title: Enhanced Innate Response In RB1 deficient Microglia Derived From Retinoblastoma Patient

status: Public on Dec 31 2022

city: Beijing

first: Jia

last: Xu

address: 17 Hougou Lane, Chongnei Street

country: China

institute: Beijing Institute of Ophthalmology (BIO)

type: Expression profiling by high throughput sequencing

summary: Retinoblastoma (Rb), the most prevalent intraocular malignant tumor in children with global survival rate less than 30%, is mainly caused by the deficiency of the tumor suppressor RB1. A line of evidence have shown that local inflammation and immune escape play important roles in the occurrence of Rb, however the underlying mechanism remains unclear. We hypothesize that the unique neuroimmune cell type, retinal microglia, has a vital role in the Rb pathogenesis. In this study, we differentiated microglia cells (iMGs) from established induced pluripotent stem cells (iPSCs) derived from a retinoblastoma patient with the defined RB1 mutations. We investigated the function of RB1 in innate immune response of microglia and found that the expression of interleukins and chemokines, especially interleukin 6 and TNF-α, were highly upregulated in LPS-stimulated RB1 deficient iMGs, which enhanced innate immune responses and created a pro-inflammation environment. These findings demonstrated that RB1 is indispensable to maintain microglia function in innate immunity and its deficiency leads to enhanced inflammation responses, which may accelerate tumor growth and malignancy. This study provides new insights for pathological mechanism and immunotherapeutic target of retinoblastoma.

overall_design: To investigate the function of RB1 in innate immune response, we performed RNA-seq in RB1wt/wt, RB1m1/wt and RB1m1/m2 iMGs after LPS stimulation.

first: Si-Jian

last: Yu

first: Yan-Ping

last: Li

first: Xiao

last: Zhang

first: Kangxin

last: Jin

first: Zi-Bing


title: Next Generation Sequencing Facilitates Quantitative Analysis of Sox9+/IRES-EGFP and Sox9+/Y440X-IRES-EGFP Limbs Transcriptomes

city: Hong Kong

first: Tiffany

last: Au

address: Sassoon Road 21, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: Unitversity of Hong Kong

summary:
Purpose: SOX9Y440X is the most commonly reported SOX9 mutation identified in human patients with Campomelic dysplasia, a dominant semi-lethal skeletal disease characterized by congenital shortening and angulation of long bones (campomelia). To understand how the SOX9Y440X mutant cause the abnormal limb development and compare with previously heterozygous Sox9 null mutant, a mouse model with Sox9Y440X mutation has been generated. The goal of this study is to carry out transcriptome analyses (RNA-seq) of E13.5 limbs collected from Sox9+/IRES-EGFP and Sox9+/Y440X-IRES-EGFP mice. GFP+ and GFP- cells were collected from each genotype by FACS. Comparing transcriptome profiles of cells from these two genotypes aims to reveal how the SOX9Y440X mutant causes abnormal limb development.
Method: Forelimbs (FL) and hindlimbs (HL) mRNA profiles of E13.5 Sox9+/IRES-EGFP (WT) and Sox9+/Y440X-IRES-EGFP (CD) mice were generated by sequencing. 4-6 pairs of FL and HL buds were collected separately for each genotype. Limb tissues were then digested into single cells, then EGFP positive and negative cells were collected by FACS for each sample. Total RNA from each sample was prepared using Ambion RNA isolation kit (Cat. AM1580). 100ng of total RNA was used from each sample for RNA-sequencing. cDNA libraries were prepared by TruSeq Stranded mRNA Sample Prep Kit (Illumina). Pair-End sequencing of 101bp was done using HiSeq 1500 Sequencer Model.
Data processing: Reads was pre-processed and aligned to the mouse GRCm38 (mm10) reference genome and expression levels were quantified using the nfcore/rnaseq workflow. The count matrix from featureCounts was used in the downstream analyses. The Nextflow pipeline for downstream analysis is available at https://github.com/fuxialexander/sox9. With R library edgeR 3.36.0, read counts were normalized using the ‘TMM’ method. We identified differentially expressed genes between the WT and CD groups in GFP+ or GFP- samples with the ‘glmQLFTest’ function and a Benjamini & Hochberg adjusted P-value cutoff of 0.05.
Conclusions: Our study represents the first detailed analysis of mouse foetal limbs transcriptomes between Sox9Y440X mutant and wild type. Our work contributes to gain insight into the molecular signalling pathways affected by SOX9Y440X in vivo.

overall_design: Forelimbs (FL) and hindlimbs (HL) buds of E13.5 Sox9+/IRES-EGFP (WT) and Sox9+/Y440X-IRES-EGFP (CD) mice were collected for RNA-sequencing. 4-6 pairs of FL and HL buds were collected separately for each genotype. We assigned forelimb and hindlimb as biological replicates.

first: Kathyrn

middle: S

last: Cheah

middle: Y

first: Raymond

middle: K

last: Yip


title: RNA-seq Identification of Candidate Genes Differentially Expressed in DRN-BA(Pyr) and DRN-BA(PV) Neurons

city: Guangzhou

first: Xiao-Dan

address: No. 74, Zhongshaner Road

institute: SUN YAT-SEN UNIVERSITY

summary: To investigate the diversity of BA-projecting DRN(5-HT) neurons, we performed RNA-seq of BA(Pyr)- and BA(PV)-projecting DRN(5-HT) neurons and compared their gene expression levels.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for BA(Pyr)- and BA(PV)-projecting DRN(5-HT) neurons.
neurons are labeled with RV-dsRed using the monosynaptic rabies tracing virus.

first: Xiao-Ming


title: The Kupffer cell-specifying factor Id3 endows macrophages with antimetastatic activity

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

country: USA

institute: Memorial SLoan-Kettering Cancer Center

summary: The anti-tumor activity of macrophages is mediated in part via phagocytosis and controlled by a balance between the recognition of live cells by activating receptors and inhibitory receptors. The latter protects host tissues during infection but allows tumoral cells to escape phagocytosis and promotes metastasis. We investigated the mechanisms that control anti-metastatic activity of macrophages and found that the transcriptional repressor and Kupffer cells (KC)-specifying factor ID3 is required and sufficient to orchestrate tumor cell killing by macrophages in vivo and in vitro and reduces by ~50% liver and lung colonization by metastatic-initiating cells invading from the portal vein in long-term orthotopic pancreatic cancer models. Loss-of-function and gain -of functions experiments indicate that ID3 controls expression of activating and inhibitory receptors, in particular the inhibitory receptor SIRPα, which boost their phagocytic activity against tumor cells. Mechanistically, ID3 prevents binding of ELK1 and the E-Box factor E2A to promoter/enhancer regions of the inhibitory receptor Sirpα gene, which limits expression of SIRPα at levels compatible with efficient phagocytosis of tumor cells and prevents its upregulation by inflammatory stimuli. This mechanism endows macrophages with anti-metastatic activity.

overall_design: KPC-1 tumor cells DNA profiles from R26LSL-DTR and Clec4fCre;R26LSL-DTR mice. DNA samples were extracted with QIAamp DNA Micro Kit, DNA were used for library construction using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 8 cycles of PCR. After sample barcoding, 100-110ng of each library were pooled and captured by hybridization with the mm_IMPACT (Integrated Mutation Profiling of Actionable Cancer Targets) assay.

first: Zihou

last: Deng

first: Stamatina

last: Fragkogianni

first: Frederic

last: Geissmann


title: Transcriptional Dysregulation Underlies Both Monogenic Arrhythmia Syndrome and Common Modifiers of Cardiac Repolarization

city: Nashville

first: Kevin

last: Bersell

state: TN

address: 2215 Garland Ave

institute: Vanderbilt University

summary: BACKGROUND: Brugada syndrome (BrS) is an inherited arrhythmia syndrome caused by loss-of-function variants in the cardiac sodium channel gene SCN5A (sodium voltage-gated channel alpha subunit 5) in ≈20% of subjects. We identified a family with 4 individuals diagnosed with BrS harboring the rare G145R missense variant in the cardiac transcription factor TBX5 (T-box transcription factor 5) and no SCN5A variant. METHODS: We generated induced pluripotent stem cells (iPSCs) from 2 members of a family carrying TBX5-G145R and diagnosed with Brugada syndrome. After differentiation to iPSC-derived cardiomyocytes (iPSC-CMs), electrophysiologic characteristics were assessed by voltage- and current-clamp experiments (n=9 to 21 cells per group) and transcriptional differences by RNA sequencing (n=3 samples per group), and compared with iPSC-CMs in which G145R was corrected by CRISPR/Cas9 approaches. The role of platelet-derived growth factor (PDGF)/phosphoinositide 3-kinase (PI3K) pathway was elucidated by small molecule perturbation. The rate-corrected QT (QTc) interval association with serum PDGF was tested in the Framingham Heart Study cohort (n=1893 individuals). RESULTS: TBX5-G145R reduced transcriptional activity and caused multiple electrophysiologic abnormalities, including decreased peak and enhanced “late” cardiac sodium current (INa), which were entirely corrected by editing G145R to wildtype. Transcriptional profiling and functional assays in genome-unedited and -edited iPSC-CMs showed direct SCN5A downregulation caused decreased peak INa, and that reduced PDGF receptor (PDGFRA [platelet-derived growth factor receptor α]) expression and blunted signal transduction to PI3K was implicated in enhanced late INa. Tbx5 regulation of the PDGF axis and increased arrhythmia risk with disruption of PDGF sigaling were both conserved in murine model systems. PDGF receptor blockade markedly prolonged normal iPSC-CM action potentials and plasma levels of PDGF in the Framingham Heart Study were inversely correlated with the QTc interval (P

overall_design: Bulk RNA-seq was performed in iPSC-derived cardiomyocytes from 4 population control cell lines, 4 Brugada syndrome lines carrying TBX5-G145R heterozygous variant cell lines, 3 isogenic controls cell lines (CRISPR/Cas9 HDR corrected from BrS lines), and 3 TBX5 isogenic heterozygous knockout cell lines

first: Dan

last: Roden

first: Qhanhu

last: Sheng

first: Jonathan

last: Brown


title: Transcriptome profiling of 13 HIV positive individuals of variable disease progression from an Indian Cohort

city: Delhi

first: Beena

last: Pillai

address: Mathura Road

country: India

institute: IGIB

summary: In our cohort study for HIV, we have classified patients in 3 different groups, primarily on the basis latency period- Long term non-progressors (LTNP), Long term non-progressors NON-controllers (LNC), and regular progressors. individuals in these groups differ phenotypically as well as have significantly different levels of CD4+T cell counts and viral loads. Goal of the study is to explore the underlying novel mechanisms behind the differences in different patient classes of HIV using Next-Generation sequencing.

overall_design:
Transcriptome profiling of three different patient classes of HIV.
[contributor]  YRGCare, Chennai

first: Rakesh

last: Dey

first: Prachi

last: Singh


title: User-Friendly Microfluidic System Reveals Native-Like Morphological and Transcriptomic Phenotypes Induced by Shear Stress in Proximal Tubule Epithelium

city: Los Angeles

first: Megan

middle: L

last: McCain

state: CA

address: 1024 Downey Way

institute: USC

summary: Drug-induced nephrotoxicity is a leading cause of drug attrition, partly due to the limited relevance of pre-clinical models of the proximal tubule. Culturing proximal tubule epithelial cells (PTECs) under fluid flow to mimic physiological shear stress has been shown to improve select phenotypes, but existing flow systems are expensive and difficult to implement by non-experts in microfluidics. Here, we designed and fabricated an accessible and modular flow system for culturing PTECs under physiological shear stress, which induced native-like cuboidal morphology, downregulated pathways associated with hypoxia, stress, and injury, and upregulated xenobiotic metabolism pathways. We also compared the expression profiles of shear-dependent genes in our in vitro PTEC tissues to that of ex vivo proximal tubules and observed stronger clustering between ex vivo proximal tubules and PTECs under physiological shear stress relative to PTECs under negligible shear stress. Together, these data illustrate the utility of our user-friendly flow system and highlight the role of shear stress in promoting native-like morphological and transcriptomic phenotypes in PTECs in vitro, which is critical for developing more relevant pre-clinical models of the proximal tubule for drug screening or disease modeling.

overall_design:
Human hTERT-immortalized proximal tubule epithelial cells purchased from ATCC were cultured as monolayers on ibidi channel slides and subsequently exposed to physiological (0.35 dynes/cm2) or near-zero levels of fluidic shear stress using a user-friendly microfluidic flow system for 3 days. Cells were subsequently lysed and RNA was sequenced.
8 samples (GSM4982338, GSM4982384, GSM4982350, GSM4982357, GSM4982391, GSM4982364, GSM4982344, GSM4982370) were reanalyzed from GSE163603. They were first sub-sampled to normalize the sequencing depth (by a factor of 2, 2, 5, 1, 1, 1, 1, and 5, respectively). Together with our data, sequences were trimmed from both ends based on a Phred quality score of 20 and a minimum read length of 25, aligned to the hg38 genome build using STAR (2.7.8a), and quantified using Gencode 38 (V2) annotation in Partek Flow Genomics Analysis software. Read counts per gene were normalized to fragments per kilobase of transcript per million mapped reads (FPKM) and then analyzed for differential gene expression using Partek Gene Specific Analysis method with fold change and FDR cut-offs of 1.5 and 0.05, respectively.

first: Natalie

middle: N

last: Khalil

first: Andrew

middle: P

last: Petersen

first: Cheng

last: Song

first: Kaelyn

last: Takamoto

first: Austin

middle: C

last: Kellogg

first: Elaine

middle: Z

last: Chen

last: McMahon


title: Blimp-1 moulds the epigenetic architecture of IL-21-mediated autoimmune diseases through an autoregulatory circuit

city: Miaoli

first: Yu-Wen

last: Liu

state: -- None selected --

address: Zhunan: 35, Keyan Road, Zhunan Town

country: Taiwan

institute: National Health Research Institutes

summary: To unravel how Blimp-1 systematically manipulates the global transcriptional landscape in CD4 T cells to contribute to autoimmune progression, we performed RNA sequencing analysis in Blimp-1 transgenic (BTg) or Blimp1-deficient (CKO) NOD mice

overall_design: Sorted total CD4 T cells from spleens of 12-week-old control, CKO and BTg NOD mice, without further T cell receptor stimulation


title: The storage conditions of high fat diet are the key factors for diet induced obesity and liver damage.

city: Shanghai

first: Cenxi

address: Songhu Road 2005

institute: Fudan University

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

overall_design: Refer to individual Series


title: RNA sequencing showing the different response pattern between lung epithelial cells and lung cancer cells after radiation

city: Wuhan

first: Xiaoshu

last: Zhou

address: Xinhua Road

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: To seek if ionizing radiation have different biological effect on lung normal cells and cancer cells, we treated lung epithelial cell line BEAS-2B, non-small cell lung cancer cell line A549 and small cell lung cancer cell line H446 with 10 Gy X-ray radiation

overall_design: Lung epithelial cell line BEAS-2B, non-small cell lung cancer cell line A549 and small cell lung cancer cell line H446 were treated with 10 Gy X-ray radiation, then 24h later, RNA-seq was performed.

first: Xinrui

last: Rao

first: Rui


title: IL-27 sensitizes immune checkpoint blockade therapy by inducing Treg fragility in high-grade serous ovarian cancer

city: shanghai

first: Moran

last: Yang

address: shenyang road 128

institute: fudan university

summary: To characterized the effect of IL-27 on the tumor immune microenvironment in vivo, we selected the subcutaneous tumor-infiltrating CD45+ lymphocytes from tumor in vehicle or recombinant mouse IL-27 treated mice,and performed single-cell RNA sequencing on lymphocytes.

overall_design: For mouse subcutaneous xenograft models, HM1 cells (1 × 10^6) were subcutaneously injected into the right flank of B6C3F1 mouse, vehicle or recombinant mouseIL-27 (100 ng per mouse) was injected intratumorally (s.c.) on day of tumor implantation and then every other day thereafter until the end of the experiment. CD45+ lymphocytes were sorted from digested mouse subcutaneous tumor by on day 14 after tumor implantation.

first: Kankan

last: Cao

first: Jiaqi

last: Lu

first: Haiou

first: Congjian

last: Xu


title: RIP-seq of SRSF7 and m6A-RIP seq of Huh7 cells

first: CHEN

last: HONG

address: 800 Dongchuan Road

institute: shanghai jiao tong university


title: Pien-Tze-Huang Promotes Hepatocellular Carcinoma Cell Ferroptosis by Inhibiting SLC7A11-GSH-GPX4 Axis

city: beijing

first: xiangying

last: yan

address: Dongzhimen Jiedao

institute: Institute of Chinese Medicine

summary: We aimed to evaluate anti-cancer efficacy of Pien-Tze-Huang (PZH), and to investigate the underlying mechanisms by integrating transcriptional regulatory network analysis and experimental validation.

overall_design: After detecting a transcriptomic profiling, the “disease-related gene--drug effective target” interaction network was constructed, and the candidate targets of PZH against malignant transformation from liver fibrosis to HCC were identified and verified in vitro.

first: Xiangying

last: Yan

first: Yudong

first: Congchong

last: Li


city: Ningbo

first: Jia

last: Su

state: China

address: Liuting Street No.59

institute: Ningbo No. 1 Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary:
Comprehensive analysis of the RNA transcriptome expression profiles and construction of the ceRNA network in heart failure patients with therapeutic heterogeneity of sacubitril/valsartan after acute myocardial infarction Patients after Acute Myocardial Infarction
Sacubitril/valsartan has a noteworthy advantage in improving ventricular remodelling, as well as reducing cardiovascular mortality and the rate of heart failure (HF) readmission. However, clinically, some patients with HF still have low sensitivity to sacubitril/valsartan, indicating sacubitril/valsartan resistance (SVR).

overall_design: the expression profiles of tRNA-derived small RNAs (tsRNAs) in SVR along with NSVR patients were determined by RNA sequencing.Five SVR and 5 matched NSVR samples were screened for differentially expressed miRNAs, circRNAs, lncRNAs along with mRNAs.

first: Yingchu

last: Hu

first: Ji

last: Cheng


title: Effect of depletion of YTH family genes on gene expression in Nipponbera rices

first: Weiwei

last: Ma

state: Zhejiang

address: #19 Dehou Stress

institute: Ningbo Academy of Agricultural Sciences

summary:
To investigate the function YTH proteins in the regulation of gene expression, we established 12 transgenic lines in which each target gene has been knocked out by CRISPR/Cas9 or knocked down by siRNA.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 45 different transgenic lines.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for two wild type controls, 10 CRISPR mediated knockout mutants, 2 siRNA mediated knockdown mutants and 1 overexpression plants with three biological replicates for each samples.

first: Xiaole

last: Wang


title: Effect of pectolinarigenin on gene expression in oleic acid (100μM) induced high lipid Huh-7 cells

city: Nanchang

first: Songhua

address: 605 Fenglin Road, Jingkai District

institute: Jiangxi Science and Technology Normal University

summary: To investigate the lipid-lower effect of pectolinarigenin,  we established a high lipid Huh-7 cells induced by oleic acid.

overall_design:
We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different cells in two groups (Control vs. Pectolinarigenin).
Comparative gene expression profiling analysis of RNA-seq data for high lipid Huh-7 cells.

first: Zhou

last: Lan


title: The storage conditions of high fat diet are the key factors for diet induced obesity and liver damage [WT vs. Nnmt KO]

first: Cenxi

last: Liu

summary: The diet induced obesity (DIO) mouse model has been widely used for obesity studies. Comparing to the composition of nutrients in the diet, the effects of storage conditions for high fat diet (HFD) on metabolic homeostasis have not been systemically investigated. In the current study, we tested the effects of HFD stored in different conditions and found the mice fed by HFD stored in the fridge (HFDfri) gained less weight than freezer (HFDfre). Further analysis revealed the changes of the relative abundance of medium chain triglyceride (MCT) in the HFDfri, which has much lower intestinal absorption rates, contributed to the body weight differences. In contrast, advanced liver damages and elevation of unfolded protein responses (UPR) was observed in the mice fed by the HFDfri. Depletion of UPR regulated gene Nnmt alleviated liver damages via inhibition of integrated stress response (ISR). Our study provided the initial evidence that HFD storage conditions have great impacts on both body weight changes and liver damages in the DIO model.

overall_design: Comparative gene expression profiling analysis of RNA-seq data

first: Chuanyou

last: Yi

first: Dandan

first: Xiao

last: Guo


title: RIP-seq of SRSF7  in Huh7

summary: RNA seq was performed after IP of Ab-SRSF7  in Huh7 cells.

overall_design: RIP assay was performed on Huh7 cells by LC-Bio (Hangzhou, China). Briefly, Huh7 cells were lysed with cell lysis buffer. The 10% lysis sample was used for input, and 90% was used for immunoprecipitation with anti-SRSF7 antibody (Catalog No. ab137247, Abcam). TRIzol reagent was used for extraction of RNA. The stranded RNA sequencing library was performed by Stranded mRNA Library Prep Kit for Illumina based on the manufacture’s instruction. The duplication bias in PCR and sequencing steps was eliminated by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Illumina Novaseq™ 6000 with PE150 model.


title: An evolved AAV variant enables efficient genetic engineering of murine T cells

city: San Francisco

first: William

last: Nyberg

address: 513 Parnassus Ave., HSW 901

institute: UCSF

summary: Precise targeting of large transgenes to T cells using homology-directed repair has been transformative for adoptive cell therapies and T cell biology. Non-toxic delivery of DNA templates via adeno-associated virus (AAV) has greatly improved knock-in efficiencies, but the tropism of current AAV serotypes restricts their use to human T cells employed in immunodeficient mouse models. To enable targeted knock-ins in murine T cells, we evolved Ark313, a synthetic AAV that exhibits high transduction efficiency in murine T cells. We performed a genome-wide knockout screen and identified QA2 as an essential factor for Ark313 infection. We demonstrate that Ark313 can be used for nucleofection-free DNA delivery, CRISPR/Cas9-mediated knockouts, and targeted integration of large transgenes. Ark313 enables pre-clinical modeling of Trac-targeted CAR-T and transgenic TCR-T cells in immunocompetent models. Efficient gene targeting in murine T cells holds great potential for improved cell therapies and opens new avenues in experimental T cell immunology.

overall_design: We performed a genome-wide CRISPR KO screen on  pirmary murine T cells from C57BL6/J H11-Cas9 mice to identify essential host genes for newly discovered AAV serotype Ark313. Cells were transdcuced with the retroviral CRISPR library before being infected with Ark313 virus expressing GFP, cells were then sorted the cells based on GFP expression in to 4 bins (1-4, from low to high). Genomic DNA was exctracted and NGS analysis was performed on PCR amplicons from the genomic DNA.

middle: A

first: Jon

last: Ark

first: Aravind

last: Asokan

first: Justin

last: Eyquem


title: Generation of anti-GD2 CAR macrophages from human pluripotent stem cells for cancer immunotherapies

city: Madison

first: Jue

last: Zhang

state: WI

address: 330 N orchard st

institute: Morgridge Institute for Research

summary:
We generate macrophages from pluripotent stem cells (PSCs) with GD2 CARs integrated into AAVS1 locus.
To produce CAR macrophages (CAR-M) we established a serum- and feeder-free differentiation protocol which generates macrophages through arterialized hemogenic endothelium.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CAR_M and WT_M cells with and without CHLA co-culture

first: John

last: Steill


title: ETV6::FRK gene expression analysis in Ba/F3 cells by whole transcriptome sequencing

city: Kyoto

first: Azusa

last: Mayumi

address: 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Pediatrics

country: Japan

institute: Kyoto Prefectural University of Medicine

summary: ETV6::FRK is a rare kinase-related fusion gene which was identified only in AML but not in ALL. Herein, we firstly identified ETV6::FRK fusion gene in a patient with pediatric B-ALL. Because FRK is Src family tyrosine kinase, we performed functional analysis of ETV6::FRK to establish molecular targeting therapy. Our case with B-ALL was refractory to conventional chemotherapy and received allogeneic bone marrow transplantation following administration of blinatumomab. Cytogenetic analysis demonstrated 46,XY,t(6;12)(q21;p13) and target capture mRNA sequencing revealed ETV6::FRK. Ba/F3 cells expressing ETV6::FRK generated by retroviral transduction (Ba/F3-ETV6::FRK) and analyzed for IL-3 independent growth. Gene expression analysis using whole transcriptome sequencing and gene set enrichment analysis (GSEA) was performed for comprehensive analysis of gene expression profile related to ETV6::FRK. It was also analyzed whether dasatinib, which is Src-kinase inhibitor, suppressed the growth of Ba/F3-ETV6::FRK in vitro and in vivo. Ba/F3-ETV6::FRK proliferated without IL-3, suggesting ETV6::FRK had proliferation activity. Western blot revealed that constitutive phosphorylation of tyrosine residue of ETV6::FRK and STAT3/STAT5, suggesting constitutive activation of FRK-STAT3/STAT5 pathway. GSEA of oncogenic gene sets (C6) from the GSEA Molecular Signatures Database revealed that, compared with control cells, Ba/F3-ETV6::FRK cells were enriched for up-regulation of SNF5 target genes and down-regulation of RB target genes involved in cell cycle regulation. In vitro killing assay showed that dasatinib killed efficiently Ba/F3-ETV6::FRK. Dasatinib also suppressed the growth of Ba/F3-ETV6::FRK in vivo and extended the survival time of the xenografted NSG mice. These findings suggest that activation of FRK-STAT3/STAT5 pathway contributes aberrant growth promotion of Ba/F3-ETV6::FRK. Our study demonstrated that dasatinib might be effective for the patient with B-ALL harboring ETV6::FRK.

overall_design: Ba/F3 cells were transduced with ETV6::FRK fusion protein by the Retro-X Tet-On Advanced Inducible Expression System (Takara Bio), and Ba/F3 cells expressing ETV6::FRK under doxycycline (DOX) dependent manner were established. To reveal which pathways were affected by ETV6::FRK, Ba/F3 cells expressing ETV6::FRK induced by DOX (Ba/F3-ETV6::FRK) or non-DOX-induced Ba/F3 cells were cultured in triplicate, and RNA was extracted from Ba/F3-ETV6::FRK or non-DOX-induced Ba/F3 48 hours later.

first: Toshihiko

last: Imamura

first: Hideki

last: Yoshida

first: Shinya

last: Osone

first: Takahiko

last: Yasuda

first: Tomoko

last: Iehara


title: K74R mutation effects in bone marrow, MSC and tumor microenvironment

city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

institute: China Medical University

summary: To investigate how KLF K74R mutation in MSC would affect tumormicroenvironment during tumorigenesis.

overall_design: Comparing gene expression differences in bone marrow, MSC and tumor between KLF K74R mutation mouse and KLF WT mouse.

first: Yu-Ting

last: Yen


title: Differentially expressed genes following YAP depletion in Esophageal Squamous Cell Cancer Cell Line

city: xinxiang

first: xiaofeng

last: zhou

address: No. 601 Jinsui Avenue

institute: xinxiang medical university

summary: Purpose: Using CRISPR to generate YAP knock-out ESCC cell lines and then detected differentially expressed genes;Results:RNA-seq results showed that the expression of CD24 was regulated by YAP.

overall_design: The experiment involves 3 replicates of a wildtype cell line (WT - Samples 1-3), and 3 replicates of the same cell line within which a single gene was knocked out(KO-Samples)

last: Zhou

first: xiumin

last: Li


title: RNA sequencing and metabolic analysis of imiquimod-induced Psoriasis-like mice with Chronic restrain stress

city: 杭州市

first: musab

middle: al

last: rudaisat

state: 浙江省

address: 浙江大学，华家池校区

institute: Zhejiang university Affiliated hospital Sir Run Run Shaw hospital

summary: Psoriasis is one of the most common dermatological disorders, characterized by increased epidermal hyperplasia and immune cell infiltration. Psychological stress has been reported to contribute to the severity, aggravation, and relapse of psoriasis. We developed a chronic restrain stress (CRS)-imiquimod (IMQ)-induced psoriasis-like mouse model and performed a comprehensive comparative transcriptomic and metabolic analysis with control mice, CRS-treated mice, and IMQ-treated mice to investigate how psychological stress affects psoriasis. We found that CRS-IMQ-induced psoriasis-like mice showed significant exacerbation of psoriasis-like skin inflammation compared with mice treated with IMQ only. Mice of the CRS+IMQ group showed increased expression of keratinocyte proliferation and differentiation genes, differential regulation of cytokines, and promotion of the linoleic acid metabolism. Our study provides new insights into the effects of psychological stress on psoriasis pathogenesis and the mechanisms involved, which provides clues for development of therapeutics or biomarkers.

first: Mus'ab

last: Al Rudaisat

first: Hao

last: Cheng


title: m6A-RIP seq of Huh7 cells

first: CHEN

last: HONG

summary: m6A seq was performed after IP of m6A antibody  in Huh7 cells.

overall_design: m6A-RIP assay was performed on Huh7 cells by LC-Bio (Hangzhou, China).Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Approximately more than 25 μg of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA). Following purification, the ribosomal-depleted RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.


title: Determining sex-specific RNA interactors of maternal Transcription factor CLAMP in Drosophila cell lines

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

institute: Brown University

summary: We performed RNA-protein interaction study iCLIP, i.e single nucleotide resolution uv crosslinking and immunoprecipitation for DNA binding transcription factor CLAMP in different cellular fractions (Chromatin fraction, Nucleoplasmic fraction,  Cytoplasmic Fraction) to explore sex-specific RNA binding properties of CLAMP in female (Kc) and Male (S2) cells

overall_design: CLAMP antibody used to immunoprecipitate RNA targets in different cellular fractions from UV crosslinked Kc (female) and S2 (male) cell line samples. Bound RNA is extracted and sequenced to determine CLAMP RNA targets and RNA sequence motifs for binding. Four replicates for each fraction and cell type performed. As control two replicates of UV treated, no antibody controls performed for each fraction and cell type.

first: Mukulika

last: Ray

first: Annie

last: Huang


title: Bulk RNAseq of HDLECs

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary: Bulk RNAseq was performed using P4 human dermal lymphatic endothelial cells (HDLECs)

overall_design: Untreated cells were detached and lysed. Total RNAs were extracted and then subjected to RNAseq analysis

first: Feng

last: Zhang

first: Yangxin

last: Chen

first: Weibin

first: Keli

last: Liu

first: Lei

last: Zeng


title: Nucleus of cytoplasmic incompetent oocytes directs the full-term development of non-human primate embryos in developmental competent cytoplasm

first: Liao

last: Zhaodi

address: 500, Qiangye Road

department: Institute of Neuroscience

institute: Chinese Academy of Sciences

summary: Oocyte quality largely determines the embryo development after fertilization. High-quality oocyte requires the competence of both cytoplasm and nucleus. However, clinically, the treatment of developmentally competent oocytes was limited. Here, in order to improve the embryo development efficiency of developmentally incompetent oocytes, we performed spindle-chromosome complex (SCC) transfer between in vitro matured (IVM) and in vivo matured (IVO) oocytes of the non-human primate. We observed that the blastocyst rate of embryos derived by transferring the SCC of IVM (IVM-SCC) oocytes into enucleated IVO oocytes was comparable with that of embryos derived by IVO oocytes. After transferring the reconstructed embryos into the uterus of surrogate mothers, two live rhesus monkeys were obtained, indicating that the nuclei of IVM oocytes support both the pre-and post-implantation embryo development of non-human primates.

overall_design: RNA-seq for the comparison of gene expression between monkey GV oocytes, in vitro matured oocytes and in vivo matured oocytes.

first: Zhaodi

last: Liao


title: Genome-wide placental DNA methylations in fetal overgrowth and associations with fetal growth factors, leptin and adiponectin

city: Toronto

first: Zhong-Cheng

last: Luo

state: Ontario

address: 60 Murray, L5-240, LTRI

department: Lunenfeld-Tanenbaum Research Institute

country: Canada

institute: Mount Sinai Hospital, University of Toronto

type: Methylation profiling by genome tiling array

summary: This study aims to identify genome-wide placental DNA differential methylation positions (DMPs) in fetal overgrowth and the associations with fetal growth factors, leptin and adiponectin. In the Shanghai Birth Cohort, we studied 30 pairs of placentals of large-for-gestational-age (LGA, birth weight>90th percentile, an indicator of fetal overgrowth) and optimal-for-gestational-age (OGA, 25th-75th percentiles, control) newborns matched by sex and gestational age. Placental DNA methylations were measured by the Illumina Infinium Human Methylation-EPIC BeadChip. Cord blood insulin, C-peptide, proinsulin, IGF-1, IGF-2, leptin and adiponectin concentrations were measured. We identified 543 DMPs (397 hypermethylated, 146 hypomethylated) comparing LGA vs. OGA at false discovery rate <5% and absolute methylation difference >0.05 adjusting for placental cell type heterogeneity, maternal age, pre-pregnancy BMI and HbA1c levels during pregnancy. We validated a hyper-methylated gene - cadherin 13 (CDH13) reported in a previous epigenome-wide association study, and validated a newly discovered differentially (hyper-)methylated gene -visual system homeobox 1 (VSX1) in an independent pyrosequencing study sample (47 LGA-control pairs). Pathway analysis did not detect any statistically significant pathway correcting for multiple tests. Adiponectin in cord blood was correlated with its gene methylation in the placenta, while other observed biomarkers were not. Fetal overgrowth was associated with a large number of altered placental gene DNA methylations. The study provides robust evidence suggesting that placental CDH13 and VSX1 genes are hyper-methylated in LGA. Placental gene methylation was correlated with cord blood biomarker for adiponectin, but not for leptin and fetal growth factors.

overall_design: Bisulphite converted DNA extracted from the placentas (fetal-side) of 30 LGA and 30 OGA pregnancies were hybridised to the Illumina Infinium HumanMethylation850 BeadChip

first: Meng-Nan

last: Yang

first: Rong

first: Tao

last: Zheng

first: Yu

last: Dong

first: Wen-Juan

last: Wang

first: Ya-Jie

last: Xu

first: Vrati

last: Mehra

first: Guang-Di

first: Xin

first: Hua

last: He

first: Fang

last: Fang

first: Fei

first: Jian-Gao

last: Fan

first: Jun

first: Fengxiu

last: Ouyang

first: Laurent

last: Briollais

first: Jiong


title: The storage conditions of high fat diet are the key factors for diet induced obesity and liver damage [HFDfre vs. HFDfri]

first: Cenxi

address: Songhu Road 2005

institute: Fudan University

first: Chuanyou

last: Yi

first: Dandan

last: Li

first: Xiao

last: Guo


title: Small RNA sequencing of Rice Efficient and Non-Efficient Genotypes to determine uptake of Nitrogen

city: Hyderabad

first: C

last: Neeraja

state: Telangana

address: Principal Scientist, ICAR-IIRR, Rajendranagar, Hyderabad 500030

department: Crop improvement

institute: ICAR-Indian Institute of Rice Research

summary: 4 rice genotypes were sequenced for nitrogen usage under low and high nitrogen conditions to determine the uptake, and later combine with RNASeq data to figure which genes were modulated

overall_design: The datasets were processed to remove adapters which are a trademark of smallRNA sequencing datasets; remove of the other ncRNA-like sequences; then perform quantification of known and identify denovo miRNAs, using Oryza sativa japonica as reference.

first: Kalyani

last: Barbadikar


title: Effect of anti-mouse TNF and IL-6 antibodies as well as their combination in a collagen-induced arthritis mouse model

city: Frankfurt am Main

first: Daniel

last: Margerie

address: Industrial Park Hoechst, Building H831

department: R&D, Digital Data Sciences

country: Germany

institute: Sanofi-Aventis Deutschland GmbH

summary: Additive effects of anti-TNF and anti-IL-6 were evaluated in a murine collagen-induced arthritis (CIA) model by RNA-seq

overall_design: Collagen-Induced Arthritis was induced in DBA/1 mice by immunizing with chicken type II collagen twice on day 1 and 21. Starting day 21, mice (n=13/group) were treated with either isotype control antibody, anti-TNF antibody, anti-IL-6 antibody, or the combination of the latter twice per week for a total duration of 5 weeks. RNA-seq of whole paw homogenate was performed on day 91

first: Nadine

last: Biesemann


title: Metabolic reprogramming underlies cavefish muscular endurance despite selective loss of muscle mass and contractility

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

institute: Stowers Institute for Medical Research

summary: We report the shift in skeletal muscle investment strategies of the Mexican cavefish following cave colonization

overall_design: Skeletal muscle extraction and RNA-sequencing of three lab-reared cavefish population (tinaja/molino/pachon), one lab-reared surface fish population (Rio Choy), one wild-caught cavefish population (pachon cave), and one wild-caught surface fish population (Rio Choy).

first: Luke

last: Olsen

first: Nicolas

last: Rohner

first: Michaella

last: Levy

first: J

last: Medley

first: Richard

last: Alexander

first: Emma

last: Wilcock

first: Kexi

first: Laurence

last: Florens

first: Sean

last: McKinney

first: Robert

last: Peuß

first: Jenna

last: Persons

first: Alexander

last: Kenzior

first: Ernesto

last: Maldonado

first: Andrew

last: Gluesenkamp

first: Edward

last: Mager

first: David

last: Coughlin


title: Profiling of alternative polyadenylation events in Arabidopsis thaliana

city: Philadelphia

first: Wei Chun

last: Chen

state: PA

address: 3601 Spruce St

department: Program in Gene Expression and Regulation, Center for Systems and Computational Biology

institute: The Wistar Institute

summary: Use 3ʹ region extraction and deep sequencing (3'READS) and bioinformatics techniques to profile alternative polyadenylation and gene regulation in plant Arabidopsis thaliana exposed to light and darkness

overall_design: 3'READS libraries from plant cells under light and dark condition (3 replicates each)

first: Wei

first: M

last: Guillermina Kubaczka

first: Micaela

last: Godoy Herz

first: Dinghai

last: Zheng

first: Aysegul

last: Guvenek

first: Alberto

middle: R

last: Kornblihitt

first: Bin

last: Tian


title: Additive efficacy of a novel bispecific anti-TNF/IL-6 NANOBODY compound in translational models of Rheumatoid Arthritis

first: Daniel

last: Margerie

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Transcriptomic profile of two tomato cultivars and their reciprocal hybrids

city: Rosario

first: Agustina

middle: Paula

last: Fortuny

address: Ocampo y Esmeralda

country: Argentina

institute: IBR (CONICET-UNR)

summary: The tomato cultivars Querubín FCA (Q) and Gema FCA (G) as parental genotypes and the hybrids Q x G and G x Q were selected to perform and investigation of the gene actions involved in gene expression profile. In this work, we aimed to study the differences between parental lines and the presence of heterosis and reciprocal effects in the reciprocal hybrids.

overall_design: Red ripe fruits of two tomato RILs (Querubín FCA [Q] and Gema FCA [G]) obtained from an interspecific cross between the cultivated tomato S. lycopersicum and the wild relative S. pimpinellifolium, as well as their reciprocal hybrids Q x G and G x Q were used as plant material. For each genotype, three biological replicates were analysed by RNA-seq.

first: Diego

last: Mengarelli

first: Javier

middle: H

last: Pereira da Costa

first: Gustavo

last: Rodriguez

first: María

middle: I

last: Zanor


title: Effect of anti-TNF/IL-6 NANOBODY® VHH, Humira, Sylvant, TNF, IL6 and TNF+IL6 in RA-FLS/T cell cocultures

summary: Additive effects of TNF and IL-6 were evaluated in cell-based model for rheumatoid arthritis (RA) and then compared to treatment with anti-TNF/IL-6 NANOBODY® VHH, Humira and Sylvant by RNA-seq

overall_design: Fibroblast-like synoviocytes from RA donors (RA-FLS, Cell Applications, Inc.) were cocultured with CD4 T cells from healthy human donors (n=9, 3 RA-FLS donors combined with 3 different CD4 T cell donors). PBMC’s were isolated from whole blood using Ficoll-Paque (GE Healthcare). CD4 T cells were purified from PBMCs by negative selection (Milteny Biotec) and directly added to attached RA-FLS in a 10:1 ratio (CD4: RA-FLS). Additive effects of TNF and IL-6 were evaluated by stimulating RA-FLS/T cell coculture with recombinant TNF (Sigma), IL-6/sIL-6R (R&D) or a combination. Similar experiments were performed with clinically approved anti-TNF and anti-IL-6 antibodies (Humira and Sylvant, from pharmacy), their combination and our bispecific anti-TNF/IL-6 NANOBODY® VHH after stimulation with 100ng/ml recombinant IL-17A, sIL-6R (R&D) and anti-CD3 (Biolegend). For these experiments, antibodies were compared to IgG1 isotype control, while anti-TNF/IL-6 NANOBODY® VHH was compared to a NANOBODY isotype control.

first: Nadine

last: Biesemann


title: Germinalmatrix-Intraventricular Hemorrhage induced Early Gene Expression Profile in Subventricular zone (SVZ) of developing rabbit forebrain

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

summary: Intraventricular hemorrhage (IVH) remains a major neurological complication of prematurity that results in cerebral palsy, hydrocephalus, and cognitive deficits. No effective therapy exists to prevent these disorders in infants with IVH. IVH triggers inflammation, cellular infiltration and white matter injury following neurobehavioural deficits.

overall_design: In this study, we have assessed early gene expression profile after hemorrhage in SVZ tissue from rabbit forebrain with without hemorrhagic pups.

first: Dina

last: Finkel

first: Selvakumar

last: Subbian

first: Edmund

middle: F

last: La Gamma

first: Govindaiah

last: Vinukonda


title: Hypercapnia alters Wnt production from PDGFR+ lung fibroblasts

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary:
Hypercapnia has deleterious effects on cell function, including inhibition of alveolar epithelial cells (AEC) and fibroblast proliferation without causing cell death.
Classical studies and lineage-trace models demonstrated that fibroblast cells can affect the structurally and functionally distinct alveolar type 1 cells (AT1) and alveolar type 2 cells.
This fibroblast cells reprogramming depends on certain signaling pathways that plays critical roles in tissue development and homeostasis throughout the organism lifespan.

overall_design: Transcriptomic profiles of flow sorted PDGFR alpha+ fibroblast cells from C57Bl/6 mice exposed to 10%  CO2 undernormoxic conditions for 0, and 10  days were generated by standard illumina RNA-Seq protocols.

first: Laura

last: Dada

first: Jacob

last: Sznajder


title: The Polyamine-Hypusine Circuit Controls an Oncogenic Translational Program Necessary for MYC-Driven Lymphomagenesis [RNA-seq]

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

summary: Hypusinated EiF5A likely impacts diverse cellular pathways, through direct regulation of its translational targets or via secondary effects on other biological processes. We examined the global effects of knockdown of EiF5A and Dhps on the transcriptome and translational landscape of MYC-induced lymphoma.

overall_design: To evaluate the effects of EiF5A or Dhps depletion on transcription and translation, RNA-seq analyses of Em-Myc;Rosa26 -rtTA2 lymphoma cells that inducibly express sh-Ren, sh-EiF5A or sh-Dhps were performed along with ribosome profiling.

first: Shima

last: Nakanishi

first: Jiannong

last: Li

first: Anders

middle: E

last: Berglund

first: Youngchul

last: Kim

first: Ling

first: Chunying

last: Yang

first: Raghu

middle: G

last: Mirmira

first: John

last: Cleveland


title: Transcriptome sequencing of pancreas and adipose tissues in obesity-related alcohol-induced acute pancreatitis

city: chengdu

first: Linbo

last: Yao

address: West China Hospital

institute: West China Hospital, Sichuan University

summary: Transcriptomics and network pharmacology reveal the protective effects of chaiqin chengqi decoction on obesity-related alcohol-induced acute pancreatitis: involvement of the antioxidant protein response and downregulation of the PI3K/Akt signaling pathway

overall_design: Two pancreatic tissues in the control group and three pancreatic tissues in the model group; Three adipose tissues in each of the control group and the model group

first: Xinmin

first: Mei

last: Yuan

first: Xiaoying

first: Monika

last: Jakubowska

first: Pawel

last: Ferdek

first: Lei

last: Dai

first: Jingyu

first: Tao

last: Jin

first: Lihui

last: Deng

first: Xianghui

last: Fu

first: Dan

last: Du

first: Tingting

last: Liu

first: Criddle

last: David

first: Robert

last: Sutton

first: Wei

first: Qing

last: Xia


title: Therapeutic Targeting Ewing Sarcoma through Inhibition of the FACT Complex (RNA-Seq II)

city: shanghai

first: Jialin

last: Mo

address: South Chongqing Road, Shanghai 200025. P.R. China

institute: Shanghai Jiao Tong University School of Medicine

summary: EWS/ETS fusion transcription factors, most commonly EWSR1-FLI1, drive initiation and progression of Ewing sarcoma (EwS), a highly aggressive childhood cancer of bone and soft tissues. Even though direct targeting EWSR1-FLI1 is a formidable challenge, epigenetic or transcriptional modulators have been recently proved to be promising therapeutic targets for indirectly disrupting its expression and/or function. Here, we performed transcriptome and functional genomics dataset analyses, and combined with small molecule screening of EwS lines to identify novel epigenetic/transcriptional-targeted therapeutic strategies. SSRP1 and SUPT16H, two subunits of the Facilitates Chromatin Transcription (FACT) complex, are both found to be EWSR1-FLI1-induced essential oncogenes in EwS. The FACT-targeted drug CBL0137 exhibits potent therapeutic efficacy against multiple EwS preclinical models in vitro and in vivo. Mechanistically, the FACT complex and EWS-FLI1 form oncogenic positive feedback loop via mutual transcriptional regulation and activation, and cooperatively promote cell cycle/DNA replication process and IGF1R-PI3K-AKT-mTOR pathway to drive EwS oncogenesis. The FACT inhibitor drug CBL0137 effectively targets the EWSR1-FLI1-FACT circuit, resulting in transcriptional disruption of EWS-FLI1, SSRP1 and their downstream effector oncogenic signatures. Our study illustrates a crucial role of the FACT complex in facilitating the expression and function of EWSR1-FLI1 and demonstrates FACT inhibition as a novel therapeutic strategy against EwS via indirect targeting the oncogenic fusion TF, providing preclinical support for adding EwS to CBL0137’s future clinical trials.

overall_design: mRNA profiling:RNA was prepared from vehicle or CBL0137 (1μM) treated human Ewing sarcoma cells SKNMC for 24 h. Trim galore was used to automatically detect and trim adapters. Reads were mapped to hg19 reference genome using Hisat2. Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0). Absolute value of fold change (FC) > 1.5 and false discovery rate (FDR) < 0.05 was used as cut-off value to select significant target genes. FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account.

first: Kezhe

last: Tan

first: Yu

last: Dong

first: Yujie

last: Tang


title: SGLT2 inhibitors and zebrafish

city: Turku

first: Riku

last: Kiviranta

address: Kiinamyllynkatu 10

department: Institute of Biomedicine

country: Finland

institute: University of Turku

summary: The CANVAS program revealed that the SGLT2 inhibitor canagliflozin increases the risk for lower-limb (minor) amputations in type 2 diabetics about a two-fold. On the contrary, the large RCTs with empagliflozin and dapagliflozin did not demonstrate a similar observation. Thus, a question arises whether the increased risk for minor amputations is associated only with canagliflozin or whether it is a class effect of SGLT2 inhibitors. Vascular disorders including defective angiogenesis are among the leading causes of lower-limb amputations. Therefore, here we examined the effects of empagliflozin, dapagliflozin, and canagliflozin on angiogenesis using zebrafish embryos and HUVECs.

overall_design: Genome-wide expression investigation and pathway changes in  control, Empagliflozin and Canagliflozin treated Zebrafish embryos in.

first: Hannu

last: Järveläinen

first: Annele

last: Sainio

first: Minna

last: Niemelä


title: WGBS and RNA-seq of HUVECs transfected with siNC or siTET2

city: Shanghai

first: Kou

last: wenxin

address: 301 middle yanchang road

institute: tongji university

type: Methylation profiling by high throughput sequencing

summary: Cardiac fibrotic process is the synergetic activities of fibroblast, myofibroblast and endothelial-to-mesenchymal transition (EndMT). Epigenetic regulators like DNA methylation are proved to involve in EndMT in the context of cardiac fibrosis. In our study, we explored the role of TET2 in heart fibrosis and EndMT, and found the loss of TET2 could promote EndMT and cardiac fibrosis by regulating DNA methylation.

overall_design: RNA-seq: mRNA profiles of HUVEC transfected with siNC or siTET2; WGBS: Examination of different methylated modifications in HUVEC transfected with siNC or siTET2

first: Wenxin

last: Kou

first: Yefei

last: Shi

first: Bo

last: Li

first: Ming

last: Zhai

first: Shuangjie

last: You

last: Yu

first: Jianhui

last: Zhuang

first: Yifan

last: Zhao

first: Weixia

last: Jian

first: Yawei

last: Xu

first: Wenhui

last: Peng


title: Therapeutic Targeting Ewing Sarcoma through Inhibition of the FACT Complex (RNA-Seq I)

first: Jialin

last: Mo

overall_design: mRNA profiling:RNA was prepared from vehicle or CBL0137 (1μM) treated human Ewing sarcoma cells A673 for 24 h. Trim galore was used to automatically detect and trim adapters. Reads were mapped to hg19 reference genome using Hisat2. Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0). Absolute value of fold change (FC) > 1.5 and false discovery rate (FDR) < 0.05 was used as cut-off value to select significant target genes. FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account.

first: Kezhe

last: Tan

first: Yu

last: Dong

last: Tang


title: Estrogen-related receptor beta differentially regulates target genes through diverse interactions with DNA, TFIIH, and coactivators

city: Koto-ku

first: Tomoyoshi

last: Nakadai

state: Tokyo

institute: Cancer Institute of JFCR

summary: Estrogen-related receptor (ERR) beta is critical for maintenance of mouse embryonic stem cell (ESC) self-renewal under 2-inhibitor (“2i”) conditions. On the other hand, we biochemically revealed ERR activated transcription through the interaction with DNA, TFIIA, and C-terminal AF2 domain binding coactivators. To evaluate the biological significance of this finding, we analyzed the transcriptome of DNA-, TFIIH-, and coactivator-binding deficient mutant ERR beta-expressing ERR beta-knockout ESCs which showed compromised self-renewal activity. The results demonstrated that each interaction was required for regulating the specific biological/functional gene set among ERR beta-target genes.

overall_design: Established ERR beta-knockout ESC clones doxycycline-inducibly expressing wild-type, DNA-, TFIIH-, and coactivator-binding deficient mutant ERR beta, and wild-type ERR gamma-expressing ERR beta-knockout were cultured in N2B27-PD/CH medium and doxycycline for 3 days, total RNA was used for RNA-seq analysis.

first: Keiichi

last: Ito

first: Robert

last: Roeder

first: Reo

last: Maruyama

first: Kohei

last: Kumegawa


title: The Polyamine-Hypusine Circuit Controls an Oncogenic Translational Program Necessary for MYC-Driven Lymphomagenesis

first: Yonghong

last: Zhang


title: Effect of developmental (24-100 hpf) embryonic exposures to tris(4-chlorophenyl)methane and tris(4-chlorophenyl)methanol in the zebrafish

city: East Lansing

first: Karilyn

last: Sant

state: MI

address: 1355 Bogue St., Life Science B440

department: Pharmacology & Toxicology

institute: Michigan State University

summary: Tris(4-chlorophenyl)methane (TCPM) and tris(4-chlorophenyl)methanol (TCPMOH) are two marine pollutants of emerging concern, found in marine mammals and coastal bird populations. Here, we assess the response to these compounds due to developmental (24-100 hourrs post fertilization) exposures in zebrafish embryos

overall_design: We analyzed a total of 15 samples: Samples 1-5 were controls, exposed to 0.01% v/v dimethyl sulfoxide for 3 days between 24-100 hours post fertilization. Samples 6-10 were exposed to 50 nM TCPM, and Samples 11-15 were exposed to 50 nM TCPMOH. Samples were collected from 3 experimental replicates, with randomized embryos acquired from 20 breeding pairs.

first: Peyton

middle: W

last: Wilson

first: Nicholas

last: Allsing

first: Christine

last: Cho


title: Transcriptome and methylation analysis of JMML patients compare to healthy prenatal and postnatal samples.

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

country: France

institute: APHP Hôpital Robert Debré

summary: JMML (Juvenile myelomonocytic leukaemia) is a leukaemia hat only develops in young children and is thought to have a prenatal initiation. To study the relationship between JMML and normal ontogeny we studied the transcriptome of HSPC (hematopoietic stem and progenitor cells) sorted from sporadic JMML patients, healthy prenatal samples and from healthy age matched donors. Bulk transcriptome of sorted HSPC reveals that some JMML samples cluster with prenatal samples whereas other from a distinct cluster apart from any healthy samples. Methylation profile on bulk mononucleated cell on theses JMML patients, 2 healthy postnatal and 2 healthy prenatal samples is also investigated. The results show a global hypermethylation in JMML samples compared to healthy samples and a specific JMML group with a hypermethylated profile compared to all JMML samples.

overall_design: Bulk RNAseq data on sorted HSPC. Bulk RRBS data on mononuclated cells

last: Cavé

first: Marion

last: Strullu

first: Aurélie

last: Caye

first: Chloé

last: Arfeuille


title: The lncRNA DANA2 interacts with the transcription factor ERF84 to regualte drought response in Arabidopsis

city: Nanchang

first: Dong

last: Wang

state: JiangXi

address: Hong Gu Tan New Road, No. 999

institute: Nanchang University

summary: DANA2 is a positive regulator of drought response and that DANA2 works jointly with the transcription factor ERF84 to activate  the JMJ29 expression during the response to drought.

overall_design: Total RNA was isolated from 10-day old wild type Col-0,  dana2 and jmj29 mutants, in triplicate, using Illumina NovaSeq 6000.


title: The L1p/L10e-type protein DIP1 recruits the long noncoding RNA DANA1 and the PEAT complex to trigger histone deacetylation of drought responsive genes in Arabidopsis

summary: DANA1 is a positive regulator of drought response and that DANA1 works jointly with the novel chromatin-related factor DIP1 to modulate the epigenetic reprogramming of the plant transcriptome during the response to drought.

overall_design: Total RNA was isolated from 10-day old wild type Col-0 and  dana1 mutant, in triplicate, using Illumina NovaSeq 6000.


title: mRNA expression quantitative Analysis of Kasumi-1 treated with I1 compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in Kasumi-1 cell lines treated with I13

overall_design: There are 6 samples for Kasumi-1 cell line ( control and I1-treated).


title: Novel dynamic network analysis approach characterizes progressive and complex effects of weight gain and obesity on breast cancer signaling

city: Detroit

first: Aliccia

last: Bollig-Fischer

address: 4100 John R

department: Oncology

institute: Karmanos Cancer Institute & Wayne State University

summary: ER-positive tumor data was derived by RNA-sequencing of formalin-fixed paraffin-embedded specimens (FFPE) collected from 44 women diagnosed with ER+ and progesterone receptor-positive but HER2 negative (ER+/PR+/HER2-) breast cancer at the Karmanos Cancer Institute. According to a pathologist review, all tumor specimens were invasive cancer with 70% or greater cancer cell content. Patients had not received neoadjuvant cancer therapy, nor were they treated for diabetes with systemic drugs (e.g., metformin) before surgical resec- tion. Following manufacturer instructions, the Recoverall Nucleic Acid Isolation Kit for FFPE Tissue (Ambion, Austin, TX) was used to isolate RNA. Quantitation and fragmentation analysis were performed using the NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 and RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA). A Qubit fluorometric assay (Thermo Fisher Scientific) was used to quantitate and equalize dsDNA prepared using the Truseq RNA Access library preparation kit (Illu- mina, San Diego, CA). Libraries were randomized, indexed, multiplexed, and paired end sequenced (200 cycles total) on an Illumina Nextseq500. Bioinformatic quality control was done using the FastQC software (v0.11.4), adapter and low-quality reads were removed using Trimmomatic v0.36. FPKM normalization and aligning were done using TopHat v2.1.1.

overall_design: Model the impact of BMI on cell signaling pathways.

first: Cristina

last: Mitrea


title: VEGF receptor inhibitor brivanib sensitizes chemotherapy by targeting cGAS to boost antitumor immunity

first: Hang

last: Su

state: Other (Non U.S.)

address: 上海市杨浦区政民路507号上海市肺科医院

institute: Shanghai pulmonary hospital

summary: Chemoresistance challenges the clinical application of most widely used platinum-based cancer chemotherapeutics which canonically function through inducing DNA damage. The DNA sensor cyclic GMP–AMP synthase (cGAS) connects genome instability to type I IFN response which confers vulnerability to platinum treatment. Here, by using a high throughput small-molecule-microarray-based screening of cGAS interacting compounds, we identified brivanib, known as an inhibitor of the vascular endothelial growth factor receptor (VEGFR), as a novel cGAS agonist. Brivanib markedly enhanced platinum-induced STING-TBK1-type I IFN response in tumor cells indispensable of cGAS. Importantly, brivanib synergizes the effect of cisplatin in restricting the growth of xenografted Lewis Lung Cancer (LLC) cells by boosting CD8+ T cell response in a cGAS-dependent manner. Mechanistically, brivanib enhances the DNA binding affinity of cGAS by directly targeting leucine 495 of cGAS. Moreover, leucine 495 of cGAS is essential for brivanib-mediated promoting effect on cisplatin-mediated type I IFN response and inhibition of tumor growth. Clinically, higher expression of cGAS in tumor renders a more favorable response to platinum-based chemotherapeutic regimens and better prognosis in lung cancer patient. Taken together, our findings discover cGAS as an unprecedented target of brivanib and provide a rationale for the combination of brivanib with platinum-based chemotherapeutics in cancer treatment.

overall_design: Total RNA was isolated and used for RNA-seq analysis. cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ-500 platform. High-quality reads were aligned to the Mus musculus reference genome (UCSC_mm10) using Bowtie2. The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-seq by Expectation Maximization (RSEM).

first: Haipeng

last: Liu


title: Analysis of differentiatng monocytes transcriptome changes in response to type I IFNs

city: Nanjing

first: Limin

last: Yang

state: jiangsu

address: pukou 11

institute: Nanjing university

summary: To analyze the transcriptome changes of differentiating monocytes in response to type I IFNs, RNA seq was performed. The MACS-purified mouse BM monocytes were cultured in the presence or absence of I IFNs for 12 h or 24h under the condition of M-CSF, samples were harvested for total RNAs and subjected to RNA sequencing analyses.

overall_design: MACS-purified monocytes from mouse bone marrow were treated with 20 ng/mL M-CSF, together with or without 100U mouse IFNβ for 12h, or 24h. each sample had three replicates. Total RNA was harvested at the indicated time, and then the RNA samples were subjected to RNA sequencing analyses.

first: Jianghuai


title: Epithelial cholangiocarcinoma cells can contribute to desmoplasia by extracellular matrix deposition and mesenchymal transition depending on the microenvironment

city: Rotterdam

first: Monique

last: Verstegen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Surgery

country: Netherlands

institute: ErasmusMC

summary:
Cholangiocarcinoma (CCA) is a hepatobiliary malignancy with dismal prognosis. Currently available models fail to recapitulate the full complexity of CCA, particularly the desmoplastic environment and the interplay between cancer cells and the extracellular matrix (ECM). We aimed to study the role of epithelial tumor cells in ECM deposition and desmoplasia by designing a model encompassing primary epithelial CCA organoids (CCAOs) and native liver and tumor scaffolds obtained by decellularization
Background & Aims: Cholangiocarcinoma (CCA) is a hepatobiliary malignancy with dismal prognosis. Currently available models fail to recapitulate the full complexity of CCA, particularly the desmoplastic environment and the interplay between cancer cells and the extracellular matrix (ECM). We aimed to study the role of epithelial tumor cells in ECM deposition and desmoplasia by designing a model encompassing primary epithelial CCA organoids (CCAOs) and native liver and tumor scaffolds obtained by decellularization.
Results: Decellularization resulted in effective removal of cells while preserving ECM structure and retaining important characteristics of the tissue origin. When culturing CCAOs in CCA-M, compared to TFL-M and BME, the genome-wide gene expression profile much more resembled the transcriptome of primary CCA tumor tissue in vivo, with an accompanying increase in chemoresistance. CCAOs in decellularized matrix, both CCA-M and TFL-M, exhibited the formation of complex morphological structures, and revealed environment-dependent proliferation and migration dynamics, driven by the occurrence of epithelial-mesenchymal transition (EMT). CCA-M induced specific extracellular matrix protein production in CCAOs, such as  fibronectin 1 (FN1), which is related to desmoplasia and patient survival. In TFL-M, lacking the desmoplastic environment, CCAOs were able to initiate a desmoplastic reaction directly through increased production of multiple collagen types.
Conclusions: This improved model of cholangiocarcinoma, combining organoids and native extracellular matrix, recapitulates key components of CCA tumor biology, including transcriptome profiles, migration patterns, EMT, and ECM protein production. The increased production of extracellular matrix proteins suggests that epithelial tumor cells can contribute to their own desmoplastic environment.

overall_design: Methods: Patient CCA matrix (CCA-M) and tumor-free liver matrix (TFL-M) were decellularized and subsequently recellularized with CCAOs. The decellularized scaffolds were biochemically and mechanically assessed. Cell behavior, including proliferation, survival, and migration, was assessed in CCA-M, TFL-M, and basement membrane extract (BME), by live-cell imaging, immunohistochemical analysis, drug response studies and through a multi-omics approach.

first: Gilles

middle: S

last: van Tienderen

middle: M

first: Luc

middle: J

last: van der Laan


title: H3K9 demethylation-mediated transcriptional activation is required for male meiosis in Arabidopsis thaliana

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Dimethylation at histone H3 lysine 9 (H3K9me2), a critical mark for heterochromatin formation and transcriptional silencing, is usually methylated at transposable elements and repetitive sequences but unmethylated at bodies of protein-coding genes. It is known that deposition of H3K9me2 is essential for proper prophase progression in both mammals and plants. Nevertheless, function of removing H3K9me2 for meiosis is unknown. In this study, we show that H3K9 demethylases, IBM1 and JMJ27, together regulate chromosome pairing and segregation in early meiosis, through protecting thousands of protein-coding genes from ectopic H3K9me2, including meiotic-essential genes. In addition to IBM1 and JMJ27, we also found that the cohesin complex cofactors Precocious Dissociation of Sisters 5 (PDS5s) regulate the expression of essential meiotic genes by interacting with H3K9 demethylases, acting downstream of H3K9 demethylation. Therefore, H3K9 demethylases and PDS5s coordinately regulate male meiosis through regulating the expression of meiotic-essential genes. These findings provide insights into a novel function of removing H3K9me2 for meiosis and deeper understanding of the H3K9 demethylation-mediated transcriptional activation pathway.

overall_design: We compared the transcriptomes and genome profiles of H3K9me2 for Col, ibm1, ibm1 jmj27, and pds5.

first: Jinping

last: Cheng

first: Linhao

last: Xu

first: Valentin

last: Bergér

first: Chao

first: Klaus

middle: D

last: Grasser

first: Arp

last: Schnitger


title: Expression profiling of B cells subsets

city: Oullins

first: Fabrice

last: Chatonnet

address: 165 Chemin du Grand Revoyet

institute: INSERM

summary: Terminal B cell differentiation into antibody-secreting cells (ASC) is a critical process for adaptive immune responses. Although many efforts have been made in the recent years to decipher the cellular and molecular events sustaining this differentiation, both in mouse and human models, several key steps still need further elucidation. We used a combined RNA-seq and ATAC-seq approach to decipher the chromatin and gene expression events driving ASC differentiation from naive or memory B cells. Out goal with the dataset was to explore the divergent molecular properties of naive and memory B cells that sustain their differential abilities to differentiate into ASC.

overall_design: Three B cell subsets from human peripheral blood were analyzed by RNA-seq in triplicates.

first: Amandine

last: Pignarre

first: Gersende

last: Caron

first: Thierry

last: Fest


title: The Polyamine-Hypusine Circuit Controls an Oncogenic Translational Program Necessary for MYC-Driven Lymphomagenesis [Ribo-seq]

first: Yonghong

last: Zhang

summary: Hypusinated EiF5A likely impacts diverse cellular pathways through direct regulation of its translational targets or via secondary effects on other biological processes. We examined the global effects of knockdown of EiF5A and Dhps on the transcriptome and translational landscape of MYC-induced lymphoma.

overall_design: To evaluate the effects of EiF5A or Dhps depletion on translation, Ribosome profiling analyses of Em-Myc; Rosa26-rtTA2 lymphoma cells that inducibly express sh-Ren, sh-EiF5A or sh-Dhps were performed along with RNA-seq.

first: Shima

last: Nakanishi

first: Jiannong

last: Li

first: Anders

last: Berglund

first: Youngchul

last: Kim

first: Ling

first: Chunying

first: Raghu

last: Mirmira

first: John

middle: L

last: Cleveland


title: RNAseq of cell populations across the pluripotency continuum

city: Camperdown

first: Hannah

last: Glover

state: NSW

address: 92 Parramatta Rd

department: Physiology

country: Australia

institute: The University of Sydney

summary: This project involved bulk-RNAseq analysis of four stages across the pluripotency continuum in two cell lines - ground state, naïve, early primitive ectoderm-like and epiblast stem cells

overall_design: 21 paired samples across 4 stages of the pluripotency continuum and two stem cell lines (A2 and D3 - EpiSCs not available in D3 cell line)

first: Michael

middle: B

last: Morris


title: Expression of thioredoxin-interacting protein (TXNIP) during megakaryopoiesis is indispensable for platelet biogenesis

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

summary: Thioredoxin-interacting protein (TXNIP) is ubiquitously expressed in blood cells, including hematopoietic stem cells (HSCs), monocytes, and platelets. Here we report a novel finding that TXNIP plays a crucial role in megakaryopoiesis and platelet biogenesis via interacting with GATA1, a transcription factor for megakaryocyte-erythroid differentiation. Txnip-/- mice displayed immature megakaryocytes in the bone marrow with thrombocytopenia, which had gotten worse as the mice aged. Transcriptome analysis revealed that the transcriptional activity of GATA1 was significantly enhanced in the Txnip-/- megakaryocyte precursors (MkPs) than wild type (WT) cells. During megakaryopoiesis in ex vivo, Txnip-/- MkPs remained small in cell size with less mitochondrial mass, and more glycolysis for ATP production, as opposed to the normal megakaryocyte maturation. The effects of TXNIP in megakaryocytes were recapitulated in human cord blood CD34+ HSC-derived differentiation. Taken together, this study demonstrates the importance of spatiotemporal expression of TXNIP in platelet biogenesis. We propose for the first time that TXNIP might play a critical role in determining a lineage between megakaryocytes and erythroid cells from a common megakaryocyte-erythroid progenitor via regulation of transcriptional activity of GATA1.

overall_design: Three replicated samples for wild type and knockout were analyzed .

first: Eunju

last: Shin

first: Ji-Yoon

last: Noh


title: Downregulated CDH3 is significantly correlated with better prognosis from lung adenocarcinomas and decreases proliferation and migration in lung cancer cells in vitro

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

institute: beijing cancer hospital

summary: CDH3 is a single-span transmembrane domain glycoprotein that mediates cell-cell adhesion. It is normally expression in basal cells, luminal epithelial cells and monocytes of lung airway epithelial cells. However, the CDH3 gene is also frequently overexpressed in many cancers. Expression of CDH3 is an indicator of poor prognosis in human breast cancer and a marker for real-time monitoring of resistance to first/second generation EGFR-TKIs. In this present manuscript, we describe that high CDH3 expression is correlated with shorter overall survival of patients in lung adenocarcinomas and low CDH3 expression inhibits cells’ proliferation and migration

overall_design: Different gene expression in H1299 and HCC827 cells with transient CDH3 knockdown at 48 post-transfection hrs.

first: Wanru

last: Ma


title: Germinalmatrix-Intraventricular Hemorrhage induced Early Gene Expression Profile in Subventricular zone (SVZ) of developing rabbit forebrain

city: Greenville

first: Weihua

last: Huang

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

summary: Intraventricular hemorrhage (IVH) remains a major neurological complication of prematurity that results in cerebral palsy, hydrocephalus, and cognitive deficits. No effective therapy exists to prevent these disorders in infants with IVH. IVH triggers inflammation, cellular infiltration and white matter injury following neurobehavioural deficits.

overall_design: In this study, we have assesed early gene expression profile after hemorrhage in SVZ tissue from rabbit forebrain with without hemorrhagic pups.

first: Dina

last: Finkel

first: Edmund

last: La Gamma

first: Govindaiah

last: Vinukonda


title: Complete transcriptome of bir-2 knockdown C. elegans nematodes with and without exposure to pathogenic bacteria Enterococcus faecalis.

city: Rindge

first: Shallee

middle: Tyler

last: Page

state: New Hampshire

address: 40 University Dr, Marcucella Hall

department: Coll. Health & Natural Sci.

institute: Franklin Pierce U

summary:
Purpose: The goals of this study are to examine the role of C. elegans gene bir-2 in innate immunity.  The method is to compare differences in gene expression of transcriptomes of C. elegans in the presence and absence of a bir-2 knockdown and with and without pathogenic bacteria.
Results: We mapped about 4 million sequence paired-end reads of 251 nucleotide length for each of the 16 samples, trimmed the reads with Trimmomatic (v.0.38), mapped to the WBGene C. elegans genome (build WBcel235.99) using HISAT2 (v.2.1.0), assembled and merged transcripts with StringTie.  SamTools were used to convert the BAM files. Differential expression was evaluated using DESEQ2 in R. Approximately 4% of the transcripts showed differential expression between the WT and bir-2 knockdown, with a fold change ?2 and p value <0.05.!Series_summary = Methods: C. elegans were grown, in quadruplicate, exposed to HT115 bacteria expressing RNAi for bir-2 with and without E. faecalis exposure. Total RNA was purified and Illumina poly-A selection, library construction (KAPA RNA Hyperprep) and deep sequencing,  using Illumina HiSeq2000 at UNH Hubbard Genome Center. The sequence reads were passed through FASTQC and Trimmomatic, and were analyzed at the transcript isoform level.
Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

overall_design: Whole animal mRNA profiles of C. elegans nematodes +/- bir-2 knockdown +/- E. faecalis

middle: T

first: Rebecca

last: Haluch


title: Aminoglycosides induce a bacterial senescent state that increases antibiotic tolerance in treatment-naïve cells

city: Boulder

first: Christian

middle: Thomas

last: Meyer

state: CO

address: 3415 Colorado Ave, JSC Biotech; UCB 596

department: BioFrontiers

institute: University of Colorado Boulder

summary: Antibiotics are a triumph of modern medicine, but their power to cure infections is being eroded through the evolution and dissemination of resistance.  Evolution of genetic resistance is in part facilitated by non-genetic resistance mechanisms that increase antibiotic tolerance buying time for evolutionary innovation.  Using live cell imaging, we discovered that Escherichia coli treated with aminoglycosides permanently lose the ability to divide within 4 hours, yet a majority of cells maintain membrane integrity and metabolic 2 days post treatment, and some continuing activity for up to > 4 days post treatment – a bacterial senescent-like state.  These cells, which we term zombies, exhibit dynamic gene expression and metabolomic profiles even after exiting the cell cycle.  Gene expression data revealed upregulated the phage shock protein response maintained membrane integrity.  Remarkably, these zombie cells, though unable to form new colonies, increase antibiotic tolerance of treatment-naïve cells, implying chemical communication.  Chemical supplementation and genetic knockouts showed that zombies communicate to treatment-naïve cells by secreting indole.  In summary, our study revealed a bacterial senescent-like state, induced by aminoglycosides, that modifies the antibiotic tolerance of multiple bacterial species.

overall_design: RNA-seq analysis of E. coli zombies during exposure to kanamycin (30ug/mL).  6 timepoints, 3 replicates/timepoint

first: C

first: G

middle: N

last: Bruni

first: B

last: Dodd

first: J

last: Kralj


title: Single-cell RNA-seq of Fibroadipogenic progenitors from WT and Dysferlin KO mice

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

summary: Droplet-based single-cell RNA-seq of fibroadipogenic progenitors (FAPs) isolated from whole limb skeletal muscles of 8 month old WT and Dysferllin KO mice.

overall_design: Examination of different transcriptional profiles of FAP cells from WT and muscle disease conditions

first: Prech

last: Uapinyoying

first: Marshall

last: Hogarth

first: Surajit

last: Battacharya

first: Davi

last: Mazala

first: Carsten

last: Bonnemann

first: Jyoti

last: Jaiswal


title: KIAA1522 Promotes Colorectal Carcinoma Liver Metastases via Activation of the Notch Signaling Pathway

city: Qingdao

first: Xin

last: Yi

address: 758 Hefei Road

institute: Qilu hospital of Shandong University (Qingdao)

summary:
Purpose: Our research aims to identify the expression, clinical value, biological significance and signaling pathway of KIAA1522 in colorectal carcinoma liver metastases (CRLM).
Materials and Methods: To elucidate the role of KIAA1522 in CRC, its expression and survival analysis were assessed using GEPIA databases. Then we evaluated expression of KIAA1522 immunohistochemically in tissue samples of 57 patients with CRLM. The correlations between expression of KIAA1522 and clinical significance, prognosis of these 57 patients with CRLM were analyzed. Western blotting, CCK-8, colony formation, Flow cytometry, Transwell invasion, and wound healing assays were performed to explore the function of KIAA1522 in colon cancer cell lines. Finally, transcriptome sequencing and gene set enrichment analysis was used to identify the pathways involved.
Results: Our results demonstrated that KIAA1522 was highly expressed in CRLM tissues and colon cancer cell lines, and expression of KIAA1522 in primary sites was significantly positively correlated with that in metastatic sites. Furthermore, KIAA1522 overexpression was associated with unfavorable clinicopathological characteristics. Survival analyses revealed that KIAA1522 overexpression predicted lower overall survival rates in patients with CRLM. Functional studies suggested that KIAA1522 facilitated proliferation, migration and invasion of colon cancer cell lines in vitro. Moreover, KIAA1522 upregulated the Notch signaling pathway, as confirmed by transcriptome sequencing and gene set enrichment analysis.
Conclusion: In conclusion, these data suggest that upregulation of KIAA1522 might enhance tumorigenicity and metastasis of colon cancer cell lines through potentiating the Notch signaling pathway activity. Expression of KIAA1522 plays oncogenic roles in CRLM and might serve as a novel molecular target in CRLM treatment.

overall_design: Examination of SW480 colon cancer cells with pIRES2-ZsGreen1-KIAA1522 overexpression and  control empty plasmid transfection.

first: Conghui

last: Hu

first: Chen

last: Zhang

first: Kai

last: Shao

first: Hui

last: Sun

first: Yuanhui

last: Jiang

first: Xuting

last: Zhi


title: The underlying mechanism by which SFRS8 exerted carcinogenesis and its potential targets in MM

first: Yuanjiao

state: China

address: Xianlin Road

institute: nanjing university of chinese medicine

summary: An RIP experiment was performed in ARP1 cell following the instructions of the article.~5-20 × 10e6 cells were harvested and lysed. Protein A/G MagBeads pre-coated with 5μg of the antibody of interest  (SFRS8, abcam) and incubated with cell lysate supernatant overnight at 4°C.The beads containing immunoprecipitated RNA-protein complex were treated with 150μL of Proteinase K buffer to digest the proteins. Specific binding RNAs were isolated by using TRIzol

overall_design: Examination  in ARP1 cells.

first: YuanJiao

first: Ye

last: Yang

first: Chunyang

last: Gu


title: RNA Sequencing Analysis of control vs KDM4Ai treated cells as a monotherapy or in combination with PARPi

city: Glasgow

first: Tae Ju

last: Park

address: 21 Shelley Rd

country: United Kingdom

institute: Paul O' Gorman Leukaemia Research Centre

summary: Leukaemic blasts share common pathological features with other cancers including genome instability and impaired DNA damage response and repair (DDR). The limited efficacy of DDR inhibitors, such as poly (ADP-ribose) polymerase inhibitors (PARPi) as single agents in acute myeloid leukaemia (AML) is partly owing to activation of alternative DDR pathways and cytotoxicity to healthy tissues. Their strengths may lie in combination strategies targeting other essential proteins required for leukaemogenesis.  We have identified the histone demethylase, KDM4A, as a critical epigenetic regulator required for AML cell survival. Depletion of KDM4A causes aberrant DDR pathway activation and subsequent DNA damage. We hypothesised that KDM4A inhibitors (KDM4Ai) increase AML cell reliance on specific DDR pathways for survival and may sensitise them to PARPi. We aimed to analyse transcriptional profiling (RNA Seq) changes associated with varying concentrations of KDM4A inhibition in monotherapy and as a combination therapy with a single PARPi treatment following 36hrs treatment. In summary, our study identifies a novel potential therapeutic strategy for AML. KDM4Ai sensitises cells to PARPi through impairing further NHEJ repair and enhancing PARP trapping leading to selective leukaemic cell death. These results warrant future clinical evaluation of this promising combination strategy in AML and other cancers.

overall_design: THP1 cells representitive of MLL-AF9 AML were treated for 36hrs with DMSO (Vehicle Control), ~IC50 KDM4Ai, High Conc. KDM4Ai, EC50 PARPi in monotherapy and combination of ~IC50 KDM4Ai and EC50 PARPi in triplicate

first: Laura

last: Monaghan

first: Joana

last: Silvestre

first: Taeju


title: METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression [TRAC-seq]

city: Guangzhou

first: Ma

last: Jieyi

address: Zhongshan II road

institute: SYSU

summary: The tRNA N7-methylguanosine (m7G) modification is not essential for yeast growth, but in mammals mis-regulations of tRNA m7G modification cause stem cell defect and developmental disorders. Here we found that tRNA m7G methyltransferase complex components METTL1 and WDR4 are elevated in lung cancer tissues and associated with poor lung cancer prognosis. Functionally, depletion of METTL1 or WDR4 suppresses proliferation, migration, and invasion of lung cancer cells. In addition, forced expression of METTL1 or WDR4 promotes lung cancer progression depending on the tRNA m7G methyltransferase activity. Mechanistically, METTL1 knockdown leads to reduced tRNA m7G modification and decreased expression of m7G-modified tRNAs. Depletion of METTL1 selectively reduces the translation of a subset of oncogenic transcripts, including the genes related to cell proliferation in a m7G related codon dependent manner. Our study uncovered a new layer of translation regulation mechanism mediated by tRNA m7G modification, provided strong evidence to support the important physiological function of mis-regulated tRNA modification in cancer, and suggested that targeting METTL1 could be a promising strategy for lung cancer treatment.

overall_design: TRAC-Seq were developed to identify the tRNA m7G methylome in lung cancer cell line A549.

first: Jieyi

last: Ma

first: Shuibin

last: Lin


title: ChIP-seq analysis of human non-transformed breast epithelial cell lines MCF10A with ARID1A knockdown

city: Shanghai

first: Jie

last: Wang

address: 416 Rm., MingdaoBldg., 131 Dongan Rd., Shanghai 200032, P.R.China

institute: Fudan University

summary: We performed ChIP-Seq analysis for the binding of ARID1A abundance genome-wide. These studies were performed in MCF10A, the human non-transformed breast epithelial cell line, with ARID1A knockdown and control group.

overall_design: ChIP-Seq analysis in MCF10A with ARID1A knockdown and control group.

first: Hai-Bo

last: Yan

first: Qian

first: Ying-Hua

first: Peng-Yuan

first: Feng

last: Liu


title: shRNA Knockdown of NFATC2 in the THP-1 cell line as a model of MLL-AF9 acute myeloid leukaemia

summary: Knockdown of NFATC2 in AML cell lines using a lentiviral shRNA approach was shown to be detrimental to cell survival in vitro. We hypothesised that NFATC2 is essential for AML oncogenic signalling in these cells and its depletion would result in the perturbation of the affected pathways

overall_design: Three biological replicates of NFATC2 knockdown by shRNA in the THP-1 AML cell line. RNA harvested 48 hours after transduction with lentivirus.

first: Shaun

last: Patterson


title: Cas9 interactions with host RNAs and transposable elements impair neurodevelopment (RNA-seq)

city: Guangzhou City

first: Denghui

last: Chen

address: No. 74 Zhongshan 2nd Road

department: Zhongshan School of Medicine

institute: Sun Yat-sen University

summary: The CRISPR (clustered regulatory interspaced short palindromic repeats)/ Cas9 (CRISPR-associated protein 9) system-based precise genome editing has revolutionized biomedical studies. As the CRISPR/Cas9 system has been also recently considered to permanently cure genetic diseases via human germline genome editing, a careful risk assessment of this genome engineering tool is required in human early development. Here we perform comprehensive analysis to evaluate the potential impact of Cas9 in human early embryogenesis. We find that even in the absence of synthetic guide RNA, Cas9 can be still guided by endogenous RNAs, and cut the genome of human embryonic cells at low frequency, and the resulting DNA damage induces the intrinsic immune response. Moreover, Cas9 interferes with the spliceosome, and with the suppressor machinery (e.g. L1TD1, APOBEC3G and PIWIL4) of LINE-1 (L1) retrotransposition. Even the transient presence of Cas9 in human embryonic cells induces robust de novo L1 retrotransposition that exacerbates DNA damage, and results in compromised neurodevelopment. Besides the ethical issues, these inevitable and detrimental Cas9-associated impacts on human embryonic development raise such serious safety concerns as to question the clinical use of human germline genome editing.

overall_design: RNA-seq were applied on hESC_WT, hESC_iCas9 and hESC_idCas9 to profile their transcriptomes.

first: Yuanglang

last: Hu

first: Ruiqi

last: Li

first: Chuanbo

first: Mingzhu

first: Hanwen

last: Yu

first: Jichang


title: METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression

first: Ma

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

overall_design: Refer to individual Series


title: METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression [RNA-seq]

overall_design: Ribosome nascent-chain complex-bound mRNAs (RNC-mRNAs) sequencing was used to study the differentially translated genes in the METTL1 knockdown and control cells.

first: Jieyi


title: Cas9 interactions with host RNAs and transposable elements impair neurodevelopment (CUT&Tag)

overall_design: We investigated Cas9 and MRE11-binding profiles on the genome of Cas9-expressing hESCs using CUT&Tag. CUT&Tag was performed in two biological replicates of hESC_WT, hESC_iCas9 and hESC_idCas9 (under doxycycline treatment or not) with the indicated antibody and IgG as control.

last: Sun


title: Non-programmed dissemination of cancer cell clusters induce malignant properties  through Integrin beta 1 activation

city: Cheonan

first: Ngu

middle: Van

last: Trinh

state: Chungcheongnam

address: 25Bongjeong-ro, Cheonan-si, Korea

institute: SoonChunHyang Institute of Medi-Bio Science

summary: We found that epithelial cluster recruiment soluble fibronectin and then activating beta1 Integrin induce epithelial-mesenchymal transition and enhance cancer cells’ malignant after cell dissemination. Non-programmed dissemination of cluster cells triggers ERK cascade and then accelerate tumor growth and metastasis. Our finding reveals that cell cluster plays a vital role in the non-programmed dissemination of breast cancer cells’ metastasis, offering a potential new therapeutic target for metastasis patients.

overall_design: MCF7 Breast Cancer cells (ATT) collected as single cells (SC) or cluster cells (CL) and then growth on suspension (DE-SC and DE-CL), then reattached on regular plate to mimic disseminated tumor cells ( RE-SC and RE-CL). Total 6 cell samples were generated and did RNA sequencing

first: Trinh

middle: V

last: Ngu

first: Seongho

last: Ryu


title: Next Generation Sequencing Facilitates Quantitative Analysis of wild-type and erf4 mutant Transcriptomes

first: Anming

last: Ding

state: Shandong

address: No.11 Keyuanjingsi Rd.

institute: Tobacco Research Institute of CAAS

summary: Analysis of gene expression level. The hypothesis tested in the present study was that erf4 mutant affects PMEI genes expression which inhibited PME activity in the seed coat mucilage

overall_design: mRNA profiles from 7 DPA seeds of wild-type and erf4 mutant (SALK_073394) were generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000.

first: A

first: Y

last: Kong


title: Polycomb repressive complex 1 and 2 (PRC1 and PRC2) role in controling skin pigmentation [RNA-Seq]

city: Bronx

first: Deyou

last: Zheng

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Polycomb repressive complexes 1 and 2 (PRC1 and 2)-mediated epigenetic regulation establishes  gene expression necessary for skin pigmentation.

overall_design: Epidermal keratinocyte was purified from P71 control, Eed KO and Ring1a/b 2KO back skin by FACS sorting. The controls for the two KOs are different. RNA from the sorted cells was analyzed by RNA-seq.

first: Meng

first: Pooja

last: Flora

first: Phillip

last: Galbo

first: Elena

last: Ezhkova


title: RNA-sequencing analysis of skin in ND- and HFD-fed mice after the application of phorbol12-myristate13-acetate (PMA)

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

summary: To investigate the effects of a high-fat diet (HFD) on the skin, RNA-seq was performed on the ear skin after 8 weeks of normal diet (ND) and HFD-fed mice. We also examined the effects of a HFD on irritant dermatitis by PMA.

overall_design: 4 ND-fed mice, 4HFD-fed mice, 4 ND-fed mice with PMA treatment, 4 HFD-fed mice with PMA treatment

first: Kenji

last: Kabashima

first: Florent

last: Ginhoux


title: Polycomb  complexes in skin epithelium development I

summary: Polycomb group (PcG) proteins are essential epigenetic transcriptional regulators. Traditionally, PcG proteins function as two multi-subunit complexes, Polycomb repressive complex 1 (PRC1) and PRC2, which largely overlap in their genomic binding and cooperate to establish repressive chromatin domains demarcated by H2AK119ub and H3K27me3. Here, using the developing skin epidermis as a paradigm, we uncovered a  functional redundancy between Polycomb complexes in the repression of unwanted non-lineage genes.

overall_design: Newborn mouse epidermal progenitor cells  were FACS purified. Immunoprecipitated chromatin was analyzed by ChIP-seq.

first: I

last: Cohen

first: D

first: E


title: Polycomb  complexes in skin epithelium development II


title: Polycomb repressive complex 1 and 2 (PRC1 and PRC2) role in controling skin pigmentation [ChIP-Seq]

overall_design: Back skin epithelium was purified from P71 control mice by FACS sorting.  Immunoprecipitated chromatin was analyzed by ChIP-seq.

first: Hequn

last: Liu


title: Polycomb  complexes in skin epithelium development III

overall_design: Newborn mouse epidermal cells  were purified from Eed;Ring1a/b triple knock out and control mice. RNA from the sorted cells was analyzed by RNA-seq.