahlbusch

first: Joerg

last: Kotzka


title: Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice

overall_design: Refer to individual Series


title: Specificity protein 6 governs human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements [RNA-seq]

first: Chen

last: Yanglin

overall_design: To investigate the function of SP6 in the regulation of trophoblast cell generation， we established GATA3-mCherry knock in （G3M），SP6 knock out (SP6 KO) and inducible exogenous SP6 overexpression（DOX/noDOX）EPSCs cell lines. These cells were differentiated to cytotrophoblast-like cells respectively.

first: Yanglin

last: Chen


title: Bulk RNA-sequencing of MYCN-overexpressing chicken retinal cell lines

city: Uppsala

first: Finn

last: Hallböök

address: Dag Hammarskjölds v 20

department: Dept Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

summary:
Background: MYCN gene is a transcription factor whose amplification and overexpression can lead to tumorigenesis. In retina, MYCN overexpression is related to tumorigenesis of retinoblastoma, a childhood cancer. Purpose: To find out differentially expressed genes in MYCN-overexpressing cells, which will give information of MYCN-related gene expression and possibly find out new pathways in mechanism of retinoblastoma tumorigenesis with MYCN overexpression.
Methods: MYCN-overexpressing cells were taken from MYCN electroporated E14 chicken retina and kept in culture. Unelectroporated E14 chicken retina central region was dissected as a control. Total RNA was extracted and sequenced on Illumina NovaSeq 6000. The data were used for differential expression analysis and GO/Pathway enrichment analysis.

overall_design: Bulk RNA sequencing of three biological replicates of MYCN-overexpressing cell lines in culture and with three replicates of E14 dissected chicken retinas as control

first: Hanzhao

last: Zhang

first: Dardan

last: Konjusha

first: Nima

last: Rafati


title: Comparison of gene expression in the nucleus accumbens of rats expressing or not the conditioned place preference to cocaine

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

institute: IBENS

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