title: Transcriptome profile of Responders and Nonresponders T cells infiltrated lymphocytes (TILs) co-cultured with autologous tumor cells from patients with melanoma.

city: Houston

first: Melisa

middle: Angela

last: Martinez-Paniagua

state: Texas

address: S222 Engg Bldg 1, 4226 Martin Luther King Blvd.

department: William A. Brookshire Department of Chemical and Biomolecular Engineering

institute: University of Houston

summary: Adoptive cell therapy (ACT) based on ex vivo expanded autologous tumor-infiltrating lymphocytes (TILs) can mediate durable antitumor responses even in heavily pretreated patients. However, only a subset of patients responds to ACT; efforts to identify correlates of response have focused on profiling the tumor or the TIL but rarely in an interactive environment. Interactive profiling can provide unique insights into the clinical performance of TILs since the fate, function, and metabolism of TILs are influenced by autologous tumor-derived factors. Here, we performed a suite of cell-sparing assays dubbed holistic analysis of the bioactivity of interacting T cells and autologous tumor cells (HABITAT). HABITAT profiling of TILs used for human ACT and their autologous tumor cells included function-based single-cell profiling by timelapse imaging microscopy in nanowell grids (TIMING); multi-omics using RNA-sequencing and proteomics; metabolite inference using genome-scale metabolic modeling, and pulse-chase assays based on confocal microscopy to profile the uptake and fate of fatty acids (FA). Phenotypically, the ACT TILs from both responders (Rs) and nonresponders (NRs) were comprised of predominantly effector memory T cells (TEM cells) and did not express a high frequency of programmed death ligand-1 (PD-L1) and showed no differences in TCR diversity. Our results demonstrate that while tumor cells from both Rs and NRs are efficient at uptaking FAs, R TILs are significantly more efficient at utilizing FA through fatty acid oxidation (FAO) than NR TILs under nutrient starvation conditions. While it is likely that lipid and FA uptake is an inherent adaptation of TIL populations to lipid-rich environments, performing FAO sustains the survival of TILs and allows them to sustain antitumor cytolytic activity. We propose that metabolic plasticity enabling FAO is a desirable attribute of human TILs for ACT leading to clinical responses.

overall_design: Three responders' and three nonresponders' TIL samples were co-cultured for 12 hours with their respective autologous tumor cells from melanoma patients in complete media.

first: Cara

last: Haymaker

first: Jonathan

last: Robinson

first: Michal

last: Harel

first: Caitlin

last: Creasy

first: Jay

last: Adolacion

first: Xingyue

last: An

first: Mohsen

last: Fathi

first: Ali

last: Kumar

first: Amit

last: Amritkar

first: Scott

middle: E

last: Woodman

first: Rodabe

last: Amaria

first: Tamar

last: Geiger

first: Patrick

last: Hwu

first: Chantale

last: Bernatchez

first: Navin

last: Varadarajan


title: Effect of knockout (KO) of Usp28 on gene expression in embryonic stem cells(ESCs) cultured under 2iL condition

status: Public on May 01 2023

city: Chongqing, China

first: jiangjun

last: wang

address: Chongqing, China

department: Depart of Histology and Embryology

country: China

institute: Cell Biology Department

type: Expression profiling by high throughput sequencing

summary: For validating the role Usp28 in regulating mouse ESC self-renewal, sgRNAs were designed to generate Usp28 KO cell lines. We then performed gene expression profiling analysis using data obtained from RNA-seq control (CTL) and Usp28 KO ESCs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CTL and Usp28 KO ESCs.

first: Jiangjun

last: Wang

first: Chen

last: Zhang

first: Yi

last: Huang

first: Yan

last: Ruan

last: Hu

first: Jiaqi

first: Fengsheng

first: Meng

last: Yu

first: Yixiao

last: Xu

first: Lianlian

last: Liu

first: Yuda

last: Cheng

first: Ran

last: Yang

first: Yutong

last: Dong

first: Jiali

first: Jiaxiang

last: Xiong

first: Yanping

last: Tian

first: Qiangguo

last: Gao

first: Junlei

first: Rui

last: Jian


title: Molecular changes in the maize roots transcriptome due to soil microbes

city: Lincoln

first: Chi

state: NE

address: 1901 Vine Street

country: USA

institute: University of Nebraska - Lincoln

type: Non-coding RNA profiling by high throughput sequencing

summary: The association between soil microbes and plant roots is present in all natural and agricultural environments. Microbes can be beneficial, pathogenic, or neutral to the host plant development and adaptation to abiotic or biotic stresses. Progress in investigating the functions and changes in microbial communities in diverse environments have been rapidly developing in recent years, but the changes in root function is still largely understudied. The aim of this study was to determine how soil bacteria influence maize root transcription and microRNAs (miRNAs) populations in a controlled inoculation of known microbes over a defined time course. At each time point after inoculation of the maize inbred line B73 with ten bacterial isolates, DNA and RNA were isolated from roots. The V4 region of the 16S rRNA gene was amplified from the DNA and sequenced with the Illumina MiSeq platform. Amplicon sequencing of the 16S rRNA gene indicated that most of the microbes successfully colonized maize roots. The colonization was dynamic over time and varied with the specific bacterial isolate. Small RNA sequencing and mRNA-Seq was done to capture changes in the root transcriptome from 0.5 to 480 hours after inoculation. The transcriptome and small RNA analyses revealed epigenetic and transcriptional changes in roots due to the microbial inoculation. This research provides the foundational data needed to understand how plant roots interact with bacterial partners and will be used to develop predictive models for root response to bacteria.

overall_design: gene expression profiling analysis of  the maize inbred line B73 with ten bacterial isolates at 1o time point after inoculation.

first: Jingjie

last: Hao

first: Bin

first: Daniel

last: Schachtman


title: Targeting IRG1 in tumor-associated macrophages for cancer therapy

city: Shang Hai

first: LEILEI

last: CHEN

address: Dongan Road 131#

institute: Fudan University

summary: Immune-responsive gene 1 (IRG1) is a mitochondrial aconitate decarboxylase and can produce the immunomodulatory metabolite itaconic acid (ITA). However, its role in modulating the function of tumor-associated macrophages (TAMs) remains elusive. Here, we show that IRG1 is expressed in TAMs in human tumors and mouse models of cancer. Tumor cells induce Irg1 expression in macrophages which dampens the inflammatory response and restricts M1-like TAM polarization. In contrast, Irg1-deficent macrophages acquire more proinflammatory M1-like features, promote immunogenic antigen presentation, and enhance cytotoxic T cell infiltration into tumor sites. Consequently, Irg1 deficiency suppresses the growth of mouse syngeneic tumors, including melanoma, colorectal cancer, breast cancer, and pancreatic cancer. Irg1-deficient macrophages not only dictate the tumoricidal effect but enhance the efficacy of anti-PD(L)1 immunotherapy. In conclusion, our data identify IRG1 as a myeloid immune check point gene and foster the development of genetic or pharmacologic targeting of IRG1 for skewing macrophages toward an anti-tumor phenotype to treat a broad spectrum of cancer.

overall_design: We performed single-cell RNA sequencing on Irg1+/+ and Irg1-/- mice and obtained CD45+ cells from B16-F10 melanoma tumors.

first: Lei

middle: L

last: Chen

first: Yu

middle: J

first: Min

last: Fu


title: Engineering T cells to encode natural post-integration barriers to HIV-1 replication

city: Madison

first: Ryan

last: Behrens

address: 555 Science Dr

institute: University of Wisconsin-Madison

summary: HIV-1 virion production is inefficient in cells derived from mice and other rodents.  Inefficient production maps, in part, to a species-specific polymorphism in the cellular gene, CCNT1. In human cells, the HIV-1 Tat protein hijacks the positive transcription elongation factor (p-TEFb) complex, composed of CCNT1 and the cellular kinase CDK9, to promote viral transcript elongation and thereby increasing net viral gene expression and virion production. In mouse cells, Tat-dependent viral transcription is poor, reflecting the inability of Tat to engage p-TEFb because of a species-specific tyrosine residue at position 261 in the mouse ortholog of CCNT1.  Humans encode a cysteine at the equivalent position which Tat requires for efficient p-TEFb usage. Here, we used CRISPR/Cas9 genome engineering to substitute the native cysteine with the rodent-encoded tyrosine (C261Y) in the human Jurkat T cell line (E6-1 clone).  We derived two independent Jurkat T cell clones with all endogenous CCNT1 encoding the C261Y substitution.  In an effort to understand net impacts to cellular and viral gene expression, we compared the transcriptomes of uninfected parental Jurkat T cells (E6-1 clone) to the two derived clones (C1 and C2, CCNT1.C261Y).

overall_design: Transcriptome comparison (polyA-enriched RNA-seq) of human Jurkat T cells (E6-1 clone) to two derivative clones (C1 and C2) encoding CCNT1 with an engineered C261Y substitution via CRISPR knock-in.  Total RNA was extracted from three replicate cell cultures.

middle: T

first: Nathan

middle: M

last: Sherer


title: RNASeq of skin tissues by Mesenchymal stem cells treatment on DNCB induced mice model

city: Hangzhou

first: Chunting

last: Hua

state: Zhejiang

address: 3 East Qingchun Road

institute: Sir Run Run Shaw Hospital

summary: Evaluate the therapeutic effects of different delivery route of MSC treantment in DNCB induced atopic dermatitis mice model.

overall_design: 12 Balb/C mice were randomly divided into 4 groups and the hairs of dorsal skin were shaved two days before sensitization. For sensitization, 1% DNCB was applied to the shaved area of the dorsal skin. Mice of the solvent control group were treated with vehicle only (acetone: olive oil = 3:1 v/v). Subsequently, the dorsal skin  were repeatedly challenged with 0.5% DNCB solution. Each mice in the MSC treatment group received the dose of 2×106 MSCs in 100μL culture solution. For scMSC group, 100μL MSC solution were injected subcutaneously in the dorsal skin area. For scivMSC group, 50μL MSC solution were injected subcutaneously in the dorsal skin area and another 50μL MSC solution were injected into tail vein.

first: Hao


title: RNASeq of blood by Mesenchymal stem cells treatment on DNCB induced mice model

overall_design: 12 mice were randomly divided into 4 groups and the hairs of dorsal skin were shaved two days before sensitization. For sensitization, 1% DNCB was applied to the shaved area of the dorsal skin. Mice of the solvent control group were treated with vehicle only (acetone: olive oil = 3:1 v/v). Subsequently, the dorsal skin  were repeatedly challenged with 0.5% DNCB solution. Each mice in the MSC treatment group received the dose of 2×10^6 MSCs in 100μL culture solution. For scMSC group, 100μL MSC solution were injected subcutaneously in the dorsal skin area. For scivMSC group, 50μL MSC solution were injected subcutaneously in the dorsal skin area and another 50μL MSC solution were injected into tail vein.


title: Senescent endothelial cells are predisposed to SARS-CoV-2 infection and subsequent endothelial dysfunction

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

country: Japan

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: The coronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains to spread worldwide. COVID-19 is characterized by the striking high mortality in elderly; however, its mechanistic insights remain unclear. Systemic thrombosis has been highlighted in the pathogenesis of COVID-19, and lung microangiopathy in association with endothelial cells (ECs) injury has been reported by post-mortem analysis of the lungs. Here, we experimentally investigated the SARS-CoV-2 infection in cultured human ECs, and performed a comparative analysis for post-infection molecular events using early passage and replicative senescent ECs. We found that; 1) SARS-CoV-2 infects ECs but does not replicate and disappears in 72 hours without causing severe cell damage, 2) Senescent ECs are highly susceptible to SARS-CoV-2 infection, 3) SARS-CoV-2 infection alters various genes expression, which could cause EC dysfunctions, 4) More genes expression is affected in senescent ECs by SARS-CoV-2 infection than in early passage ECs, which might causes further exacerbated dysfunction in senescent ECs. These data suggest that sustained EC dysfunctions due to SARS-CoV-2 infection may contribute to the microangiopathy in the lungs, leading to deteriorated inflammation and thrombosis in COVID-19. Our data also suggest a possible causative role of EC senescence in the aggravated disease in elder COVID-19 patients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for young and secescent HUVECs with SARS-CoV-2 infection.

first: Koji

last: Ikeda


title: Effects of Mitochondrial Disturbances on Transcriptional Profile of Arabidopsis ucp double mutant plants

city: Botucatu

first: Ivan

middle: Godoy

last: Maia

state: São Paulo

address: Rua Professor Doutor Antonio Celso Wagner Zanin, Instituto de Biociências - UNESP

department: Ciências Químicas e Biológicas (Setor Genética)

country: Brazil

institute: UNESP (Universidade Estadual Paulista "Júlio de Mesquita Filho")

summary: Three genes encoding mitochondrial uncoupling proteins (UCPs) have been described in Arabidopsis thaliana (UCP1 to UCP3). In plants, they are characterized as regulators of oxidative stress, and, for instance, much of the biological data were obtained for the UCP1 and UCP2 isoforms compared with UCP3. To gain further insights, we investigated the transcriptome profiles of ucp1 ucp3 double mutant plants during vegetative phase. We found that the double knockdown of UCP1 and UCP3 promotes important transcriptional reprogramming with clear alterations in the expression of genes related to mitochondrial and chloroplast function as well as those responsive to abiotic stress, suggesting that profound disturbances occur throughout the cell. These findings support a better elucidation for effects of UCP genes and provide insights into the role of UCP3 isoform together with UCP1 in the entire plant.

overall_design: Transcriptome profiles of Col-0 and ucp1 ucp3 double mutant plants using RNA-seq (three biological replicates).

first: R

middle: P

last: Lima

first: J

middle: S

last: Oliveira

first: L

middle: C

last: Nascimento

first: I

middle: G


title: Genome-wide methylation analysis of cerebrospinal fluid circulating tumor DNA: a new biomarker for recurrent glioblastoma [MeDIP-Seq]

city: Beijing

first: Lixin

last: Ma

address: Haidian District

department: Neurosurgery

institute: Sanbo Brain Hospital

type: Methylation profiling by high throughput sequencing

summary: Background: Glioblastoma (GBM) is a common malignancy of the central nervous system (CNS) that is prone to recurrent and has a short survival period. Clinical biomarkers for the diagnosis and prognosis of recurrent GBM are lacking.Methods: We collected 4 cerebrospinal fluid (CSF) samples and 1 normal CSF sample from recurrent GBM, as well as paired tissue samples. Genome-wide methylation profiles of CSF circulating tumor DNA (ctDNA) and tissue mRNA transcription profiles were analyzed, and genes were screened by univariate Cox analysis, Lasso regression analysis, and multivariate Cox analysis by the Chinese Glioma Genome Atlas (CGGA) database. Data analysis and visualization were performed using R software, SPSS software, and Graphpad Prism.Results: By taking the intersection of differentially methylated regions (DMRs) and differentially expressed genes (DEGs), 892 genes were selected for Lasso regression analysis and multivariate Cox analysis, and 12 hub genes were finally screened to construct diagnostic and prognostic models. The diagnostic (AUC=0.982) and prognostic (5-years AUC=0.931) models based on the 12 hub genes had high accuracy.Conclusions: This study reveals that 12 hub genes in CSF ctDNA can diagnose and prognosticate recurrent GBM and provide new biomarkers for clinical research into the mechanisms of GBM recurrent.

overall_design: In this study, we collected cerebrospinal fluid samples as well as matched tumor tissue samples from four patients with glioblastoma, in addition to one normal cerebrospinal fluid sample and one normal brain tissue sample as controls. We sequenced the methylation of four glioblastoma cerebrospinal fluid samples and one normal cerebrospinal fluid sample, and the other four glioblastoma tissue samples and one normal brain tissue sample were sequenced for gene expression profiling.

first: Lin

last: Dai


title: Genome-wide methylation analysis of cerebrospinal fluid circulating tumor DNA: a new biomarker for recurrent glioblastoma

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

overall_design: Refer to individual Series


title: Preliminary Study of the Mechanism of Fenofibrate in the Treatment of Nonalcoholic Fatty Liver Disease based on Bioinformatic Analysis

city: 中国

first: hang

last: chen

state: - 请选择 -

address: 北城街道

institute: 昆明医科大学

summary: The aim of this study was to explore the possible action mechanism of fenofibrate in treating non-alcoholic fatty liver disease (NAFLD) through bioinformatic analysis. Statistical and bioinformatic analyses were conducted through Gene Ontology, Gene Set Enrichment Analysis (GSEA), and Kyoto Encyclopedia of Genes and Genomes (KEGG). The control, high-fat diet (HFD), and HFD + fenofibrate (HFD + Fen) groups were analyzed for differentially expressed genes (DEGs). In the HFD versus control dataset analysis, 493 DEGs were identified, of which 200 were upregulated and 293 were downregulated. In the HFD + Fen versus HFD dataset, 449 DEGs, comprising 376 upregulated and 73 downregulated genes, were observed. Two KEGG pathways and one key gene were identified. The key gene mup family appeared to mediate the mechanism underlying NAFLD. Treatment of NAFLD with fenofibrate may occur through the core gene mup.

overall_design: Thirty mice were randomly assigned to a control group (n = 10), high-fat group (n = 10), and fenofibrate treatment group (n = 10). The high-fat and fenofibrate treatment groups received a 14-week high-fat diet intervention. The control group was on a normal diet for 14 weeks. After 10 weeks, the fenofibrate treatment group received fenofibrate gavage treatment, and then continued to receive a high-fat diet for 4 weeks. After 14 weeks, the liver tissues were collected. RNA/DNA extraction was performed to build a library, and liver transcriptome sequencing (RNA-Seq) was performed.

first: Hang

first: Dan

last: Zhang

first: Jian-jun

last: Liu

first: Lan-qing


title: TFCP2 is a transcriptional regulator of heparan sulfate assembly and melanoma cell growth

city: Athens

first: Ryan

middle: Joseph

last: Weiss

state: GA

address: 315 Riverbend Road

department: Biochemistry and Molecular Biology

institute: University of Georgia

summary: Heparan sulfate (HS) is a long, linear polysaccharide that is ubiquitously expressed in all animal cells and plays a key role in many cellular processes, including cell signaling and development. Dysregulation of HS assembly has been implicated in pathophysiological conditions, such as tumorigenesis and rare genetic disorders. HS biosynthesis occurs in a non-template driven manner in the endoplasmic reticulum and Golgi through the activity a large group of biosynthetic enzymes. While much is known about its biosynthesis, little is understood about the regulation of HS assembly across diverse tissue types and disease states. To address this gap in knowledge, we recently performed genome-wide CRISPR/Cas9 screens to identify novel regulatory factors of HS biosynthesis. From these screens, we identified the alpha globin transcription factor, TFCP2, as a top hit. To investigate the role of TFCP2 in HS assembly, we targeted TFCP2 expression in human melanoma cells using the CRISPR/Cas9 system. TFCP2 knockout cells exhibited decreased fibroblast growth factor binding to cell surface HS, alterations in HS composition, and slowed cell growth compared to wildtype cells. Additionally, RNA sequencing revealed that TFCP2 regulates expression of multiple enzymes involved in HS assembly, including the secreted endosulfatase, SULF1. Pharmacological targeting of TFCP2 activity similarly reduced growth factor binding and increased SULF1 expression, and knockdown of SULF1 expression in TFCP2 mutant cells restored melanoma cell growth. Overall, these studies identify TFCP2 as a novel transcriptional regulator of HS and highlight HS-protein interactions as a possible target to slow melanoma growth.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for A375 cells and TFCP2 knockout cell derivatives


title: Effect of RIG-I activation and thymidine phosphorylase inhibition using Tipiracil on gene expression of human endothelial cells.

city: Portland

first: sudarshan

last: anand

address: 2720 S Moody Ave

department: CDCB

institute: oregon health & science university

summary: To investigate the role of RIG-I activation and thymidine phosphorylase inhibition human endothelial cells, we used a dsRNA agonist on HUVECs and HMVECs to activate RIG-I signaling, and further treated with tymp inhibitor TPI. We then performed differential gene expression analysis using data obtained from RNA-seq from each treatment group.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUVEC and HMVECs treated with a control or RIG-I agonist and Tipiracil.

first: Baris

last: Adrian

first: Fraile-Bethencourt

last: Eugenia

first: Khou

last: Sokchea

first: Anand

last: Sudarshan


title: Transcriptome Profiling Reveals the Progression of Primary Pneumonic Plague

first: Yifeng

last: Wang

state: China

address: Feitai region Dongda road

institute: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology

summary: The global transcriptome profile of lung tissue in mice after exposure to aerosolized yersinia pestis  strain 201

overall_design: Lung mRNA profiles of 8 week-old females wild type (WT) mice infected with yersinia pestis strain 201 for 0,24,48,and 72 hours post infection

last: Xiao

first: Huiying

last: Yang

first: Erhei


title: Protective effect of Cyanidin on Myocardial infraction mice

city: GuangZhou

first: Gang

last: Deng

address: 106 Zhongshan Er Road, Guangzhou, P.R

institute: Guangdong Provincial People's Hospital

summary: Myocardial infarction (MI) is a worldwide disease with high morbidity and mortality and a major cause of chronic heart failure, seriously affecting patients' quality of life. Natural medicine has been used to cure or prevent cardiovascular disease for decades. As a natural flavonoid, Antocyanide has been used to treat many diseases due to its antioxidative, anti-inflammatory, and others. However, the molecular mechanism of Cyanidin (Cyn) in MI is not precise. As demonstrated by the result, after MI, some genes such as Fibronectin 1(Fn1) and Matrix metalloproteinases (MMP2/9) is highly overexpressed, and Cyn protects myocardial cell apoptosis by regulating these genes. These results were warranted by autodocking simulation.

overall_design: We performed RNA sequencing analysis derived from mouse infarcted cardiac tissues or normal left ventricle (LV).

first: Deng

last: Gang

first: Moussa

middle: I

last: Nasser

first: Zhu

last: Ping


title: Gene expression profile at single cell level of GFP labeled islet β cells from streptozotocin (STZ) treated Ins/β-lineage-labeled  mice

city: Nanjing

first: Yu

last: Qian

state: Jiangsu

address: 300 Guangzhou Road

department: Department of Endocrinology

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Islet β cells suffer from de- and trans-differentiation after injury. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of β cells in from STZ-induced diabetes.

overall_design: Ins/β-lineage-labeled (Ins1-CreERT; Rosa26-mT/mG) mice underwent 5-day STZ treatment after 5-day tamoxifen (TAM) treatment and 2-wk washout. At 12wk after STZ treatment, islets were isolated and dispersed into single cells. GFP positive cells were isolated by Fluorescence-activated cell sorting (FACS)  and analyzed using scRNAseq.

first: Heming

last: Jiang

first: Qi

last: Fu


title: Inhibition of H3K9me2-specific histone methyltransferase, G9a/GLP, reveals transcripts regulated by the establishment of H3K9me2 in hematopoietic stem and progenitor cells

city: Duarte

first: Dustin

middle: E.

last: Schones

state: CA

address: 1500 E Duarte, 2131B North Gonda

institute: Beckman Research Institute of the City of Hope

summary: We have performed RNA-seq from DMSO control treated, G9a/GLP inhibitor (UNC0638) treated, and DNA-demethylating agent (Decitabine) treated CD34+ hematopoietic stem and progenitor cells. This experiment was performed to identify transcripts that were uniquely affected by the loss of H3K9me2 in hematopoietic stem and progenitor cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for CD34+ hematopoietic stem and progenitor cells treated with DMSO, UNC0638, or Decitabine

first: Michael

last: Lee


title: RAV1 and BES1 mutually inhibit each other’s expression and oppositely co-regulate the genes for growth and defense in Arabidopsis

city: Seoul

first: DAMI

last: YANG

address: Cheonpa-ro 47 gil 100, Yongsan-gu

department: Department of Biological Sciences

country: South Korea

institute: Sookmyung Women's University

summary: RAV1 (RELATED TO ABI3/VP1) is a plant-specific B3 domain and AP2 domain-containing transcription factor and acts as a negative regulator of growth in many plant species. Expression of the RAV1 was down-regulated by BR, and through the large-scale transcriptome analyses its expression was previously shown to be targeted by BES1 and BZR1 that are critical transcription factors for BR-signaling process. Using the RAV1-overexpressing transgenic plants, here we showed that RAV1 overexpression reduced BR signaling capacity, resulting in the up-regulation of BR biosynthetic genes and down regulation of BES1 expression. Furthermore, we demonstrated that BES1, not BZR1, directly bound to the RAV1 promoter and repressed RAV1 expression, and vice versa, RAV1 also bound to the BES1 promoter and repressed BES1 expression. This mutual inhibition was specific to between RAV1 and BES1, because RAV1 showed binding activity to BZR1 promoter but did not repressed BZR1 expression. To validate this mutual inhibition of RAV1 and BES1, we generated transgenic bes1-D plants overexpressing RAV1 and observed that constitutively activated BR-signaling phenotypes in bes1-D were attenuated due to the repression of endogenous BES1 expression. To investigate transcriptomic expressional changes that are regulated by RAV1 and BES1, we performed RNA-sequencing analysis from RAV1-overexpressing transgenic plants and bes1-D mutant plant. We identified differentially expressed genes (DEGs) by RAV1 and BES1, respectively, as well as the genes that are oppositely co-regulated by RAV1 and BES1. And we found that RAV1 and BES1 regulate different transcriptome but co-regulate a specific set of genes that are responsible for the balance between growth and defense. Taken together, these results suggested that mutual inhibitory transcriptional activities of the RAV1 and BES1 provide fine regulatory mechanisms for plants growth and development mediated by BR signaling.

overall_design: Examinination of mRNA expression patterns in Arabidopsis RAV1 over-expression lines and bes1-D mutants

first: Dami

first: Hyun-young

last: Shin

first: Hyun

middle: K

last: Kang

first: Yun

last: Shang

first: So

middle: Y

last: Park

first: Dong-Hoon

last: Jeong

first: Kyoung

middle: H

last: Nam


title: Dorsal hippocampal transcriptome analysis after Auditory Fear Conditioning and pharmacological GR modulation

city: Leiden

first: Jacobus

middle: Cornelis

last: Buurstede

state: Zuid-Holland

address: Albinusdreef 2

department: Endocrinology

country: Netherlands

institute: Leiden University Medical Center

summary:
Aim: We investigated the role of GR in Auditory Fear Conditioning memory consolidation by application of a pharmacological filter using selective glucocorticoid receptor modulators.
Methods: Adult male mice were exposed to Auditory Fear Conditioning training and subsequently injected with 3.0 mg/kg corticosterone, 20 mg/kg CORT108297, 80 mg/kg CORT118335, 40 mg/kg RU486 or vehicle. Dorsal hippocampi were dissected 3 hours after injection and snap-frozen. Total RNA was isolated and send for 100bp paired-end sequencing by BGI.

overall_design: Hippocampal mRNA profiles of male mice after Auditory Fear Conditioning combined with multiple GR-ligands.

first: Onno

last: Meijer


title: Triple therapy reduced metastasis in triple-negative breast cancer.

city: Shanghai

first: Dawei

last: Wang

address: 197 Ruijin Road II

institute: Shanghai Jiao Tong University School of Medicine

summary:
Purpose: To understand the underlying mechanisms of oncolytic virus therapy in breast cancer.
Methods: The primary tumors of 4T1 in BALB/C mice were exstracted and analyzed by RNA-seq.
Results: In consistent with previous studies, we found some anti-tumor factors were up-regulated. Interestingly, several immunosupressive genes were activited.
Conclusion: Our study identified the intercellular and intracellular factors restricting the optimized oHSV efficacy and supported the rationally designed triple therapy for clinical translation.

overall_design:
Breast tumors in BALB/C mice were extracted, followed by RNA-seq. There were 4 groups, and 4 mice per group.
Control group: Intratumoral and intraperitoneal injection of PBS.
Ab group: Intraperitoneal injection of PD-1 antibody.
Dual group: Intratumoral injection of oHSV and intraperitoneal injection of OLA.
Triplet group: Intratumoral injection of oHSV and intraperitoneal injection of OLA and PD-1 antibody.

first: Yujia

last: Cai

first: Yiye

last: Zhong


title: Conserved transcriptional connectivity of regulatory T cells in the tumor microenvironment informs novel combination cancer therapy strategies [mouse]

city: New York

first: Dana

last: Pe'er

state: NY

address: 417 E 68th St

department: Computational and Systems Biology

institute: Memorial Sloan Kettering Cancer Center

summary: While regulatory T (Treg) cells are traditionally viewed as professional suppressors of antigen presenting and effector T cells in both autoimmunity and cancer, recent findings of distinct Treg functions in tissue maintenance suggest that their regulatory purview extends to a wider range of cells and is broader than previously assumed. To elucidate tumoral Treg “connectivity” to diverse tumor-supporting accessory cell types, we explored immediate early changes in their single cell transcriptomes upon punctual Treg depletion in experimental lung cancer and injury-induced inflammation. Prior to any notable T cell activation and inflammation, fibroblasts, endothelial and myeloid cells exhibited pronounced changes in their gene expression in both cancer and injury settings. Factor analysis revealed shared Treg-dependent gene programs, foremost, prominent upregulation of VEGF signaling-related genes upon Treg deprivation in either setting, as well as in Treg-poor vs Treg-rich human lung adenocarcinomas. Accordingly, punctual Treg depletion combined with short-term VEGF blockade showed markedly improved control of PD-1 blockade-resistant lung adenocarcinoma progression in mice compared to the corresponding monotherapies, highlighting a promising factor-based querying approach to elucidating novel rational combination treatments of solid organ cancers.

overall_design:
Three mouse sets of data are deposited.
1. KP Lung Adenocarcinoma and stromal cells were collected from KrasLSL-G12D/WTTrp53fl/fl  Foxp3GFP-DTR  (KP-DTR) mice harboring ~3 months old Adenicarcinomas, following 48 hr treatment with Diphteria toxin (DT) to deplete Tregs, or PBS as control. Cells were isolated by Fluorescence-activated cell sorting (FACS), gating on CD45, CD31, GP38, MHCII CD11b, GR1 CD4 and CD8 and analysed by Bulk RNA-seq (08820, 08233)
2. KP Lung Adenocarcinoma and stromal cells were collected from KrasLSL-G12D/WTTrp53fl/fl  Foxp3GFP-DTR  (KP-DTR) mice harboring ~3 months old Adenicarcinomas, following 48 hr treatment with Diphteria toxin (DT) to deplete Tregs, or PBS as control. Cells were isolated by FACS gating on CD45- and CD45+ signal and analyzed using scRNAseq (07734).
3. KP-DTR mice were treatead with bleumycine for 21 days, followed by 48 hr treatment with Diphteria toxin (DT) to deplete Tregs, or PBS as control. Cells were isolated by FACS gating on CD45- CD45+ and EpCAM+ signal and analyzed using scRNAseq (10506)

first: Ariella

last: Glasner

first: Samuel

middle: A

last: Rose

first: Roshan

last: Sharma

first: Herman

last: Gudjonson

first: Jesse

last: Green

first: Sham

last: Rampersaud

first: Isabella

last: Valdes

first: Michail

last: Schizas

first: Stanislav

last: Dikiy

first: Alejandra

last: Mendoza

first: Wei

last: Hu

first: Zhong-min

first: Alexander

last: Rudensky


title: Translation initiation of the MgtL leader peptide is essential for the expression of mgtA in Escherichia coli

city: Sherbrooke

first: Eric

last: Massé

state: QC

address: 3201, Jean Mignault

department: Biochemistry

country: Canada

institute: University of Sherbrooke

summary: Riboswitches are cis-acting regulating RNA elements mostly found in the 5’-UTR of bacterial mRNAs. The Salmonella enterica mgtA riboswitch controls mgtA expression upon the sensing of intracellular Mg2+ ions. A leader peptide (MgtL) is contained within the mgtA riboswitch and its translation has been previously shown to be affected by Mg2+ concentrations. The current regulatory model suggests that the efficiency of MgtL translation is inversely related to mgtA transcription. Herein we show that the orthologue mgtA riboswitch of Escherichia coli also contains a leader peptide but, unlike S. enterica, that its translation is proportionally related to mgtA expression. Our results also suggest that ribosome stalling at mgtL is crucial for mgtA expression. Together, our results indicate that in E. coli, the expression of the MgtL leader peptide and mgtA are positively coordinated according to the intracellular Mg2+ concentration, a unique mechanism among known riboswitches.

overall_design: Comparative ribosome profiling analysis for escherichia coli k-12 under 20 µM MgSO4 and 50 µM MgSO4.

first: Mélanie

last: Geffroy

first: Anne

last: Stringer

first: Philippe

last: Balthazar

first: Karine

last: Prévost

first: Joseph

last: Wade

first: D

last: Lafontaine


title: Effects of e-cigarette smoke on transcription profiles of PASMCs and AECII in mice

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

summary: Cigarette smoke is a major risk factor for the development and progression of chronic obstructive pulmonary disease. Tobacco smoking is also the main cause of lung cancer and the main preventable cause of other lung and heart disease. Strategies to eliminate cigarette smoking have led to the emergence of new tobacco-related products as alternatives for cigarette smoking or tools for smoking cessation. Electronic cigarettes (E-cigarettes) have been introduced to the market in recent years as an alternative to smoking conventional cigarettes. E-cigarettes are nicotine delivery devices by heating and converting to aerosol a liquid mixture composed of propylene glycol, vegetable glycerine, flavouring chemicals, and nicotine.   Despite the lack of appropriate studies, e-cigarettes are nowadays widely used and advertised as safe cigarette replacements and the number of users is rapidly growing. Unlike cigarette smoke, where the determinant effects are well studied and documented, very limited amount of research has been done on the health effects and public health of e-cigarettes.   The study aims to investigate the effects of e-cigarette vapour extract on gene expression in different primary isolated mouse lung cells [pulmonary arterial smooth muscle cells (PASMC) and alveolar epithelial type two cells (AECII)]. The cells will be exposed to e-cigarette vapour extract (ECVE).

overall_design: Two cell types were treated with 3 conditions. Cells were isolated from 8 mice.

first: Elsa

last: Tadele

first: Norbert

last: Weissmann


title: Effect of hepatic depletion of Ftcd on gene expression during hepatocarcinogenesis in DEN-induced and untreated C57BL/6 mice

first: Siying

last: Wang

address: No.25, Lane 2200 Xie-Tu Road.

summary:
To investigate the global function of Ftcd in the regulation of hepatocarcinonegesis, we established DEN-induced or untreated liver-specific Ftcd knockout(referred as Ftcd LKO) murine model in which Ftcd has been knocked out by loxp/alb-cre system, take the wildtype(referred as WT) mice as control.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 different Ftcd LKO mice and 6 different WT mice at 12 months after DEN treatment, as well as RNA-seq of 3 different 12-month-old Ftcd LKO and WT mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for tumourous tissues or nontumorous liver tissues from Ftcd LKO mice or WT littermates with or without DEN treatment

first: Haojie

last: Jin


title: circRNAs microarray analysis in plasma of Parkinson’s Disease

city: Huai'an

first: Lingling

last: Zhong

address: Huanghe Road West

institute: The affiliated Huai’an No. 1 People’s Hospital of Nanjing Medical University

type: Non-coding RNA profiling by genome tiling array

summary: Parkinson's disease (PD) is a chronic and progressive degenerative disease of the central nervous system. Degenerative neuropathy can occur in patients with PD even before typical clinical symptoms appear in the preclinical stage. Therefore, if the early diagnosis of degenerative diseases can be timely and the correlation with the disease progression can be explored, the disease progression will be slowed down and the quality of life of patients will be improved. In this study, the circRNA microarray was employed to screen the dysregulated circRNA in plasma samples of PD

overall_design: CapitalBio Technology Human CircRNA Array v2 was designed with four identical arrays per slide (4 x 180K format), with each array containing probes interrogating about 170,340 human circRNAs. Those circRNA target sequences were all from Circbase，Deepbase and Rybak-Wolf20151. Each circRNA was simultaneous detected by a long probe and a short probe. The circRNA array also contain 4974 Agilent control probes.The circRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998). Finally, we performed tree visualization by using Java Treeview (Stanford University School of Medicine, Stanford, CA, USA).


title: Genome-wide methylation analysis of cerebrospinal fluid circulating tumor DNA: a new biomarker for recurrent glioblastoma [mRNA-Seq]

first: Lixin

last: Ma

summary: Background: Glioblastoma (GBM) is a common malignancy of the central nervous system (CNS) that is prone to recurrent and has a short survival period. Clinical biomarkers for the diagnosis and prognosis of recurrent GBM are lacking.Methods: We collected 4 cerebrospinal fluid (CSF) samples and 1 normal CSF sample from recurrent GBM, as well as paired tissue samples. Genome-wide methylation profiles of CSF circulating tumor DNA (ctDNA) and tissue mRNA transcription profiles were analyzed, and genes were screened by univariate Cox analysis, Lasso regression analysis, and multivariate Cox analysis by the Chinese Glioma Genome Atlas (CGGA) database. Data analysis and visualization were performed using R software, SPSS software, and Graphpad Prism.Results: By taking the intersection of differentially methylated regions (DMRs) and differentially expressed genes (DEGs), 892 genes were selected for Lasso regression analysis and multivariate Cox analysis, and 12 hub genes were finally screened to construct diagnostic and prognostic models. The diagnostic (AUC=0.982) and prognostic (5-years AUC=0.931) models based on the 12 hub genes had high accuracy.Conclusions: This study reveals that 12 hub genes in CSF ctDNA can diagnose and prognosticate recurrent GBM and provide new biomarkers for clinical research into the mechanisms of GBM recurrent.

overall_design: In this study, we collected cerebrospinal fluid samples as well as matched tumor tissue samples from four patients with glioblastoma, in addition to one normal cerebrospinal fluid sample and one normal brain tissue sample as controls. We sequenced the methylation of four glioblastoma cerebrospinal fluid samples and one normal cerebrospinal fluid sample, and the other four glioblastoma tissue samples and one normal brain tissue sample were sequenced for gene expression profiling.

first: Lin

last: Dai


title: Per- and Polyfluoroalkyl Substances Cause Changes in MicroRNA Expression within Extracellular Vesicles

city: Chapel Hill

first: Kyle

last: Roell

address: 135 Dauer Drive

institute: University of North Carolina Chapel Hill

summary: These analyses set out to evaluate changes in microRNA signatures within extracellular vesicles isolated from liver cells exposed to a mixture of PFAS.

overall_design: We tested an equimolar mixture containing three PFAS compounds: PFHxA, PFOA, and PFOS; with each individual chemical at a concentration of 35uM. This PFAS mixture was used to treat HepG2 cells with a 24 hour time-point. Media was subsequently collected and used to isolate extracellular vesicles, enriching for exosomes. MicroRNA was extracted from isolated exosomes and sequenced to evaluate changes in expression associated with exposure.

first: Celeste

last: Carberry

first: Lauren

middle: E

last: Koval

first: Julia

last: Rager


title: Ferroptosis-related Gene Signature Predicts Glioma Cell Death and Glioma Patient Progression

first: hanjie

last: liu

address: Nansihuanxi street，NO.119

institute: 1. Beijing Neurosurgical Institute and Beijing Tiantan Hospital

summary: cell culture:The human glioma cell line U87MG was obtained from the Cell Resource Center, Peking Union Medical College (Beijing, China), and U251MG was acquired from the American Type Culture Collection (Manassas, VA). Temozolomide (TMZ) resistant U87MG cells (U87TR) and TMZ resistant U251MG cells (U251TR) of glioblastoma (GBM) sub-cell lines, were established through repetitive exposure to increasing TMZ concentrations in vitro in our laboratory. Cells were cultured in DMEM culture medium supplemented with 10% FBS with a standard humidified incubator under 5% CO2 at 37°C.

overall_design: RNA sequencing of glioma cell lines:Total RNA from U251MG, U87MG, U251TR and U87TR cell lines were extracted and quantified. A total amount of 3 μg RNA per sample was used as input material for library preparation. The library preparations went through standard Illumina Hiseq platform and 150 bp paired-end reads from transcriptome sequencing were generated. After quality control procedures, the data were mapped to human hg38 reference by STAR (Dobin et al., 2013).

first: Tao

last: Jiang

first: Hanjie

last: Liu


title: miRNA regulated by Xanthohumol is linked to  cognitive impairment in mice

city: Shaanxi

first: Yang

address: Yangling

institute: Northwest A&F University

summary: To explore whether the cognitive effect  of xanthohumol on mice is affected by the hypothalamic-pituitary-gonad system, and  to fully reveal the potential regulatory mechanism of xanthohumol on mice cognition,   we performed RNA-seq, miRNA-seq, and real-time qPCR to distinguish expression  differences between xanthohumol and saline treated mice brain cells in both HPG dysfunction/normal conditions.This study provides comprehensive miRNA and mRNA expression profile data of  xanthohumol and saline treated mice brain cells in HPG dysfunction and normal  conditions, which advances our understanding of the regulation of cognitive impairment mediated by miRNA.

overall_design: Hippocampal tissues of ovariectomized and sham-operated mice treated with xanthohumol and normal saline

first: Zezhi

last: Li

first: Jingcheng

last: Zhang

first: Xin

last: Yang

first: Yuhe

last: Qiao

first: Caixia

last: Feng

first: Shengze

last: Yu

first: Hui

last: Jing

first: Wenjuan

first: Li

last: Ren

first: Qimei

last: Duan

first: XiaoQiang

first: Wei

last: Cao


title: Comprehensive analysis of the immune implication of NOTCH1 gene in stomach adenocarcinoma

city: Fuzhou

first: Liangqing

address: No 20, ChaZhong Road, TaiJiang District, Fuzhou 350000, China.

institute: The First Affiliated Hospital of Fujian Medical University

summary: In order to better understand the relationship between NOTCH1 gene and immunity in gastric adenocarcinoma cells, we performed the silent interference of NOTCH1 gene on three gastric adenocarcinoma cell lines AGS, MKN-45 and MGC-803. We extracted the total RNA from the interfered and untreated blank control cells, and performed lncRNA library construction and sequencing. The results of bioinformatics analysis showed that the silencing of NOTCH1 gene in gastric adenocarcinoma cells activated several immune-related signal transduction pathways, including T cell receptors, chemokines, JAK-STAT, Toll-like receptors, ECM receptors and other signals. Conduction pathway. These results confirm that NOTCH1 may down-regulate the immune response of gastric adenocarcinoma.

overall_design: cell lines AGS, MKN-45 and MGC-803（ NOTCH1 interfered and untreated blank control） were used for RNA sequencing.

first: L


title: IFN-γ induces ZEB1 expression through STAT1-dependent upregulation of JMJD3 to promote lung adenocarcinoma cell aggressiveness

city: Wuhan City

first: jianjian

last: yang

address: No. 1095, Jiefang Avenue, Wuhan City, Hubei Province

department: Department of Thoracic Surgery

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China.

summary: Active IFN-g signaling is a common feature of tumors responding to PD-1 checkpoint blockade. IFN-g exhibits both anti- and pro-tumor activities. Here, we demonstrated that IFN-g induced ZEB1 expression and promoted epithelial-to-mesenchymal-transition in lung adenocarcinoma cells. ZEB1 was required for IFN-g-promoted EMT, cell migration, and metastasis. We performed a transcriptome analysis using RNA-seq to comprehensively describe the altered epithelial cell phenotype following IFN-g treatment.

overall_design: A549 and HCC827 cells were treated with 100 IU/ml IFN-g for 1h, 8h, and 24h, respectively. total RNA of A549 and HCC827 cells was harvested and analyzed by RNA sequencing (RNA-seq)

first: Jianjian

first: Lequn

first: Xiangning

last: Fu


title: lncSLCC1(RP11-400N13.2)-regulated genes in Colorectal Cancer

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

summary: To investigate the global genes regulated by lncRNA-SLCC1(RP11-400N13.2), high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between DLD-1 cells transfected with control siRNA or lncSLCC1 siRNA.

overall_design: RNA-seq was performed in DLD-1 colorectal cancer cells after control siRNA or lncSLCC1 siRNA transfection

first: Yan

last: Tingting


title: CD11c+ Dendritic cells from MLN in MC38 tumor bearing WT or Myd88-knockout mice treated with LGG combined with anti-PD-1

city: Beijing

first: Liangliang

last: Wang

address: #30 Shuangqing Road

institute: Tsinghua University

summary: We treated WT or Myd88-knockout mice bearing MC38 tumors with oral administration of live LGG combined with anti-PD-1 antibody or not . CD11c+ DCs were isolated from MLN and then RNA-seq performed. The goals of this study are to identify the activated cellular pathways in DCs with oral administration of live LGG or the combination treatment. Samples were sequenced on an Illumina Hiseq instrument. The short sequence reads were aligned to mouse mm10 reference genome using STAR (2.4.0) and then assembled and quantified by HTSeq (0.6.1) with Gencode M8 as annotation. DESeq2 was used for differential gene expression analysis among subgroups. Hierarchical clustering and principal component analysis were plotted applying FactoMineR and gplots libraries in R. log2 [FPKM] was calculated for each gene. We found that cytokine-related pathways, response to interferon pathway and T cell activation pathway were activated in combination treatment group  and Response to interferon beta pathways was activated when LGG alone treated.

overall_design: Examination of CD11c+ DCs isolated from MLN in MC38 tumor bearing WT or Myd88-knockout mice treated with LGG, anti-PD-1 or anti-PD-1 plus LGG.  Both conditions were run in triplicate.

first: Xin

last: Zhao

last: Si


title: AHR regulated genes in Colorectal Cancer

summary: To investigate the global genes regulated by AHR, high-throughput mRNA sequencing (RNA-Seq) was performed to compare the expression profile between DLD-1 cells transfected with control siRNA or AHR siRNA.

overall_design: RNA-seq was performed in DLD-1  colorectal cancer cells after control siRNA or AHR siRNA transfection


title: Expression data from human normal fibroblasts (NFs) and cancer associated fibroblasts (CAFs) [HTA-2_0]

first: Junlong

last: Zhuang

address: 321# Zhongshan Road

institute: Institute of Urology, Drum Tower hospital

summary:
CAFs are the major regulators in tumor microenviroment which promote cancer progression. We want to know which mRNAs changed in human CAFs compared to NFs.
We used microarrays to detail the mature mRNA expression and identified distinct classes of 2-fold changed mRNAs during this process.

overall_design: NFs and CAFs were isolated from human bladder cancer tissues. And cells were used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jun

last: Yan


title: Cell-sorted monoytes from PR8-infected mice

city: Grand Forks

first: Danielle

last: Perley

state: North Dakota

address: 1301 N Columbia Rd

institute: University of North Dakota Genomics Core

summary: Primary monocytes from PR8-infected mice were magnetically sorted and processed for RNA-sequencing

overall_design: Mice were infected with 250 PFU PR8 and 7 days post-infection, lungs were harvested and processed to produce single cells. Single cells were magnetically sorted using Miltenyi Biotech's enrichment kit and purity was assessed via flow cytoemtry.

first: M

middle: N

last: Khan

first: Ganesh

last: Ambigapathy

first: Mitchell

last: Klomp


title: RNA sequencing identifies key differences in patient derived xenograft models of primary and metastatic pediatric neuroendocrine tumors

city: Birmingham

first: Colin

middle: Quinn

last: Quinn

state: AL

address: 1670 University Blvd, Room 662

department: Surgery

institute: University of Alabama at Birmingham Heersink School of Medicine

summary: Here we report the RNA sequence of a primary patient-derived xenograft neuroendocrine tumor and compare it to the RNA sequence of an intraperitoneal metastatic tumor that was established using the respective primary tumor. Using this data, we identified key differences that validated the metastatic tumor to indeed have a more mestatic genotype. Noteworthy differences were the upregulation of matrix metalloproteinases and downregulation of PTK2, both associated with metastatic neuroendocrine tumors in patients. Furthermore, we found upregulated pathways that could potentially be targeted through  small molecule inhibition. One such example is ERK1/2 had a higher expression in the metastatic tumor and using a MEK inhibitor, were able to successfully deplete metastasis of the tumor in an in vivo model. These data will be helpful in translating the therapeutics tested to a clinical arena.

overall_design: Examination of RNA in a primary versus a metastatic pediatric neuroendocrine patient-derived xenograft tumor.

first: Elizabeth

last: Beierle


title: RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic

city: Tianshui

first: Fang

last: Ma

state: Qinzhou District

address: South Xihe Road

department: College of Bioengineering and Technology

institute: Tianshui normal university

summary:
Purpose:Our data significantly advance understanding of probiotic regulatory mechanism of miRNA in  ileum of Taiping chicken
Methods: Using RNA-seq analysis to study the gene expression in ileum tissue after Taiping chicken was given probiotics
Results: A total of 164,629,826 and 156,180,764 raw reads were generated from the CT and MP, respectively. After removing the interference data, about 164,028,872 and 155,579,470 clean reads were obtained
Conclusions: through high-throughput sequencing of the six libraries from ileum of Taiping chicken, the expression level of mRNA has significant changes after  given probiotics

overall_design: Control group (CT), birds were fed a corn-soybean basal diet , Probiotics group (MP), birds were given a basal diet supplemented with 2 mL of probiotics per litre of water


title: A Transcriptomic Snapshot of Labor Timing and Development in Human Decidua

city: Los Angeles

first: Amal

last: Katrib

address: 609 Charles E Young Dr E

institute: University of California, Los Angeles

summary:
Introduction: Disruption in the synergistic machinery of human parturition can cascade into an ill-timed onset of labor, jeopardizing pregnancy outcomes and contributing to perinatal morbidity and mortality. Parturition is invoked by a phenotypic shift towards a pro-inflammatory predominant state; however, the mechanistic underpinnings as well as tissue-specific role and pathophysiological implications remain elusive. Predicting labor trajectory is further hindered due to confounding by concurrent processes either unrelated or exclusive to advancing gestation. It is thus critical to employ a strategic plan when probing the genetic and environmental tug-of-war that underlies parturition.
Methods: We collected human deciduas to explore the genetic control of inflammation within the immunologically-distinct part of the placenta. We performed a genome-wide profiling of the trascriptome to incorporate environmental and fetal stimuli effects on phenotypic divergence. Samples were segregated into term labor (n=16), premature labor (n=16), and nonlaboring C-section (n=18) to distinguish between factors governing gestation duration and those involved in the final pathway of labor. Leveraging the high resolution of next-generation sequencing, we analyzed gene-, isoform-, and network scale-level variability across labor states and then interrogated clinical traits to extract key players in labor timing and development.
Results: All samples exhibited a global upregulated expression of adhesion, vascular, humoral, and endocrine genes enriched in the placenta and critical to pregnancy sustenance. Nonlaboring deciduas revealed the most divergent transcriptional landscape, with significant enrichment for dysregulated vacular extracellular matrix remodeling and muscle contractility. Premature deciduas showed a more prominent immune-mediated fetal rejection, infection response, and lipid metabolism signature.
Conclusion: Our study provides a comprehensive steady-state snapshot of co-/post-transcriptional changes across various modes of parturition. Using multilayered analytics, it suggests the withdrawal of immune suppression at the maternal-fetal interface during labor development, a process that is further enhanced with pre-existing intrauterine infection and systemic stress to potentially modulate labor timing.

overall_design: Comprehensive examination of 50 mRNA profiles of human decidual samples collected following birth from normal spontaneous vaginal (n=16), cesarean section (n=18), and preterm (n=16) pregnancy cases.

first: Jinsil

last: Kim

first: Lan

last: Lin

first: Jeffrey

last: Murray

first: Yi

last: Xing


title: Stress resilience-enhancing drugs preserve tissue structure and function in degenerating retina via selective phosphodiesterase inhibition

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

summary: To determine the gene expression changes in the retina of Abca4-/-Rdh8-/- (dKO) mice, we collected retina samples from dKO animals under various experimental conditions, generated single-cell suspensions, and performed scRNA-Seq (10X Genomics).

overall_design: In each of the five experimental groups, four retinae from two mice were pooled to prepare single-cell suspensions at a final concentration of 1,000 cells/µl. For each group, freshly dissociated cells (~15,000) were loaded into a 10x Genomics Chromium Single Cell system using v3 chemistry following the manufacturer's instructions.

first: Jennings

last: Luu

first: Henri

last: Leinonen

first: Elliot

last: Choi


title: Blood RNA profiling after an RNA editor-exonuclease axis perturbation

city: Boston

first: Areum

last: Han

state: MA

address: Karp Family Building, 7th Floor. 300 Longwood Ave.

institute: Boston Children's Hospital

summary: The goal of this study is to reveal the role of the RNA editor-exonuclease axis during erythropoiesis. We bled E18.5 Zcchc6-/- and Dis3l2-/- mice and profiled transcriptome of their mature red blood cells/reticulocytes.

overall_design: mRNA profiles of mature red blood cells/reticulocytes (TER119+) of E18.5 Zcchc6-/- and Dis3l2-/- and corresponding wild type mice.

first: Michael

last: Morse

first: Brianna

last: Hilton


title: Direct Induction of Trophoblast Stem Cells from Human Fibroblasts

city: Jerusalem

first: Yosef

last: Buganim

address: Jerusalem, IMRIC-Hadassah Medical School

department: Developmental Biology and Cancer Research

country: Israel

institute: HUJI

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

overall_design: Refer to individual Series


title: Direct Induction of Trophoblast Stem Cells from Human Fibroblasts (RRBS)

summary: Transcription profile analysis revealed similarity/dissimilarity between human blastocyst derived trophoblast stem cells (hbdTSCs), human induced trophoblast stem cells (hiTSCs), human foreskin fibroblasts (HFFs) and pluripotent stem cells (hESCs, hiPSCs)

overall_design: HFFs reprogrammed into hiTSC lines by transient ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) were subjected to RRBS-protocol to assess differentially methylated regions, along with samples of HFFs, hbdTSCs, hESCs and hiPSCs


title: Direct Induction of Trophoblast Stem Cells from Human Fibroblasts (RNA-seq)

overall_design: HFFs reprogrammed into hiTSC lines by transient ectopic expression of GATA3, OCT4, KLF4, MYC (GOKM) were subjected to RNA-seq, along with samples of HFFs, hbdTSCs, hESCs and hiPSCs


title: Microarray expression profiles of circular RNA in malignant pleural effusion

first: Ziliang

last: Hou

state: Beijing

address: NO.82 Xinhuananlu, Tongzhou District

department: PCCM

institute: Beijing Luhe Hospital

summary: To explore the expression pattern of circular RNAs (circRNAs) and their biological functions in malignant pleural effusion, we surveyed the circRNA expression profiles of 3 lung adenocarcinoma-associated malignant pleural effusion (LA-MPE) and 3 tuberculous pleural effusion (TPE) from clinical patients using Clariom D human microarray.

overall_design: The pleural effusions were divided into two experimental groups: test group (LA-MPE) and control group (TPE). After being centrifuged, the cell pellets were resuspended in TRIzol reagent to extract the total RNA. CircRNA expression profiles were then explored by Clariom D human microarray from Affymetrix.

first: Yakun

last: Wen


title: Characterization of subcutaneous white adipose tissue gene expression profile in control and chronic kidney disease patients

city: VILLEURBANNE

first: Christophe

middle: O

last: Soulage

address: 15 avenue Jean Capelle

department: BioSciences

country: France

institute: INSA-Lyon

summary: Many metabolic disturbances, such as protein-energy wasting, inulin resistance, and dyslipidemia are common features of chronic kidney disease (CKD). However, to date, the underlying mechanisms of these disturbances remain elusive. Many in vitro studies have demonstrated that white adipose cells exhibit dysfunctions in conditions that mimics uremic environment. In good agreement, several animal experiments have reported that chronic kidney disease was associated with lipoatrophy, adipose tissue dysfunction and ectopic lipid redistribution. The goal of this protocol was to collect and study structural and metabolic properties of white adipose tissue in CKD stage V patients to evidence adipose tissue dysfunction associated with CKD. The primary outcome measure was to study the cellularity of the adipose tissue (i.e. size of the adipose cells) and the secondary measure was to study the gene expression profile using microarray and metabolic properties of adipose tissue (i.e. lipogenesis). To this end, 11 male adult volunteers and 10 non-diabetic and non-dialyzed CKD stage V patients, matched for age, gender and body mass index (BMI) will be recruited at the Departments of Nephrology or Urology of Lyon University Hospital (Lyon, France). The biopsies of abdominal subcutaneous white adipose tissue (2-3 g) were  performed during elective urologic surgery (i.e. peritoneal dialysis catheter for CKD patients and radical prostatectomy for non CKD patients).

overall_design: 9 Male healthy subjects and  9 chronic kidney disease patients (CKD stage 5 before initiation of renal suppletion therapy) matched for age and BMI

first: Emilie

middle: M

last: Kalbacher

first: Fitsum

last: Guebre-Egziabher

first: Denis

last: Fouque

first: Emmanuelle

last: Meugnier

first: Sandra

last: Pesenti


title: Control ChIP-seq from heart (ENCSR980YAL)

status: Public on Apr 30 2023

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

type: Genome binding/occupancy profiling by high throughput sequencing

summary: For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Single Copy Loss of Tet1 disrupts neural stem cell differentiation and enhances GBM aggressiveness

city: Toronto

first: Fiona

middle: J

last: Coutinho

state: ON

address: 686 Bay Street, PGCRL 16-9801

department: Developmental and Stem Cell Biology

institute: The Hospital for Sick Children

summary: Glioblastoma (GBM) is a highly aggressive brain tumor, characterized by poorly differentiated cells that drive disease growth and relapse. In contrast to normal neural stem cells (NSCs) which show a highly orderly process of differentiation, GBM precursors exhibit differentiation failure. In order to identify new mechanisms involved in neuronal differentiation that may have bearing on understanding GBM, we performed an unbiased phenotypic screen, utilizing a library of mouse embryonic stem cell (mESC) clones carrying 1307 unique variable length haplodeletions (altogether covering 25% of the mouse genome). We identified a series of haplodeletions that conferred failed neuronal differentiation following neural lineage specification.  Several hit clones contained a deletion on mouse chromosome 10, synteneic to human chromosome 10q, and included the Tet1 gene. Loss of a single allele of Tet1 was sufficient to confer the failed neuronal differentiation on mouse neural precursors by allowing stem cell programs to override early commitment steps leading to full reversion back to a stem cell state. By deleting TET1 in human GBM precursors, we show that loss of one allele of TET1 is sufficient to cause increased self renewal, decreased differentiation, and increased tumorigenicity, demonstrating TET1 to be a key target, along with PTEN, on 10q. Reduced TET1 dosage leads to global DNA hypermethylation and increased sensitivity to DNA methylation inhibitors, suggesting their application in a subset of GBMs.

overall_design: Human primary glioblastoma cells with a crispr-induced loss of function deletion in one or both copies of TET1 are compared to TET1 wildtype cells of matched genetic background

first: Peter

middle: B

last: Dirks


title: Control ChIP-seq from HCT116 (ENCSR990OHC)


title: Expression profile and clinical significance of miRNAs at different stages of severe fever with thrombocytopenia syndrome (SFTS) in Chinese patients

city: Nanjing

first: Pengfei

last: Li

address: NO.155 Hanzhong Road, Baixia District

department: Clinical Laboratory

institute: Jiangsu Province Hospital of TCM

summary: In order to determine the microRNAs profile in peripheral blood mononuclear cell (PBMC) from severe febrile with thrombocytopenia syndrome virus infection and investigate possible diagnostic value of these differential microRNAs.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: The blood samples of SFTS and healthy people were collected. Differential miRNAs were screened by miRNA microarray analysis, and the expression of selected miRNAs were validated by quantitative reverse-transcriptase polymerase chain reaction assays (qRT-PCR).

first: Zhifeng


title: TF ChIP-seq from HCT116 (ENCSR979ZEO)


title: Control ChIP-seq from HepG2 (ENCSR542TKO)

summary:
ChIP-Seq on HepG2

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Effect of EZH2 inhibition on ARID1A mutant bladder cancer cell lines

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

summary:
ARID1A, a subunit of SWI/SNF chromatin remodeling complex. SWI/SNF complex can regulate expression of genes involved in vital biological processes such as cell cycle, DNA damage repair and development. ARID1A is known to have high mutation rate in human cancers including bladder cancer, leading to its loss of function. Publicly available whole exome sequencing data for muscle invasive and non-muscle invasive bladder cancers, show fraction of tumors with truncated ARID1A. Thus identifying therapeutic strategies for ARID1A mutant cancers is of high importance.
EZH2, a histone methyltransferase is known to over-express and play pivotal role in aggressive bladder cancer. Our preliminary studies show that treatment of EZH2 inhibitor (GSK126) on ARID1A mutant bladder cancer cells significantly reduced cancer cell viability, invasion and colony formation relative to wild type ARID1A containing cells. Here, we performed microarray experiments to assess the effect of EZH2 inhibitor on global transcriptome of both ARID1A mutant and wild type bladder cancer cell line.

overall_design: Two color microarray experiments were performed considering DMSO treated and GSK126 (EZH2 inhibitor) treated bladder cancer cells. The study included two ARID1A mutant (HT1197, HT1376) and two ARID1A wildtype (T24 and 5637) bladder cancer cell lines.

first: B

middle: V

last: Chakravarthi

first: D

middle: S

last: Chandrashekar

first: S


title: Histone ChIP-seq from heart right ventricle (ENCSR541TUX)


title: Control ChIP-seq from HepG2 (ENCSR533ASI)


title: Histone ChIP-seq from heart right ventricle (ENCSR528PVW)


title: Control ChIP-seq from HCT116 (ENCSR229ZIR)


title: Acetaminophen

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

institute: Sapporo Medical University

summary: 8 and 80 week old mice treated with acetaminophen

overall_design: Mice treated with acetaminophen


title: Histone ChIP-seq from layer of hippocampus (ENCSR527FRO)


title: TF ChIP-seq from HCT116 (ENCSR954MUZ)


title: Control ChIP-seq from left cerebral cortex (ENCSR515UIB)


title: Control ChIP-seq from left cerebral cortex (ENCSR513BAE)


title: TF ChIP-seq from HCT116 (ENCSR216SIK)


title: Control ChIP-seq from layer of hippocampus (ENCSR206ALY)


title: Control ChIP-seq from HCT116 (ENCSR936ENS)


title: Histone ChIP-seq from layer of hippocampus (ENCSR213YKJ)


title: Control ChIP-seq from heart (ENCSR477YXE)


title: Control ChIP-seq from HCT116 (ENCSR198TUZ)


title: Control ChIP-seq from WTC11 (ENCSR491BNK)

summary:
ChIP-Seq on WTC11

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from left cerebral cortex (ENCSR491RBV)


title: Control ChIP-seq from K562 (ENCSR722TKK)

summary:
K562 immortalized cell line stably expressing C-terminal eGFP-ATF4 fusion protein.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: TF ChIP-seq from HCT116 (ENCSR446FOM)


title: TF ChIP-seq from heart left ventricle (ENCSR461HOC)


title: TF ChIP-seq from HCT116 (ENCSR450DXU)


title: Control ChIP-seq from HepG2 (ENCSR720MOD)


title: TF ChIP-seq from HCT116 (ENCSR160GVO)


title: TF ChIP-seq from HCT116 (ENCSR908TBJ)


title: Control ChIP-seq from HEK293 (ENCSR151LCI)

summary:
ChIP-Seq on HEK293

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from gastrocnemius (ENCSR714ZJT)


title: Control ChIP-seq from WTC11 (ENCSR428BNQ)


title: Control ChIP-seq from layer of hippocampus (ENCSR148TRG)


title: Control ChIP-seq from HEK293 (ENCSR148MVL)


title: Histone ChIP-seq from heart left ventricle (ENCSR704JQF)


title: Control ChIP-seq from K562 (ENCSR144DXT)

summary:
ChIP-Seq on K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HCT116 (ENCSR147MKT)


title: Control ChIP-seq from HCT116 (ENCSR147CEU)


title: Histone ChIP-seq from left cerebral cortex (ENCSR943LBN)


title: TF ChIP-seq from heart right ventricle (ENCSR138FTN)


title: Control ChIP-seq from WTC11 (ENCSR678WJT)


title: Histone ChIP-seq from heart left ventricle (ENCSR678RFS)


title: Control ChIP-seq from K562 (ENCSR188MIS)


title: Control ChIP-seq from HCT116 (ENCSR862XXV)


title: Histone ChIP-seq from heart right ventricle (ENCSR678IYC)


title: Control ChIP-seq from HepG2 (ENCSR396WYG)


title: TF ChIP-seq from layer of hippocampus (ENCSR877MSN)


title: Control ChIP-seq from HepG2 (ENCSR123ESD)


title: Control ChIP-seq from gastrocnemius (ENCSR121JUM)


title: Control ChIP-seq from K562 (ENCSR385DOV)


title: TF ChIP-seq from HCT116 (ENCSR385CDF)


title: Control ChIP-seq from HCT116 (ENCSR858IFL)


title: TF ChIP-seq from HCT116 (ENCSR671ITY)


title: Control ChIP-seq from HCT116 (ENCSR661KFD)


title: TF ChIP-seq from HCT116 (ENCSR107GWZ)


title: Control ChIP-seq from HCT116 (ENCSR365VOI)


title: Control ChIP-seq from K562 (ENCSR085CJF)

summary:
ChIP-seq on human K562

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Histone ChIP-seq from heart (ENCSR846REF)


title: Histone ChIP-seq from heart right ventricle (ENCSR842TXG)


title: Control ChIP-seq from WTC11 (ENCSR828IIG)


title: Histone ChIP-seq from heart left ventricle (ENCSR359HLC)


title: TF ChIP-seq from left cerebral cortex (ENCSR644VYX)


title: Control ChIP-seq from K562 (ENCSR615INN)


title: Control ChIP-seq from HCT116 (ENCSR621MTI)


title: Control ChIP-seq from gastrocnemius (ENCSR820CZJ)


title: Histone ChIP-seq from heart left ventricle (ENCSR072GNA)


title: TF ChIP-seq from HCT116 (ENCSR352EIC)


title: Control ChIP-seq from K562 (ENCSR802WKU)


title: Control ChIP-seq from HepG2 (ENCSR800SRA)


title: Control ChIP-seq from HepG2 (ENCSR315QCW)


title: TF ChIP-seq from HCT116 (ENCSR341OQG)


title: Histone ChIP-seq from heart (ENCSR349EHZ)


title: TF ChIP-seq from HCT116 (ENCSR048RGR)


title: Control ChIP-seq from HCT116 (ENCSR307VBQ)


title: Control ChIP-seq from WTC11 (ENCSR783VJL)


title: Histone ChIP-seq from heart right ventricle (ENCSR589EMG)


title: TF ChIP-seq from HCT116 (ENCSR597TGH)


title: Control ChIP-seq from HCT116 (ENCSR317ZOF)


title: TF ChIP-seq from HCT116 (ENCSR059BCO)


title: TF ChIP-seq from HCT116 (ENCSR288YJL)


title: Control ChIP-seq from MCF-7 (ENCSR301NCS)

summary:
MCF7 immortalized cell line stably expressing C-terminal eGFP-TSC22D1 fusion protein.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf


title: Control ChIP-seq from HCT116 (ENCSR313EED)


title: Control ChIP-seq from HepG2 (ENCSR578XKJ)


title: Histone ChIP-seq from heart right ventricle (ENCSR031SHV)


title: Control ChIP-seq from WTC11 (ENCSR549JGF)


title: TF ChIP-seq from gastrocnemius (ENCSR798CCX)


title: Control ChIP-seq from HEK293 (ENCSR245JDY)


title: Histone ChIP-seq from heart left ventricle (ENCSR748OJA)


title: Control ChIP-seq from WTC11 (ENCSR730ATD)


title: Control ChIP-seq from HCT116 (ENCSR557ZCZ)


title: Histone ChIP-seq from gastrocnemius (ENCSR283HPZ)


title: Control ChIP-seq from HepG2 (ENCSR005ZFP)


title: TF ChIP-seq from heart (ENCSR024KGB)


title: Can non-invasive prenatal screening based on cell-free fetal DNA be utilized to assess chromosome abnormalities in fetuses with increased Nuchal Translucency?

city: fuzhou

first: su

last: linjuan

address: daoshanlu

institute: Fujian Provincial Maternity and Children's Hospital,

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary:
Objective: The study compared the incidence of aneuploidy and copy number variations (CNVs) in fetuses with increased nuchal translucency (NT) to those with clear indications for non-invasive prenatal screening (NIPS), aiming to evaluate the risk of routine aneuploidy (RA) and pathogenic submicroscopic abnormalities and the potential use of NIPS for fetuses with increased NT.
Methods: The study retrospectively analyzed 716 pregnant women with isolated increased NT in Group IiNT and 2960 pregnant women in the control group. The control group was divided into sub-Group A (1531 patients underwent invasive prenatal diagnosis for advanced maternal age (AMA)), sub-Group B (1331 for high-risk maternal serum screening (hMSS)), and sub-Group C (98 for both hMSS and AMA). All cases underwent karyotyping and chromosomal microarray analysis.
Results: In Group IiNT and each sub-group, there were cases of RA (17, 28, 24, and 1) and clinically significant CNVs (22, 19, 39, and 5), respectively. There was no significant difference in RA incidence between Group IiNT and the control group/subgroups. Similarly, there was no statistical difference in clinically significant CNVs and CNVs <10 Mb between Group IiNT and sub-Group B/C or the control group. Only Group IiNT and sub-Group A showed a significant difference.
Conclusion: Using NIPS with broader and deeper sequencing could theoretically potentially serve as a screening tool for identifying global chromosomal and submicroscopic abnormalities in fetuses with isolated increased NT. However, further research is required to determine the clinical application and to assess the efficacy of NIPS in detecting abnormalities.
Traditional karyotyping and SNP array was performed on all 3676 pregnancies.

overall_design:
SNP array was performed on various pregnancy types.

*** Submitter declares that some chp and CEL files have been lost. ***

first: Linjuan

last: Su

first: Liangpu

last: Xu


title: XBP1s cutnrun

city: Madison

first: Allan

last: Brasier

state: WI

address: 715 Highland

department: ICTR

institute: university of Wissconsin

summary: The unfolded protein response (UPR) has emerged as important signaling pathway mediating anti-viral defenses to Respiratory Syncytial Virus (RSV) infection.  In this study, we examine how Inositol Requiring Enzyme (IREa X-Box Binding Protein spliced (XBP1s) arm of the Unfolded Protein Response (UPR) pathway controls the innate response integrating RNA-seq and Cleavage Under Targets and Release Using Nuclease (CUT&RUN) analyses. XBP1s binds to ~4.2 K high-confidence genomic binding sites.  Surprisingly these map to only a small subset of IL10/cytokine genes.  We further find that that RSV infection enhances XBP1s occupancy on 786 genomic sites enriched in AP1/Fra-1, RELA and SP1 binding sites controlling a core subset of cytokine regulatory factors genes including IFN response factor 1 (IRF1), CSF2, NFKB1A and DUSP10.  Selective IRF1 knockdown experiments demonstrates its requirement in control of type I and -III IFNs and IFN-stimulated genes (ISGs) indicating these genes are indirectly regulated through IRF1 transactivation.  We conclude that RSV modulates the XBP1 binding complex to the IRF1 epromoter, providing novel insight into how the IRE1-XBP1s pathway potentiates airway mucosal anti-viral responses.

overall_design: hSAECs were treated in triplicate replicates including FLAG-XBP1s transduced cells with or without RSV infection (MOI = 1.0, 24 h). Untransduced cells were negative control.  After trypsinization, 4 x 106 cells were aliquoted and incubated on ice for 10 minutes in 1 ml of nuclear extraction buffer (20 mM HEPES, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine), the released nuclei were pelleted at 600x g, 5 minutes at 4 oC. A basic wash buffer (WB) consisting of 20 mM HEPES, pH7.5, 150 mM NaCl, 0.05% Triton X-1000, 0.1% BSA, 1x cOmplete proteinase inhibitor, 1x protein phosphatase inhibitor cocktail and 0.5 mM spermidine was used throughout. Between incubation steps, the nuclei were pelleted at 600x g, 3 minutes at 4 oC. Prior to antibody binding, the isolated nuclei were incubated with nutation at 4 oC for 5 minutes in WB containing 2 mM EDTA, followed by nutation at 4 oC for 25 minutes in WB. The nuclei were resuspended in antibody buffer produced by diluting 5 mg of FLAG-M2 in 500 ml of Triton X-100-free WB, and incubated with nutation overnight at 4 oC.  After washing three times in 500 ml of WB on ice (10 minutes each time), the nuclei were incubated at 4 oC for 1 h in 50 ml of WB containing 2.5 ml of EpiCypher pAG-MNase 20x stock (EpiCypher, NC). Washing as above, targeted chromatin cleavage was then conducted by incubating the nuclei on ice for 1 h in 150 ml of BSA-free WB containing 2 mM CaCl2. The cleavage was terminated by adding 150 ml of stop buffer (300 mM NaCl, 20 mM EDTA, 4 mM EGTA and 0.5 ng of E. coli Spike-in DNA (EpiCypher, NC) per 150 ml).  The samples were further incubated with nutation at 4 oC for 1 h, centrifuged at 16,000x g for 5 min at 4 oC and the supernatant was collected. Phenol-chloroform DNA precipitation with 80 mg of glycogen was performed and the Cut&Run-enriched DNA was dissolved in 20 ml of 0.1x TE buffer. Following DNA quantitation by a Qubit fluorometer, Cut&Run DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, MA) per the manufacturer’s instruction, with modification in SPRI bead clearance of adaptor ligation and library amplification reactions to retain small-sized DNA fragments (down to ~170 bp in post-library amplification size). The quality of the resultant DNA libraries was confirmed by Agilent TapeStation HS DNA assay (Agilend, CA), and paired-end Illumina NGS was carried out on NovaSeq 6000 with 5 million reads per sample.

middle: R

first: Dianhua

last: Qiao


title: Control ChIP-seq from HCT116 (ENCSR001YXI)


title: Genomic DNA copy number alterations of X-ray-induced intestinal tumors in ApcMin/+ mice

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

type: Genome variation profiling by genome tiling array

summary: To investigate DNA copy number changes in mouse  intestinal tumors induced by ionizing radiation.

overall_design: DNA copy number changes in radiation-induced mouse intestinal tumors were analyzed using array-CGH microarray.

first: Hiromi

last: Yanagihara

first: Hirotaka

last: Tachibana

last: Daino

first: Shizuko

last: Kakinuma


title: Endothelial cell senescence exacerbates pulmonary hypertension by inducing juxtacrine Notch signaling in smooth muscle cells

city: Kyoto

first: Tetsuro

last: Kusaba

state: Kyoto

address: 465 Kajii-cho, Kamigyo-ku

department: Department of Nephrology

institute: Graduate School of Medical Science, Kyoto Prefectural University of Medicine

summary: Pulmonary arterial hypertension (PAH) is a fatal disease characterized by a progressive increase in pulmonary artery pressure caused by pathological pulmonary artery remodeling. Here, we show that endothelial cell (EC) senescence plays a negative role in pulmonary hypertension via juxtacrine interaction with smooth muscle cells (SMCs). By using EC-specific progeroid mice that we recently generated, we discovered that EC progeria deteriorated vascular remodeling in the lungs, and exacerbated pulmonary hypertension in mice exposed to chronic hypoxia. Mechanistically, senescent ECs overexpressed Notch ligands, which resulted in increased Notch signaling and activated proliferation and migration capacities in neighboring SMCs. Pharmacological inhibition of Notch signaling reduced the effects of senescent ECs on SMCs functions in vitro, and improved the worsened pulmonary hypertension in EC-specific progeroid mice in vivo. Our findings show that EC senescence is a critical disease-modifying factor in PAH and that EC-mediated Notch signaling is a pharmacotherapeutic target for the treatment of PAH, particularly in the elderly.

overall_design: single nucleus RNA sequencing was used to profile mouse lung

first: Koji

last: Ikeda


title: Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

country: Australia

institute: University of Queensland

summary: DSP RNA profiling using the whole transcriptome atlas kit was performed on a cohort of placentae from participants who had contracted SARS-CoV-2 in the third trimester compared to uninfected controls.

overall_design: Differential expression was performed on the trophoblast and villous core stroma cells from the anchoring and terminal villi of placentae from the SARS-CoV-2 cohort (n=7) compared to uninfected controls (n=9).

first: Nataly

last: Stylianou


title: Case Report: Immune Modulation after PD-1 Inhibitor Therapy in a Patient with Extranodal NK/T-cell Lymphoma Secondary to Chronic Active Epstein-Barr Virus Disease Unveiled by Single-Cell Transcriptomics

city: Nantong

first: Yao

last: Wang

address: Xinchengqiao Street

institute: Affiliated Hospital of Nantong University

summary: We used  single-cell RNA sequencing (scRNA-seq) to explore the immune status of the patient before and after anti-PD-1 therapy to predict the possible trajectories of disease progression.

overall_design: Peripheral blood mononuclear cells were  isolated before and after PD-1 inhibitor therapy and analyzed using scRNAseq.

first: Minan

last: Zhang

first: Yaping

first: Wenyu

last: Shi


title: Gene expression profile at single cell level of blood leukocytes from the turbot (Scophthalmus maximus)

city: Shanghai

first: Weijie

last: Chen

address: Furonghua Road 118

institute: Simcere Zaiming Pharmaceutical Co.

summary: Cell types of turbot blood leukocytes remian unknown. We used single cell RNA sequencing (scRNA-seq) to analyze the cell types of turbot blood leukocytes.

overall_design: Blood leukoucytes of turbots were isolated by density gradient centrifugation and analyzed using scRNAseq.

first: Dahai

last: Yang


title: RNA-seq for transcription factor HOMEZ

city: Beijing

first: Yanan

address: Taipin Rd 27

institute: Beijing institute of biotechnology

summary: RNA-seq was used to identify HOMEZ target genes with a Tet-on inducible expression system

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MCF-7 cells and its derivatives (HOMEZ-induced expression at indicated times).

first: Qinong

last: Ye

first: Lihua

last: Ding


title: Comparison of the effects of paternal obesity upon gene expression in mice

city: Barcelona

first: Carlos

last: Castaño

address: Rossello 153

country: Spain

institute: CIBER

summary: We used microarrays to detail the global changes of gene expression induced by paternal obesity in liver and adipose tissues

overall_design: C57BL/6J male mice born from control parents (CT) or from control female and an obese male (F1) were sacrificed at 14 weeks of age for tissue dissection and RNA analysis

first: Marcelina

last: Parrizas


title: ChIP-seq for transcription factor HOMEZ

summary: ChIP-seq was used to identify HOMEZ binding sites of target genes

overall_design: Comparative gene expression profiling analysis of ChIP-seq data for MCF-7 cells


title: A nutriepigenetic pathway links diet to sensory plasticity

city: Ann Arbor

first: Monica

last: Dus

state: Michigan

address: 1105 N University, 4224

institute: University of Michigan

summary: RNAseq data related to the tongue epithelia of R.norvegicus rats fed either a chow and water diet or chow and water+30% sucrose

overall_design: Rats were assigned to sucrose or control groups such that weight did not differ between conditions (water: 357.75 +/- 7.8 g, sucrose: 360.75 +/- 8.8 g). Both water (control) and sugar rats were given free access to standard chow (Lab Diet 5001: 4.07kcal/g; 13.5% fat, 28.5% protein, 58% carbohydrates; % of caloric content); sucrose rats were given a bottle of 30% sucrose diluted in tap water as their only liquid source, while water rats were given plain water alone. Food intake and body weight was monitored throughout.

first: Anoumid

last: Vaziri


title: Evaluation of cell cycle phase dependent transcriptional changes by single cell RNA-seq

city: San Francisco

first: Robert

last: Blelloch

address: 35 Medical Center Way

department: Urology

institute: UCSF

summary: We performed single cell RNA MULTI-seq using 10x v3 platform with 24h induced and non-induced FOXD3 KO cells.

overall_design: FOXD3 loss was induced with 4HT for 24h (control was treated with EtOH) with two independently grown cultures per conditions. Cells were lipid barcoded according to McGinnis et al (2019) and stoichiometrically pooled. A total of 45920 cells were used as input to the 10x controller aiming for 20000 cells captured.

first: Deniz

last: Goekbuget


title: RNA N6-methyladenosine modification  in different developmental stages of Echinococcus

city: Lanzhou

first: John

last: Ohiolei

state: Gansu

address: 1 Xujiapin Road, Yanchang Bu, Chengguan District

institute: Lanzhou Veterinary Research Institute

summary: N6-methyladenosine (m6A) is the methylation of adenosine at position N6 and is notably one of the most abundant modifications found in mRNA of eukaryotes. Although it does not interrupt the coding functions of transcripts, it assists in regulating several RNA functions like splicing, stability, translocation and translation and is associated with disease development, cell proliferation, cell migration, cell invasion, autophagy, cell apoptosis, and drug resistance. In this study, we performed a colorimetric assay, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), and methylated RNA immunoprecipitation sequencing (MeRIP-seq) to assess the RNA N6-methyladenosine landscape of Echinococcus granulosus; a tapeworm species of the phylum Platyhelminthes that is responsible for a cosmopolitan zoonosis (cystic echinococcosis) of public health importance. While the levels of m6A modification were not significantly different between the life cycle stages, many important genes including notably enriched and expanded protein domains like Dyneins, Hsp70, and Cadherin thought to play important roles in adaptation to parasitism were m6A-modified. These genes were functionally enriched in biological processes like cell division, cell adhesion, microtubule-based movement, important pathways involved in parasitism (e.g. MAPK), and disease processes. Additionally, the m6A alterations were present in the first exon of modified genes, suggesting gene regulatory activities. Conclusively, m6A modification of the mRNA is present in Echinococcus, and is mediated by orthologues of known mammalian methyltransferases but possibly irreversible due to the absence of demethylases. The demonstration of differentially m6A-methylation in the different life cycle stages of Echinococcus suggests a role in the development and survival of the tapeworm. It also provides the groundwork for future studies in understanding the implication of RNA methylation in the treatment of echinococcoses.

overall_design: N6-methyladenosine (m6A)

first: Wan-Zhong

last: Jia

first: Bao-Quan

last: Fu

first: Yan

last: Hong-Bin

first: Xiao-Feng

last: Nian

first: Li

last: Li


title: RevGel-seq: instrument-free single-cell RNA sequencing using a reversible hydrogel for cell-specific barcoding [scRNA-seq_ScaleUp_Scipio]

city: Paris

first: Stuart

last: EDELSTEIN

state: Île-de-France

address: 29 rue du Faubourg Saint Jacques, Pépinière Paris Santé Cochin

institute: Scipio bioscience

summary: Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.

overall_design: Benchmarking experiments to assess the performances obtained using RevGel-seq (scRNA preparation).

first: Hélène

last: Eckert

first: Frédéric

last: Guérin

first: Raya

last: Poncin

first: Sara

last: Majello

first: Léa

last: Cathaly

first: Stanislas

last: Lipin

first: Barbara

last: André

last: Edelstein


title: Impact of dietary fat content and sulfur amino acid restriction on the hepatic transcriptome in male mice

city: New Brunswick

first: Tracy

middle: G

last: Anthony

state: NJ

address: 59 Dudley Rd

department: Nutritional Sciences

institute: Rutgers University

summary: This study investigated the effects of dietary sulfur amino acid restriction (SAAR) on the mouse liver transcriptome. We fed wild-type (C57Bl/6J) male mice either a control (Ctrl) or SAAR diet on either a regular-fat (RF) or high-fat HF) background for seven days. After seven days, liver samples were collected, among other tissues, and processed for RNA-sequencing. We then analyzed the changes in the transcriptome, comparing the two different Ctrl vs. SAAR comparisons against each other to identify how HF might impact the effect of SAAR on the hepatic transcriptome. Additionally, this project also involved generating proteomics data which we used to compare the similarities and differences between transcriptomic and proteomic changes in response to the different dietary treatments. We find that SAAR, independent of diet, produces a robust realignment of the transcriptome after seven days of SAAR. In contrast, proteome-wide changes were less well-aligned.

overall_design: Livers from a total of 12 male mice were processed for RNA-sequencing after 7 days of consuming either a control (ctrl) of sulfur amino acid restricted (SAAR) diet on either a regularfat (RF) or high-fat (HF) background.

first: William

last: Jonsson


title: Cholesterol homeostatic regulator SREBP2 promotes macrophage alternative activation and allergic airway inflammation

city: Hangzhou

first: Yinfang

last: Wu

address: Yuhangtang RD 866

institute: Zhejiang University

summary: Metabolic reprogramming is well-appreciated to be able to control macrophage activation. However, it remains unknown whether the SREBPs-lipogenesis pathway is involved in macrophage alternative (or M2) activation. Here, we showed that IL4-induced M2 activation was coupled with increased SREBP2 maturation and activated cholesterol biosynthetic pathway, while the SREBP1-fatty acid biosynthesis pathway remained unaffected after IL4 stimulation. Genetic or pharmacologic blockade of SREBP2 maturation significantly inhibited IL4-induced M2 activation independent of cholesterol. Instead, cholesterol inhibited M2 activation most likely through its feedback regulation of SREBP2 maturation. Mechanically, the upregulation of SREBP2 maturation was dependent on the activation of upstream MTOR, and mature SREBP2 increased the expression of KAZALD1 and subsequently activated the IGF1 signaling to promote IL4-induced M2 activation. Consistently, myeloid-specific Scap deficiency markedly decreased the number of M2 macrophages in the lung and attenuated the HDM-induced allergic airway inflammation. Taken together, these findings highlight a critical role for cholesterol homeostatic regulator SREBP2 in M2 activation, which advances our understanding of the regulation of immunometabolism for M2 activation and points to new opportunities for therapeutic control of M2 activation and allergic airway inflammation.

overall_design: mRNA profiles of BMDM treated with IL4, IL4 + fatostatin, IL4 + betulin,  IL4  + 25-HC,  IL4 + PF429424, and  IL4 + 1,10-Phen, respectively.

first: Huahao

last: Shen

first: Zhihua

last: Chen

first: Wen


title: Endothelial cells synergize with fibroblasts to form a niche for engineering alveolar epithelium

city: New Haven

first: Katherine

middle: L

last: Leiby

state: CT

address: 10 Amistad St. Rm 314

department: Biomedical Engineering

institute: Yale University

summary: We perform single-cell RNA sequencing of whole engineered lungs generated either by alveolar epithelial type 2 cell (AEC2)/fibroblast (FB) co-culture or by AEC2/FB/endothelial cell (EC) tri-culture, to investigate AEC2 and FB phenotype in the presence and absence of endothelial cells. Primary postnatal day 7 (P7) AEC2s, P7 lung FBs, and primary rat lung microvascular ECs (from 4-6 week-old rats) used for engineered cultures, as well as native P7 whole rat lung, were sequenced for comparison. We find that native-like AEC2 phenotype, alveolar structure, and cellular signaling patterns are better recapitulated via epithelial-mesenchymal-endothelial tri-culture rather than by a more simplified system. FBs cultured in the presence of endothelial cells demonstrate reduced expression of contractile markers and upregulate features of an AEC2 niche-supportive signature.

overall_design: Single-cell RNA sequencing data of AEC2/fibroblast and AEC2/fibroblast/endothelial (tri-culture) d7 engineered lungs, with AEC2 and fibroblast isolates, primary ECs, as well as P7 native rat lung (pooled from 6 rats) for comparison

first: Laura

last: Niklason